Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 18:41:20.669157450 +0000 +++ b2/build.log 2024-04-30 19:08:53.242819541 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 30 06:13:02 -12 2024 -I: pbuilder-time-stamp: 1714500782 +I: Current time: Tue Jun 3 15:04:27 +14 2025 +I: pbuilder-time-stamp: 1748912667 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -41,51 +41,83 @@ dpkg-source: info: applying 190-newest-vcf.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1256643/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 3 01:04 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='38e4829a968844108ff10481f8e819bd' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1256643' - PS1='# ' - PS2='> ' + INVOCATION_ID=24b7b0bedffa460b8a6c756ed49b22e6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=787020 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/pbuilderrc_NODy --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b1 --logfile b1/build.log htsjdk_4.1.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/pbuilderrc_gd9A --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.D63VSAQ0/b2 --logfile b2/build.log htsjdk_4.1.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-20-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 23 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1256643/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 24 13:34 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -919,7 +951,7 @@ Get: 405 http://deb.debian.org/debian trixie/main amd64 libngs-jni amd64 3.0.3+dfsg-6 [23.4 kB] Get: 406 http://deb.debian.org/debian trixie/main amd64 libngs-java amd64 3.0.3+dfsg-6 [110 kB] Get: 407 http://deb.debian.org/debian trixie/main amd64 scala-library all 2.11.12-5 [9588 kB] -Fetched 351 MB in 3s (102 MB/s) +Fetched 351 MB in 3s (106 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. @@ -2270,8 +2302,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 30 18:15:07 UTC 2024. -Universal Time is now: Tue Apr 30 18:15:07 UTC 2024. +Local time is now: Tue Jun 3 01:06:30 UTC 2025. +Universal Time is now: Tue Jun 3 01:06:30 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2807,7 +2839,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/htsjdk-4.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../htsjdk_4.1.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/htsjdk-4.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../htsjdk_4.1.0+dfsg-1_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 4.1.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2857,18 +2893,18 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.921 secs. -The client will now receive all logging from the daemon (pid: 1289198). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-1289198.out.log +An attempt to start the daemon took 0.918 secs. +The client will now receive all logging from the daemon (pid: 821943). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-821943.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5b13a210 -Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5b13a210 -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@55397567 +Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9 +Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e783cc9 +Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6 Starting Build Compiling initialization script '/build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@2423adac +Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d96c56b Compiling initialization script '/build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2888,17 +2924,17 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : -Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@33e67c6f +Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@25b67184 Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@55397567 -Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@36e4bab6 -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7db1e098 -:compileJava (Thread[Task worker for ':' Thread 3,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@787805f6 +Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@55aee263 +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a4c43a1 +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.005 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@749befda +Putting task artifact state for task ':compileJava' into context took 0.004 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a087dcb Loading the Maven rules... Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian @@ -2919,7 +2955,7 @@ Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Passing through org.hamcrest:hamcrest:jar:debian -Up-to-date check for task ':compileJava' took 2.444 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.075 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. @@ -2927,39 +2963,39 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 9.961 secs. -:processResources (Thread[Task worker for ':' Thread 3,5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 8.842 secs. +:processResources (Thread[Task worker for ':' Thread 11,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.003 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.004 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.035 secs. -:classes (Thread[Task worker for ':' Thread 3,5,main]) started. +:processResources (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.026 secs. +:classes (Thread[Task worker for ':' Thread 11,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 3,5,main]) started. +:classes (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[Task worker for ':' Thread 11,5,main]) started. :debianMavenPom executing task ':debianMavenPom' ... Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/htsjdk-4.1.0+dfsg/build/debian/htsjdk.pom -:debianMavenPom (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.084 secs. -:jar (Thread[Task worker for ':' Thread 3,5,main]) started. +:debianMavenPom (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.065 secs. +:jar (Thread[Task worker for ':' Thread 11,5,main]) started. :jar executing task ':jar' ... Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.027 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.021 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.389 secs. -:javadoc (Thread[Task worker for ':' Thread 3,5,main]) started. +:jar (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 0.292 secs. +:javadoc (Thread[Task worker for ':' Thread 11,5,main]) started. :javadoc executing task ':javadoc' ... Putting task artifact state for task ':javadoc' into context took 0.0 secs. -Up-to-date check for task ':javadoc' took 0.166 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.137 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc @/build/reproducible-path/htsjdk-4.1.0+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc'' @@ -3278,9 +3314,9 @@ /** Formats date & time */ ^ 100 warnings -:javadoc (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 9.909 secs. +:javadoc (Thread[Task worker for ':' Thread 11,5,main]) completed. Took 8.397 secs. -BUILD SUCCESSFUL in 25s +BUILD SUCCESSFUL in 22s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg' jh_build -O--buildsystem=gradle @@ -3299,8 +3335,8 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.881 secs. -The client will now receive all logging from the daemon (pid: 1290329). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-1290329.out.log +An attempt to start the daemon took 0.783 secs. +The client will now receive all logging from the daemon (pid: 822748). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-822748.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. @@ -3329,11 +3365,11 @@ Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@67456c59 Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@1500db0a Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@42287545 -:compileJava (Thread[Task worker for ':' Thread 6,5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.007 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5cf67532 +Putting task artifact state for task ':compileJava' into context took 0.003 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@47c95edc Loading the Maven rules... Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian @@ -3354,23 +3390,23 @@ Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian Passing through org.hamcrest:hamcrest:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 0.742 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.701 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 0.809 secs. -:processResources (Thread[Task worker for ':' Thread 6,5,main]) started. +:compileJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.745 secs. +:processResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. Skipping task ':processResources' as it is up-to-date (took 0.003 secs). :processResources UP-TO-DATE -:processResources (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 0.006 secs. -:classes (Thread[Task worker for ':' Thread 6,5,main]) started. +:processResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.006 secs. +:classes (Thread[Task worker for ':' Thread 3,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 0.001 secs. -:compileTestJava (Thread[Task worker for ':' Thread 6,5,main]) started. +:classes (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) started. :compileTestJava executing task ':compileTestJava' ... Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. @@ -3423,7 +3459,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [VariantContext$Validation.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SAMSequenceDictionaryExtractor$TYPE.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3472,7 +3508,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SAMSequenceDictionaryExtractor$TYPE.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [VariantContext$Validation.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3570,7 +3606,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3619,7 +3655,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SamReaderFactory$Option.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [ContentDigests$KNOWN_DIGESTS.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3668,7 +3704,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SRALazyRecord$LazyField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3717,7 +3753,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [ContentDigests$KNOWN_DIGESTS.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SRALazyRecord$LazyAttribute.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3815,7 +3851,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SRALazyRecord$LazyAttribute.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SamReaderFactory$Option.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3864,7 +3900,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:840) -Malformed class file [SRALazyRecord$LazyField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3924,13 +3960,10 @@ Passing through org.jsr-305:jsr305:jar:0.x Passing through com.google.errorprone:error_prone_annotations:jar:debian Passing through com.google.errorprone:error_prone_parent:jar:debian -Up-to-date check for task ':compileTestJava' took 1.799 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 1.104 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. -/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal - tagMap.put("XC", new Character('q')); - ^ /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:15: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal {new Byte((byte) 7)}, ^ @@ -4054,90 +4087,93 @@ /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false}, ^ +/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal + tagMap.put("XC", new Character('q')); + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 42 warnings -:compileTestJava (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 9.128 secs. -:processTestResources (Thread[Task worker for ':' Thread 6,5,main]) started. +:compileTestJava (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 7.523 secs. +:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) started. :processTestResources executing task ':processTestResources' ... Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.425 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.309 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 1.053 secs. -:testClasses (Thread[Task worker for ':' Thread 6,5,main]) started. +:processTestResources (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.885 secs. +:testClasses (Thread[Task worker for ':' Thread 3,5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 0.001 secs. -:testWithDefaultReference (Thread[Task worker for ':' Thread 6,5,main]) started. +:testClasses (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. +:testWithDefaultReference (Thread[Task worker for ':' Thread 3,5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... Putting task artifact state for task ':testWithDefaultReference' into context took 0.0 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.216 secs. It is not up-to-date because: +Up-to-date check for task ':testWithDefaultReference' took 0.193 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath6907548906275863931txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' +Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath18004479675575439867txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. Gradle Test Executor 1 STANDARD_ERROR - INFO 2024-04-30 06:16:23 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2025-06-03 15:07:46 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms @@ -4167,34 +4203,34 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequenceExtended runtime: 0ms + testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 9ms + testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 5ms + testLastCompleteContigRead runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 1ms + testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 14ms + testLastCompleteContigRead runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 16ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 13ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 10ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 9ms + testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms @@ -4218,22 +4254,22 @@ testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 12ms + testNextElementOfIterator runtime: 7ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 13ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 13ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 2ms @@ -4269,7 +4305,7 @@ testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 1ms + testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms @@ -4281,7 +4317,7 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 1ms + testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms @@ -4296,7 +4332,7 @@ testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 1ms + testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -4323,38 +4359,38 @@ testReset runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 1ms + testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 12ms + testReset runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 12ms + testReset runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 13ms + testReset runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 4ms + testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 3ms + testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2024-04-30 06:16:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:07:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@5d8c4407, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2024-04-30 06:16:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@1a3dcfb8, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2025-06-03 15:07:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2024-04-30 06:16:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:07:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 200 tests Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2024-04-30 06:16:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:07:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2024-04-30 06:16:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:07:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 @@ -5415,450 +5451,442 @@ Finished 400 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.14361637924253403397.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.18304095849403386773.bai - #BAMIndexWriterTest diff /tmp/javaBai.14361637924253403397.bai /tmp/cBai.18304095849403386773.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.2750161010191483551.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.15830538535078931576.bai + #BAMIndexWriterTest diff /tmp/javaBai.2750161010191483551.bai /tmp/cBai.15830538535078931576.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.423934933978038613.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.450120304021985101java.bai - #BAMIndexWriterTest diff /tmp/javaBai.450120304021985101java.bai.txt /tmp/cBai.423934933978038613.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.17387163724022175056.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.613650840951684057java.bai + #BAMIndexWriterTest diff /tmp/javaBai.613650840951684057java.bai.txt /tmp/cBai.17387163724022175056.bai.txt Finished 600 tests -Finished 800 tests -Finished 1000 tests -Finished 1200 tests -Finished 1400 tests -Finished 1600 tests -Finished 1800 tests -Finished 2000 tests Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 15ms to write + 4ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 6ms to write + 3ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT - Creating file /tmp/BCOST.3360182376575514773.gz + Creating file /tmp/BCOST.1766175562148577771.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.4405145101319595227.gz + Creating file /tmp/testCustomDeflater.14881755396101322987.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.5203238221386409287.gz -Finished 2200 tests + Creating file /tmp/BCOST.9768897646454591960.gz +Finished 800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2024-04-30 06:17:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:17:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2024-04-30 06:17:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:17:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2024-04-30 06:17:36 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-04-30 06:17:36 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2024-04-30 06:17:36 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-04-30 06:17:36 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2025-06-03 15:08:46 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2025-06-03 15:08:46 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2025-06-03 15:08:46 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2025-06-03 15:08:46 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:17:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2024-04-30 06:17:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:17:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:08:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:08:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2024-04-30 06:17:40 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-04-30 06:17:40 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2024-04-30 06:17:40 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-04-30 06:17:40 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2025-06-03 15:08:49 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2025-06-03 15:08:49 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2025-06-03 15:08:49 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2025-06-03 15:08:49 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR - WARNING 2024-04-30 06:17:40 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:17:40 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2024-04-30 06:17:40 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:17:40 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. -Finished 2400 tests + WARNING 2025-06-03 15:08:49 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:08:49 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2025-06-03 15:08:49 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:08:49 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR - INFO 2024-04-30 06:22:17 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2024-04-30 06:22:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:22:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2025-06-03 15:12:50 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2025-06-03 15:12:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:12:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2024-04-30 06:22:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:22:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2024-04-30 06:22:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:22:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. -Finished 2600 tests + WARNING 2025-06-03 15:12:50 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:12:50 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2025-06-03 15:12:50 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:12:50 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. +Finished 1000 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3235dacf, [Ljava.lang.String;@61e7c614) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9e49b67, [Ljava.lang.String;@d5d22c8) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26b34cc7, [Ljava.lang.String;@158a4b46) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@abe8545, [Ljava.lang.String;@6d5f1b6c) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5ba583e3, [Ljava.lang.String;@7497c5a2) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@73928faa, [Ljava.lang.String;@6fef2b1b) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49eb857f, [Ljava.lang.String;@1b30e9d1) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6562eede, [Ljava.lang.String;@3ab72c0d) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1e69c974, [Ljava.lang.String;@189c89bc) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@206c3122, [Ljava.lang.String;@13a91b0d) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2303952b, [Ljava.lang.String;@43bdeb30) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@cf8b21e, [Ljava.lang.String;@27063576) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7ac96e20, [Ljava.lang.String;@6ec7ad09) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54feaa2e, [Ljava.lang.String;@6216f321) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@570155f8, [Ljava.lang.String;@6427c3b2) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f212fef, [Ljava.lang.String;@76cabbc0) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39786779, [Ljava.lang.String;@ebacb40) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@e203769, [Ljava.lang.String;@16cab622) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f964e1, [Ljava.lang.String;@4cda9823) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c04a8a4, [Ljava.lang.String;@3d8dc09) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a6bd33a, [Ljava.lang.String;@538d0ff2) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1b61c430) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@4dc7f57) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@383402ed) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6b5bb706) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4e493ac8) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@6602c44e) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@5ad2bb89) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1bb56aeb) STANDARD_ERROR - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2fd0a849, [Ljava.lang.String;@2ab252c2) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e72cd4f, [Ljava.lang.String;@642b5dd0) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7016df9e, [Ljava.lang.String;@674d8ebc) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f7c7d9a, [Ljava.lang.String;@656f10ff) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b1f64f2, [Ljava.lang.String;@5a8d090c) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6422ca55, [Ljava.lang.String;@23059242) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ea22955, [Ljava.lang.String;@7882246a) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@521cdd00, [Ljava.lang.String;@49732172) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1772dc30, [Ljava.lang.String;@5181959e) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@40ba5199, [Ljava.lang.String;@18e0b741) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7ea611, [Ljava.lang.String;@343df691) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d98e885, [Ljava.lang.String;@1a5fd792) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8170ccc, [Ljava.lang.String;@308f92dc) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f459574, [Ljava.lang.String;@3b887553) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c95814a, [Ljava.lang.String;@731c5da7) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e5d1a9d, [Ljava.lang.String;@77d2b510) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@441cc7ae, [Ljava.lang.String;@8f97330) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@ba10461) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2f6d26ea) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@27c26f57) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6f0b8922) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@622a4ff0) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7b49e6cf) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@f13bcfe) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@45483a7) STANDARD_ERROR + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@7c83d750, [Ljava.lang.String;@580fd025) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37884168, [Ljava.lang.String;@43247e25) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fcd5173, [Ljava.lang.String;@2431160f) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@133e6440, [Ljava.lang.String;@7debe277) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c2fe3ec, [Ljava.lang.String;@7dd3f06b) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68462040, [Ljava.lang.String;@6db07e31) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b953716, [Ljava.lang.String;@745900bf) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b6d88c3, [Ljava.lang.String;@7e952630) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@729ec8a4, [Ljava.lang.String;@6cca34fd) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4154149c, [Ljava.lang.String;@765716dd) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2439c761, [Ljava.lang.String;@664f6bdb) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@99483e7, [Ljava.lang.String;@596f1c06) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6746fdc9, [Ljava.lang.String;@5319d1c4) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@490e9626, [Ljava.lang.String;@7e272cbc) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e984af0, [Ljava.lang.String;@348085a2) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70acc1bc, [Ljava.lang.String;@2345e6ed) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26755d6b, [Ljava.lang.String;@2b7dd7d3) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6f26bd82) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@400704f8) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@38a41476) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@243caf40) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2e774aec) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@33236b21) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@2fb5cb97) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@740195c2) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6124752a) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@482e4dce) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@487b8969) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@23a4cba8) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@529d6ce2) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1fef5016) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@132f85ec) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6fb15eeb) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3e58abd7) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@4e5ae243) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4f8b20e7) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1396e6a0) STANDARD_ERROR - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@4b7d6c8c) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2315c1ff) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@548eb8ff) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@41d87297) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@562d3dd0) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2434e318) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@2ecb1036) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@725a5d34) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@238c6216) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4ee1b2ad) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.12160031169681312870.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@77da4a88) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 2800 tests + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@58841f6d, [Ljava.lang.String;@760bbafa) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bd6b6c0, [Ljava.lang.String;@27f93e66) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@aaf93a2, [Ljava.lang.String;@3336a055) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41a566cb, [Ljava.lang.String;@3ee66948) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68ed98b2, [Ljava.lang.String;@1328696d) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@256c4496, [Ljava.lang.String;@34ecff3d) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38c313b4, [Ljava.lang.String;@4fdbaca0) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 1200 tests -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@18ef629e, 5) STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49d373cf, [Ljava.lang.String;@5dab0100) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@105c44d2, [Ljava.lang.String;@7040589b) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ab6779d, [Ljava.lang.String;@706ccdcb) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6fb540c2, [Ljava.lang.String;@ba94394) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@59f7539e, [Ljava.lang.String;@17603971) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1feb8755, [Ljava.lang.String;@290772c8) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21154d26, [Ljava.lang.String;@5f4f9958) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@393f9d, [Ljava.lang.String;@35d84281) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@50dd8534, [Ljava.lang.String;@f882bc6) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4bff85c, [Ljava.lang.String;@60704931) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7da29b32) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@345a7459) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5c3c5bc1) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@25b4f001) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4d6c3078) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@77febc08) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5fc0fddf) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@646b446c) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1244c5e3) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@32f65fff) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@9187ee5) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@1d545f24) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@439484ae) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4a95e2c5) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@639aacad) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@302909a0) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@a73803e) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@5dc604e) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4ca6a516) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7a8e4c25) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@549dc7c9) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@10425cf0) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1147d181) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@66fa8f23) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7e8b34a9) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@349e6caf) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@13708843) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@68331fc1) STANDARD_ERROR + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@1b758296) STANDARD_ERROR + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3b1247f3) STANDARD_ERROR + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.1968688999599575298.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@717f8253) STANDARD_ERROR + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@17bf13e0, 5) STANDARD_ERROR + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2024-04-30 06:25:27 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2025-06-03 15:15:35 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testForNPE STANDARD_ERROR - INFO 2024-04-30 06:25:27 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2025-06-03 15:15:35 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMNoReferenceRequired STANDARD_ERROR - INFO 2024-04-30 06:25:27 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2025-06-03 15:15:35 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR - INFO 2024-04-30 06:25:27 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2025-06-03 15:15:36 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20 @@ -6513,16 +6541,17 @@ Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 -Finished 3000 tests -Finished 3200 tests +Finished 1400 tests +Finished 1600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2024-04-30 06:25:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2024-04-30 06:25:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 1800 tests Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -6578,504 +6607,504 @@ Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.9595150780546036886.tmp -Finished 3400 tests -Finished 3600 tests -Finished 3800 tests -Finished 4000 tests -Finished 4200 tests -Finished 4400 tests -Finished 4600 tests + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.6442482656622782408.tmp +Finished 2000 tests +Finished 2200 tests +Finished 2400 tests +Finished 2600 tests +Finished 2800 tests +Finished 3000 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2024-04-30 06:25:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:15:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2024-04-30 06:25:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Finished 4800 tests -Finished 5000 tests + WARNING 2025-06-03 15:15:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 3200 tests +Finished 3400 tests +Finished 3600 tests Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Finished 5200 tests + WARNING 2025-06-03 15:15:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:25:47 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:15:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Finished 3800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2024-04-30 06:25:47 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2025-06-03 15:15:51 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR - WARNING 2024-04-30 06:25:47 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2025-06-03 15:15:51 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d745b29, [Ljava.lang.String;@3cae8178) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b037d7f, [Ljava.lang.String;@5aec6abc) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29bbfece, [Ljava.lang.String;@2d23d098) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22077796, [Ljava.lang.String;@4f691d1a) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@188eaae2) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1fdf792e) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@95acdaa) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Finished 5400 tests + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@13190496) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6c68cff9) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@241d582c) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@152b1975) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@132bf41f) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@4d74a585, [Ljava.lang.String;@7e1cb410) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45f33a47, [Ljava.lang.String;@1540b1c) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@14b85626, [Ljava.lang.String;@98f9732) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ceef4e2, [Ljava.lang.String;@140a907f) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c18e0a6, [Ljava.lang.String;@7826ecad) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4230461f, [Ljava.lang.String;@7217c4ac) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b458f86, [Ljava.lang.String;@c2e70) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a0d2599, [Ljava.lang.String;@181c03c) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@277c857f, [Ljava.lang.String;@4007a8e8) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@246f85bc, [Ljava.lang.String;@2ff9973b) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f9266bf, [Ljava.lang.String;@2eea4989) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@52df8dec, [Ljava.lang.String;@409242a8) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2cd32b55, [Ljava.lang.String;@27b031e2) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1ff8fd3f, [Ljava.lang.String;@3c45a593) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e54e440, [Ljava.lang.String;@616cf8c) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@60818cec, [Ljava.lang.String;@604536c6) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@560f29d6, [Ljava.lang.String;@51a05ff9) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@3d74dea9) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1131ac64) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@17cc8e2f) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7deff0ab) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@609a8352) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@27bcc14) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@7e557ede) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6fe92f70) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@41dec66f, [Ljava.lang.String;@3b72ac56) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c4dfaf5, [Ljava.lang.String;@504e82eb) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@475ee7bb, [Ljava.lang.String;@3a59d01a) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@425b1872, [Ljava.lang.String;@708d13ef) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@406dfdf3, [Ljava.lang.String;@42496cd5) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2fe2944, [Ljava.lang.String;@6d6c03de) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4636299d, [Ljava.lang.String;@2ba57293) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c770d6, [Ljava.lang.String;@5ba3d4e5) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bec9aa7, [Ljava.lang.String;@5f6cb196) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37020d3d, [Ljava.lang.String;@711fb110) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5af0ff85, [Ljava.lang.String;@2b80e24f) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3999c154, [Ljava.lang.String;@70be755) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@125f58c4, [Ljava.lang.String;@439a9d80) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@506defe1, [Ljava.lang.String;@4eec9211) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7cb775e0, [Ljava.lang.String;@1b9e86dd) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@55c90623, [Ljava.lang.String;@1a8afbd0) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@187bb9da, [Ljava.lang.String;@3343c44) STANDARD_ERROR + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@16291d65) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@3e696b) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@3b01d11d) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@777bf220) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7387840b) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2a84c2df, [Ljava.lang.String;@65ddcef) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@469d1a6b, [Ljava.lang.String;@38ed3237) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4c5f7328, [Ljava.lang.String;@48434bef) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62e1b9c9, [Ljava.lang.String;@d03ad1c) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29d0a511, [Ljava.lang.String;@473c71e8) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@67ef77ee, [Ljava.lang.String;@68609eb6) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77bb2bb7, [Ljava.lang.String;@45d968a2) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@564382aa, [Ljava.lang.String;@20596cf5) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@48277608, [Ljava.lang.String;@baa91df) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1e5e75ed, [Ljava.lang.String;@7465ce25) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42b74689, [Ljava.lang.String;@1d3bd968) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b5cf679, [Ljava.lang.String;@723933b4) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6fbd37c5, [Ljava.lang.String;@33e0f5ea) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@73dc726f, [Ljava.lang.String;@69251aea) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@52a1b50b, [Ljava.lang.String;@76d7eb14) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3b693271, [Ljava.lang.String;@810c752) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f1ea013, [Ljava.lang.String;@4b6b8406) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@5428ea3c) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@3cfe5e89) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5671bcd2) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1accb96c) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6ad491d8) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@6ab17e64) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@456507f0) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.7383518776904701120.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@763ae75c) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@333a9316) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@6d6b6ee) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@2ce7d20f) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6a793f10) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2308a71f) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@76c3cfde) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@316fb37f) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@14b3e8ab) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1d3b321c) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@37a26b6b) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@68e83d5) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@272a32ae) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1c9d806a) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1726a6d6) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@1d8b5585, [Ljava.lang.String;@4cdf6609) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3b67c38d, [Ljava.lang.String;@2b7972f3) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1220329f, [Ljava.lang.String;@f18653a) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d2ac651, [Ljava.lang.String;@23578e64) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2fdcdbfc, [Ljava.lang.String;@364ee866) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@fc5988f, [Ljava.lang.String;@5ddd6e30) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@154852b1, [Ljava.lang.String;@5ff63552) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@256652a3, [Ljava.lang.String;@6d13cb55) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4187bc56, [Ljava.lang.String;@3f2ee212) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@318d3d59, [Ljava.lang.String;@1ecd8e9) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77adc72a, [Ljava.lang.String;@69707963) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 4000 tests + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21f714a2, [Ljava.lang.String;@55b8beed) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bd9c9d6, [Ljava.lang.String;@3e15e1b6) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7685448, [Ljava.lang.String;@288f9a18) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4270e3e6, [Ljava.lang.String;@582b4292) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3329f657, [Ljava.lang.String;@31d268d6) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53f6f1cb, [Ljava.lang.String;@63d8d9ac) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@374e89c3) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@38cf6215) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@37effc3f) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4462b97f) STANDARD_ERROR + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@342fdf0b) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@2b25cf93) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@74e31747) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.3800032499323280799.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4ca6bb07) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7df7b45f) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@25c182f1) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1890e435) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@233b7153) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@62aff41) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@164ccde5) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@45b5616) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1bc1dc48) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@b8d567e) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@4866415b, 5) STANDARD_ERROR - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:25:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@45dd7bea, 5) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:15:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@d8f5ca2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2784039e], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:25:50 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@201d5a88, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5391807a], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:25:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2025-06-03 15:15:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72437e01, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7467a8f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@553307d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@26913969, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@345e1f9a], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:25:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72437e01, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7467a8f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@553307d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@26913969, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@345e1f9a], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:25:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72437e01, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7467a8f7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@553307d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@26913969, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@345e1f9a], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:25:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Finished 5600 tests -Finished 5800 tests -some stuffFinished 6000 tests +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2343855a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@150dbd1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15777215, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@54cd886, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4db43140], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:15:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Finished 4200 tests +Finished 4400 tests +some stuffFinished 4600 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file9125696051509082103.bad -Finished 6200 tests -Finished 6400 tests + Could not delete file file12829976832041055813.bad +Finished 4800 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT Time to construct a tree with 50000 nodes: 29 milliseconds - Queried for the same 100-length mapping 214397977 times in 10 seconds. + Queried for the same 100-length mapping 209851170 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6600 tests + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 5000 tests +Finished 5200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6800 tests -Finished 7000 tests + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 5400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) +Finished 5600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -7233,13 +7262,12 @@ Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058 + .) STANDARD_OUT Diagnosing chrX:48774611-48775058 + . (len 448) chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 -Finished 7200 tests -Finished 7400 tests +Finished 5800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:26:06 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 7600 tests - Gradle is still running, please be patient... + INFO 2025-06-03 15:16:08 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6000 tests +Finished 6200 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 @@ -7261,103 +7289,103 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - d b - a + d e c -Finished 7800 tests -Finished 8000 tests + a +Finished 6400 tests +Finished 6600 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2025-06-03 15:16:34 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD VN:1.0 SO:FALSE ) STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2025-06-03 15:16:34 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2025-06-03 15:16:34 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2025-06-03 15:16:34 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD VN:1.0 SO:cOoRdinate ) STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2025-06-03 15:16:34 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2024-04-30 06:26:34 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2024-04-30 06:26:34 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2025-06-03 15:16:34 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2025-06-03 15:16:34 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.14170264746838317495..cram - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2024-04-30 06:26:34 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.1568143910345870867..cram + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2025-06-03 15:16:34 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension18382404068261087157.cram + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension12599895228598270492.cram Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR - Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.17198274230218226457.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.3256785474167497241.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension4189212954870707337.cram - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2024-04-30 06:26:34 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension5602041274548275673.cram + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2025-06-03 15:16:34 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension6884590729963019389 + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension8220755866087596270 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension17465590380191835254.png + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension3280966596230784115.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://89de91f4-acd9-42d5-9871-18fb18ac6270/work/testMakeWriterPathsam + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4a3e844d-ebac-49bd-a9e8-fbcfd7763535/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://109e3503-7b33-4856-886d-91081fcdaeb6/work/testMakeWriterPathbam + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f0d0b879-c4e6-4547-9b3d-47a6c2cb0317/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ee24604a-7555-427f-9893-55090315d59e/work/testMakeWriterPathcram + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8b42eb1b-2189-4374-97c3-54b797340b52/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://07f4b4b6-3409-4d1e-b9e6-56c568be0b2d/work/testMakeWriterPathsam + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c86421eb-158b-4385-91f7-93e69c80d63c/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8fe7587e-1750-40e7-9721-80afb675b2d7/work/testMakeWriterPathbam + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://68c30191-e1a4-49e8-b62f-fb86c71f9743/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR - INFO 2024-04-30 06:26:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ed7df605-48a3-4d55-b9da-f7acd1915882/work/testMakeWriterPathcram + INFO 2025-06-03 15:16:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8ab1edc9-3d21-4563-9721-829070cb61b3/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 -Finished 8200 tests -Finished 8400 tests +Finished 6800 tests +Finished 7000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2024-04-30 06:26:47 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2025-06-03 15:16:46 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest STANDARD_ERROR ngs-java: DLL download was disabled @@ -7389,172 +7417,172 @@ Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[1](SRR2096940, CM000681.1, 55627015, 10591) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAQueryTest.testReferenceAlignedCounts[2](SRR2096940, CM000681.1, 55627016, 0) SKIPPED -Finished 8600 tests Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReference[0](SRR2096940, CM000681.1, 95001, 95050, AGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCAT) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReferenceMt[0](SRR353866, [AAAB01001871.1:1-50 = TGACGCGCATGAATGGATTAACGAGATTCCCTCTGTCCCTATCTACTATC, AAAB01001871.1:901-950 = ACCAAGCGTACGATTGTTCACCCTTTCAAGGGAACGTGAGCTGGGTTTAG, AAAB01008987.1:1-50 = TTTTGGACGATGTTTTTGGTGAACAGAAAACGAGCTCAATCATCCAGAGC, AAAB01008859.1:1-50 = CAAAACGATGCCACAGATCAGAAGTTAATTAACGCACATTCTCCACCCAC]) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2024-04-30 06:26:48 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2024-04-30 06:26:48 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2025-06-03 15:16:47 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2025-06-03 15:16:47 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam +Finished 7200 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2024-04-30 06:26:48 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2024-04-30 06:26:48 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2024-04-30 06:26:48 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2024-04-30 06:26:48 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2025-06-03 15:16:48 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2025-06-03 15:16:48 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2025-06-03 15:16:48 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2025-06-03 15:16:48 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2024-04-30 06:26:48 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2025-06-03 15:16:48 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2024-04-30 06:26:49 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... - INFO 2024-04-30 06:26:49 SamReaderFactoryTest Finished queries in 35ms + INFO 2025-06-03 15:16:48 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2025-06-03 15:16:48 SamReaderFactoryTest Finished queries in 60ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2024-04-30 06:26:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:16:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR - WARNING 2024-04-30 06:26:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:16:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR - WARNING 2024-04-30 06:26:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:16:48 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 8800 tests + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2024-04-30 06:26:49 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2025-06-03 15:16:49 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2024-04-30 06:26:49 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2025-06-03 15:16:49 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:16:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-04-30 06:26:49 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2025-06-03 15:16:49 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2025-06-03 15:16:49 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-04-30 06:26:49 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2025-06-03 15:16:49 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2025-06-03 15:16:49 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED -Finished 9000 tests +Finished 7400 tests +Finished 7600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED -Finished 9200 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:16:49 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR - WARNING 2024-04-30 06:26:49 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2024-04-30 06:26:49 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2025-06-03 15:16:49 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2025-06-03 15:16:49 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. +Finished 7800 tests Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir @@ -7577,141 +7605,141 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir +Finished 8000 tests +Finished 8200 tests +Finished 8400 tests +Finished 8600 tests +Finished 8800 tests +Finished 9000 tests +Finished 9200 tests Finished 9400 tests Finished 9600 tests Finished 9800 tests Finished 10000 tests + Gradle is still running, please be patient... Finished 10200 tests -Finished 10400 tests -Finished 10600 tests -Finished 10800 tests -Finished 11000 tests -Finished 11200 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[59](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[60](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[61](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[62](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[63](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[64](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[65](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[66](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[67](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[68](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[69](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:26:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 11400 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[183](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:26:51 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. -Finished 11600 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[461](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[462](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[463](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[464](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[465](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[466](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[467](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[468](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[469](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[470](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[471](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 11800 tests -Finished 12000 tests +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[398](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[399](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[400](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[401](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[402](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[403](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[404](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[405](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[406](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[407](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[408](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[414](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:18:03 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[426](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[427](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[428](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[429](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[430](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[431](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[432](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[433](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[434](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[435](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[436](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:18:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 10400 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2024-04-30 06:28:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:18:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2024-04-30 06:28:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:18:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2024-04-30 06:28:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Finished 12200 tests -Finished 12400 tests + WARNING 2025-06-03 15:18:04 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 10600 tests +Finished 10800 tests Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops @@ -7732,6 +7760,14 @@ at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:840) +Finished 11000 tests +Finished 11200 tests +Finished 11400 tests +Finished 11600 tests +Finished 11800 tests +Finished 12000 tests +Finished 12200 tests +Finished 12400 tests Finished 12600 tests Finished 12800 tests Finished 13000 tests @@ -7855,17 +7891,17 @@ WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release Results: SUCCESS (35817 tests, 35791 successes, 0 failures, 26 skipped) -Finished generating test XML results (0.33 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.292 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.288 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 12 mins 37.694 secs. -:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 6,5,main]) started. +Finished generating test html results (0.241 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 11 mins 55.929 secs. +:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 3,5,main]) started. :testWithOptimisticVCF4_4 executing task ':testWithOptimisticVCF4_4' ... Putting task artifact state for task ':testWithOptimisticVCF4_4' into context took 0.0 secs. -Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.028 secs. It is not up-to-date because: +Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.045 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath9387866982432323449txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' +Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath3557541738552212450txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' Successfully started process 'Gradle Test Executor 2' Gradle Test Executor 2 started executing tests. Gradle Test Executor 2 finished executing tests. @@ -7876,20 +7912,20 @@ Results: SUCCESS (0 tests, 0 successes, 0 failures, 0 skipped) Finished generating test XML results (0.0 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithOptimisticVCF4_4 Generating HTML test report... -Finished generating test html results (0.001 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithOptimisticVCF4_4 -:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 1.587 secs. -:test (Thread[Task worker for ':' Thread 6,5,main]) started. +Finished generating test html results (0.004 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithOptimisticVCF4_4 +:testWithOptimisticVCF4_4 (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 1.435 secs. +:test (Thread[Task worker for ':' Thread 3,5,main]) started. :test executing task ':test' ... Putting task artifact state for task ':test' into context took 0.0 secs. Up-to-date check for task ':test' took 0.04 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath11789975779435961858txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' +Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7145509439580589075txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' Successfully started process 'Gradle Test Executor 3' Gradle Test Executor 3 started executing tests. Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms @@ -7919,7 +7955,7 @@ testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms @@ -7928,10 +7964,10 @@ testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms @@ -7940,7 +7976,7 @@ testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms @@ -7967,16 +8003,16 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testFirstSequenceExtended runtime: 1ms + testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 7ms + testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 4ms + testLastCompleteContigRead runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 1ms @@ -7985,22 +8021,22 @@ testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 10ms + testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 11ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 10ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 9ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 2ms + testLastCompleteContigRead runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstOfChr1 runtime: 1ms + testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms @@ -8018,22 +8054,22 @@ testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 0ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 7ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 7ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms @@ -8084,7 +8120,7 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms @@ -8099,7 +8135,7 @@ testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 1ms + testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -8117,7 +8153,7 @@ testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 1ms @@ -8129,13 +8165,13 @@ testReset runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 10ms + testReset runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 11ms + testReset runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 10ms + testReset runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms @@ -8144,20 +8180,20 @@ testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2024-04-30 06:29:09 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:19:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@169c6e28, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2024-04-30 06:29:09 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:19:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2024-04-30 06:29:09 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:19:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 200 tests Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2024-04-30 06:29:09 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:19:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2024-04-30 06:29:09 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:19:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 @@ -9218,441 +9254,433 @@ Finished 400 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.13212171085316457083.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.172046548055026987.bai - #BAMIndexWriterTest diff /tmp/javaBai.13212171085316457083.bai /tmp/cBai.172046548055026987.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.1747479980684561059.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.11804104086333295410.bai + #BAMIndexWriterTest diff /tmp/javaBai.1747479980684561059.bai /tmp/cBai.11804104086333295410.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.11548434139478637919.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.834872268968872081java.bai - #BAMIndexWriterTest diff /tmp/javaBai.834872268968872081java.bai.txt /tmp/cBai.11548434139478637919.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.4296675977070378954.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.17040063018247560354java.bai + #BAMIndexWriterTest diff /tmp/javaBai.17040063018247560354java.bai.txt /tmp/cBai.4296675977070378954.bai.txt Finished 600 tests -Finished 800 tests -Finished 1000 tests -Finished 1200 tests -Finished 1400 tests -Finished 1600 tests -Finished 1800 tests -Finished 2000 tests Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 5ms to write + 8ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 2ms to write + 3ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT - Creating file /tmp/BCOST.7061692740338153866.gz + Creating file /tmp/BCOST.4954632807742220128.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.14175871889989790288.gz + Creating file /tmp/testCustomDeflater.16415492608929428904.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.16545191982765114502.gz -Finished 2200 tests + Creating file /tmp/BCOST.9677100648622238739.gz +Finished 800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2024-04-30 06:30:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:30:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2024-04-30 06:30:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:30:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2024-04-30 06:30:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-04-30 06:30:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2024-04-30 06:30:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-04-30 06:30:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2025-06-03 15:20:45 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2025-06-03 15:20:45 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2025-06-03 15:20:45 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2025-06-03 15:20:45 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:30:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2024-04-30 06:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:20:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:20:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2024-04-30 06:30:12 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-04-30 06:30:12 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2024-04-30 06:30:12 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-04-30 06:30:12 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2025-06-03 15:20:48 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2025-06-03 15:20:48 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2025-06-03 15:20:48 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2025-06-03 15:20:48 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR - WARNING 2024-04-30 06:30:12 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:30:12 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2024-04-30 06:30:12 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:30:12 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. -Finished 2400 tests + WARNING 2025-06-03 15:20:48 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:20:48 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2025-06-03 15:20:48 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:20:48 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR - WARNING 2024-04-30 06:34:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:34:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:24:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:24:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2024-04-30 06:34:37 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:34:37 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2024-04-30 06:34:37 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-04-30 06:34:37 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2025-06-03 15:24:50 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:24:50 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2025-06-03 15:24:50 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2025-06-03 15:24:50 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. +Finished 1000 tests Gradle is still running, please be patient... -Finished 2600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44e8a46a, [Ljava.lang.String;@63cb488) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e4fc0e4, [Ljava.lang.String;@bed9eac) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7088d985, [Ljava.lang.String;@65b30cbf) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5baf431a, [Ljava.lang.String;@1138a661) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@66ad114d, [Ljava.lang.String;@3d6aa1a8) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22a25d3a, [Ljava.lang.String;@19541178) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2d97eff1, [Ljava.lang.String;@2a168e2) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70f93fe, [Ljava.lang.String;@3d0abb2e) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3bb21436, [Ljava.lang.String;@1bf2485c) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5cde7865, [Ljava.lang.String;@1a9a6099) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@74bd0b88, [Ljava.lang.String;@3702467) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26ae94ff, [Ljava.lang.String;@41a6b05f) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7eb0c2b, [Ljava.lang.String;@123eb1d4) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@363618b5, [Ljava.lang.String;@44d004b3) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f3198ea, [Ljava.lang.String;@6f43c411) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@23c4c4f, [Ljava.lang.String;@4318880b) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@484c6334, [Ljava.lang.String;@77591ddb) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fab6626, [Ljava.lang.String;@68a558f) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43877f0e, [Ljava.lang.String;@54feaa2e) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27c8143c, [Ljava.lang.String;@570155f8) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@653c2282, [Ljava.lang.String;@6f212fef) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@c93e43) STANDARD_ERROR - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7be8aedf) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@108f9823) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@33af1f92) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@15cab86b) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@6beb8597) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@27ab2509) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@759165c3) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@8f0bb9c, [Ljava.lang.String;@28ec9d3c) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5703b18d, [Ljava.lang.String;@56ed8401) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f8c422, [Ljava.lang.String;@14fef042) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@251277c7, [Ljava.lang.String;@468e10c7) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78307f72, [Ljava.lang.String;@500ab7ad) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15582e6, [Ljava.lang.String;@4a6e772a) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@51a4e2ef, [Ljava.lang.String;@24396102) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fbdf1ce, [Ljava.lang.String;@62de2afa) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f8f7942, [Ljava.lang.String;@53f1a1) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fd83bee, [Ljava.lang.String;@49d793f3) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@595b1b3e, [Ljava.lang.String;@7079df60) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1dadae69, [Ljava.lang.String;@5c0fbefb) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79e289b7, [Ljava.lang.String;@1d7d272a) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f38f5d4, [Ljava.lang.String;@411ec08c) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69ef4f32, [Ljava.lang.String;@cfe9f49) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35c3399c, [Ljava.lang.String;@1f964a67) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b306ecf, [Ljava.lang.String;@5382c776) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@29b3401c) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3cbfc257) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@12e9a823) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@31091864) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@a2cee93) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7edf2413) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@5852f258) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7c3c7291) STANDARD_ERROR + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@25e620e6, [Ljava.lang.String;@44f79a6a) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@156fa4bb, [Ljava.lang.String;@7801b4e4) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e7a2681, [Ljava.lang.String;@5f1e3173) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36daebe5, [Ljava.lang.String;@6fdcde86) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a51d849, [Ljava.lang.String;@7358588a) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70ea8845, [Ljava.lang.String;@2117197b) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6492095d, [Ljava.lang.String;@6c97bc8) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26d9b9dc, [Ljava.lang.String;@532f3f6e) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6800d77f, [Ljava.lang.String;@4d6355c5) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e33fdc7, [Ljava.lang.String;@5e4f9225) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a31e859, [Ljava.lang.String;@29225a70) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1898e16a, [Ljava.lang.String;@41859619) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@671a5ae4, [Ljava.lang.String;@6535ec96) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@470b3822, [Ljava.lang.String;@60879b90) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1a0d0433, [Ljava.lang.String;@4154149c) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@612f83d8, [Ljava.lang.String;@2439c761) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@276467ed, [Ljava.lang.String;@99483e7) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@d8797d1) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@60579d55) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@3f8ec06f) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@51ebc774) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@52e68e5c) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2a5e9327) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@eb9ac9c) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@743dcf84) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2312b0) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5b24828) STANDARD_ERROR - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1866e845) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@7e936cef) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@11c7e3e9) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6436ff5f) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4e91d781) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@3daab09b) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@69037a54) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@c7794de) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1005dc2d) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6a94fe9b) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@45efe86) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@4b1d34ec) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@16b4fc4d) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1e00d1bc) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@a916a76) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@13231f38) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@2d0186de) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@17c9c640) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@3432b99e) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@601d1609) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.17572956246248730660.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@47269c65) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 2800 tests + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5e9515fe, [Ljava.lang.String;@28a4c1e9) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30bd5994, [Ljava.lang.String;@1fe84e57) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b79c399, [Ljava.lang.String;@135e4946) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27eceb14, [Ljava.lang.String;@10d28028) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4682b7b9, [Ljava.lang.String;@3be72e7c) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7e6c62b1, [Ljava.lang.String;@31d1d0d9) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ff6d56d, [Ljava.lang.String;@5d724e38) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 1200 tests -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@33f557e5, 5) STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6494f524, [Ljava.lang.String;@6893dbc8) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29a6e90c, [Ljava.lang.String;@6bf9e608) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@246e46d0, [Ljava.lang.String;@268ae346) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15733ed2, [Ljava.lang.String;@3c5ed10a) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@608a19c, [Ljava.lang.String;@7ee4db53) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e9cf143, [Ljava.lang.String;@261c2955) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42df468e, [Ljava.lang.String;@6ee10344) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fa284e5, [Ljava.lang.String;@6dec6917) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@64bc0bc2, [Ljava.lang.String;@63fb81c3) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@626e0b9b, [Ljava.lang.String;@1d385889) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@558feb61) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@36b7c2d8) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@35bd291d) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@8e5daaf) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6e58dc03) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7e15db06) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@71de70d1) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@40d61bac) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2e326211) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@64aed219) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@ddefa82) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@aeff070) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@60422725) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@13ac6733) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5ecf902) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4759af46) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@499d6978) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@16cf28a8) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@48561120) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6f6d905c) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@650c4c56) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2ae0b8b7) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@39fa920) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@115d4230) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@409a016d) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@404a26a4) STANDARD_ERROR + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@107936f4) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2f6338e5) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@67767425) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5f62f206) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.9734174648722611297.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2dca71bd) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@346fcd96, 5) STANDARD_ERROR + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2024-04-30 06:37:31 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2025-06-03 15:27:38 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 @@ -10309,16 +10337,17 @@ Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 -Finished 3000 tests -Finished 3200 tests +Finished 1400 tests +Finished 1600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2024-04-30 06:37:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2024-04-30 06:37:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 1800 tests Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -10374,504 +10403,504 @@ Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.15737494180588331610.tmp -Finished 3400 tests -Finished 3600 tests -Finished 3800 tests -Finished 4000 tests -Finished 4200 tests -Finished 4400 tests -Finished 4600 tests + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.10342644787588597466.tmp +Finished 2000 tests +Finished 2200 tests +Finished 2400 tests +Finished 2600 tests +Finished 2800 tests +Finished 3000 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2024-04-30 06:37:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:27:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2024-04-30 06:37:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Finished 4800 tests -Finished 5000 tests + WARNING 2025-06-03 15:27:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 3200 tests +Finished 3400 tests +Finished 3600 tests Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Finished 5200 tests + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-04-30 06:37:46 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2025-06-03 15:27:53 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Finished 3800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2024-04-30 06:37:47 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2025-06-03 15:27:53 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR - WARNING 2024-04-30 06:37:47 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2025-06-03 15:27:53 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@706f293d, [Ljava.lang.String;@50235641) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f8a8cd9, [Ljava.lang.String;@22d60b7c) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7a15030b, [Ljava.lang.String;@713220d0) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@402adafa, [Ljava.lang.String;@27650402) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@334c8663) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5bfc643) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@36d0183d) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Finished 5400 tests - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1ffe640a) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4f53a1d4) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1ffba27f) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@428cbb57) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4aa778f5) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@19b3c644, [Ljava.lang.String;@43cddb90) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@706ea96d, [Ljava.lang.String;@36a37952) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@57f22181, [Ljava.lang.String;@6d3cf7ab) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d74a585, [Ljava.lang.String;@7e1cb410) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45f33a47, [Ljava.lang.String;@1540b1c) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@14b85626, [Ljava.lang.String;@98f9732) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ceef4e2, [Ljava.lang.String;@140a907f) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c18e0a6, [Ljava.lang.String;@7826ecad) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4230461f, [Ljava.lang.String;@7217c4ac) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b458f86, [Ljava.lang.String;@c2e70) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a0d2599, [Ljava.lang.String;@181c03c) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@277c857f, [Ljava.lang.String;@4007a8e8) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@246f85bc, [Ljava.lang.String;@2ff9973b) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f9266bf, [Ljava.lang.String;@2eea4989) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d62f836, [Ljava.lang.String;@461dfaa2) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@295efed1, [Ljava.lang.String;@793f7a4) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7707aa2d, [Ljava.lang.String;@135d33e8) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6469e460) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2a3322ed) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1c32a0e6) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2d748564) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@61996cf6) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@b319d51) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@6ac16bdd) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1fbfd1d6) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5488f9ea, [Ljava.lang.String;@2b94cc04) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@65701ad0, [Ljava.lang.String;@4ead36e0) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@366702bb, [Ljava.lang.String;@197f72c3) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37d8b041, [Ljava.lang.String;@3c4369cb) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36a56cdc, [Ljava.lang.String;@5fe2d78d) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@301ec8c1, [Ljava.lang.String;@59a0faf5) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@487b3e25, [Ljava.lang.String;@267cead9) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19071978, [Ljava.lang.String;@7d391967) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@bdc229c, [Ljava.lang.String;@2e45ac83) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1de060c7, [Ljava.lang.String;@394e162d) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2ce853b8, [Ljava.lang.String;@785c69ec) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b9333c9, [Ljava.lang.String;@1287b953) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@58c02614, [Ljava.lang.String;@576a536) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5b9f8bba, [Ljava.lang.String;@5491d8cb) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30c74afa, [Ljava.lang.String;@4be8f5a4) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4582a95b, [Ljava.lang.String;@4137800e) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f4bbeaf, [Ljava.lang.String;@499825cf) STANDARD_ERROR + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@543d3de2) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@1715b7bf) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5444d8b5) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2eaf50aa) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@483e3e02) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2ac50a79, [Ljava.lang.String;@78900859) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54679d83, [Ljava.lang.String;@462ea03f) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36b9598, [Ljava.lang.String;@624899f6) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2a84c2df, [Ljava.lang.String;@65ddcef) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@469d1a6b, [Ljava.lang.String;@38ed3237) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4c5f7328, [Ljava.lang.String;@48434bef) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62e1b9c9, [Ljava.lang.String;@d03ad1c) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29d0a511, [Ljava.lang.String;@473c71e8) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@67ef77ee, [Ljava.lang.String;@68609eb6) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77bb2bb7, [Ljava.lang.String;@45d968a2) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@564382aa, [Ljava.lang.String;@20596cf5) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@48277608, [Ljava.lang.String;@baa91df) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1e5e75ed, [Ljava.lang.String;@7465ce25) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42b74689, [Ljava.lang.String;@1d3bd968) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39a2fb74, [Ljava.lang.String;@64a91d6e) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@781f3d2b, [Ljava.lang.String;@6ef62b2e) STANDARD_ERROR - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e50208f, [Ljava.lang.String;@31f3aff1) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6670c512) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@72c62b97) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2dc3a73) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@670baa33) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@ff2e88a) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@5c3fcc50) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@519dc562) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.3478312991303092177.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@1091d712) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@17c91cd2) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5b380222) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@10f7d6c3) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@623554b6) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2ee42a03) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@419bcb5c) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@60dfe0a) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4287145e) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@60a1562c) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@118b7a71) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@59deac9d) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@58480d4a) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@46e2d5b1) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@458cfd81) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@6fc70a4e, [Ljava.lang.String;@393e9fb1) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@312965c5, [Ljava.lang.String;@6d2981a7) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2429b974, [Ljava.lang.String;@df4488a) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@533a7b8b, [Ljava.lang.String;@51f83f4e) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@253a1f88, [Ljava.lang.String;@6a270c10) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3aa5fb03, [Ljava.lang.String;@6b3050ad) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c66672, [Ljava.lang.String;@755ab9de) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c575d99, [Ljava.lang.String;@36f79e83) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77487e5, [Ljava.lang.String;@282dd29d) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@433b8757, [Ljava.lang.String;@571b725e) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@495b8f28, [Ljava.lang.String;@2d869380) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 4000 tests + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c1056bc, [Ljava.lang.String;@4576194e) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f78d45e, [Ljava.lang.String;@7c1760e5) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@683edb4f, [Ljava.lang.String;@35a448d6) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c15865c, [Ljava.lang.String;@4d045c13) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@100d4fcd, [Ljava.lang.String;@177b01be) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b504264, [Ljava.lang.String;@4a4cec98) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@e85d062) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@6d45d904) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@259f472d) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@19b8551) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@b738659) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@57f21d3b) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@591652b) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.4570699093413518132.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@73e78369) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7075fd2e) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1c9fac72) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@207f438) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@252eed6) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6e169242) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@11a23c8) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5b7c3a52) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4f4551b2) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2a23d31b) STANDARD_ERROR + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:55 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@45207315, 5) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:37:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@57e6f2a9, 5) STANDARD_ERROR + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:27:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@647e7cb7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@547d78cb], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@66b3fafe, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@56d9efae], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:27:56 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2025-06-03 15:27:56 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49dae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b6bddcc, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1282ed96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1323a85f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27156a8e], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:27:56 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49dae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b6bddcc, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1282ed96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1323a85f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27156a8e], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:27:56 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49dae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b6bddcc, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1282ed96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1323a85f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27156a8e], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-04-30 06:37:49 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Finished 5600 tests -Finished 5800 tests -some stuffFinished 6000 tests +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7106a2c7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c649c4a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4167f6e4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@45b4a65, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23e09c3c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2025-06-03 15:27:56 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Finished 4200 tests +Finished 4400 tests +some stuffFinished 4600 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file8767957066350501193.bad -Finished 6200 tests -Finished 6400 tests + Could not delete file file10312350155809276216.bad +Finished 4800 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 34 milliseconds - Queried for the same 100-length mapping 176595493 times in 10 seconds. + Time to construct a tree with 50000 nodes: 30 milliseconds + Queried for the same 100-length mapping 214359980 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6600 tests + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 5000 tests +Finished 5200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6800 tests -Finished 7000 tests + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 5400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) +Finished 5600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -11029,12 +11058,12 @@ Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058 + .) STANDARD_OUT Diagnosing chrX:48774611-48775058 + . (len 448) chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 -Finished 7200 tests -Finished 7400 tests +Finished 5800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-04-30 06:38:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 7600 tests + INFO 2025-06-03 15:28:10 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6000 tests +Finished 6200 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 @@ -11056,261 +11085,260 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - b - a d e c -Finished 7800 tests -Finished 8000 tests + b + a +Finished 6400 tests +Finished 6600 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2025-06-03 15:28:34 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD VN:1.0 SO:FALSE ) STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2025-06-03 15:28:34 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2025-06-03 15:28:34 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2025-06-03 15:28:34 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD VN:1.0 SO:cOoRdinate ) STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2025-06-03 15:28:34 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2024-04-30 06:38:32 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2024-04-30 06:38:32 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2025-06-03 15:28:34 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2025-06-03 15:28:34 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.11032455663600022059..cram - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.17251361361741487238..cram + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension8775432608370856993.cram + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension1835310855957523149.cram Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR - Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.18207260867672354233.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.10939782239141989243.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension12562055774463340261.cram - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension12709178603073247359.cram + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension4413654420908957463 + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension9588431482652211133 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension5013357549288129526.png + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension13756555188097146974.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://3b91462e-2636-4044-ace3-118962209b24/work/testMakeWriterPathsam + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://a4453744-6589-48c3-8aa2-4e95a3e7ae0c/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://511ea4b9-c88b-4343-a1ff-17323841a92a/work/testMakeWriterPathbam + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://193f36ab-cca5-4bff-b7da-f498d380be3c/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://6348f92c-072c-4e57-9245-c70a84187146/work/testMakeWriterPathcram + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://77cc6c5c-db41-4c78-b978-cca734673979/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4f5e595b-7b98-48e0-be94-cfacf1b4b644/work/testMakeWriterPathsam + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://590000ef-d7d1-4e61-a89e-bb4e0198e5f1/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://e54325d4-9de7-4fc6-b89f-06fa34d7c73c/work/testMakeWriterPathbam + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://71ba114c-2962-4917-b29b-e94eb234e536/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR - INFO 2024-04-30 06:38:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4dbc195b-3c57-4afc-b45f-10ada8a37c29/work/testMakeWriterPathcram + INFO 2025-06-03 15:28:34 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://0da2f541-84ab-4dca-a341-27177ccc4952/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 -Finished 8200 tests -Finished 8400 tests +Finished 6800 tests +Finished 7000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2024-04-30 06:38:45 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. -Finished 8600 tests + ERROR 2025-06-03 15:28:46 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2024-04-30 06:38:45 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2024-04-30 06:38:45 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2025-06-03 15:28:46 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2025-06-03 15:28:46 SamFiles The index file /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam +Finished 7200 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2024-04-30 06:38:46 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2024-04-30 06:38:46 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2024-04-30 06:38:46 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2024-04-30 06:38:46 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2025-06-03 15:28:47 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2025-06-03 15:28:47 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2025-06-03 15:28:47 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2025-06-03 15:28:47 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2024-04-30 06:38:46 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2025-06-03 15:28:47 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2024-04-30 06:38:46 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... - INFO 2024-04-30 06:38:46 SamReaderFactoryTest Finished queries in 28ms + INFO 2025-06-03 15:28:47 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2025-06-03 15:28:47 SamReaderFactoryTest Finished queries in 58ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2024-04-30 06:38:46 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:28:47 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR - WARNING 2024-04-30 06:38:46 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:28:47 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR - WARNING 2024-04-30 06:38:46 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2025-06-03 15:28:47 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 8800 tests + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-04-30 06:38:46 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2025-06-03 15:28:47 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2025-06-03 15:28:47 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR - WARNING 2024-04-30 06:38:46 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-04-30 06:38:46 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2025-06-03 15:28:47 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2025-06-03 15:28:47 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED -Finished 9000 tests +Finished 7400 tests +Finished 7600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED -Finished 9200 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:46 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:47 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR - WARNING 2024-04-30 06:38:47 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2024-04-30 06:38:47 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2025-06-03 15:28:48 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2025-06-03 15:28:48 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir @@ -11333,141 +11361,141 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir +Finished 7800 tests +Finished 8000 tests +Finished 8200 tests +Finished 8400 tests +Finished 8600 tests +Finished 8800 tests +Finished 9000 tests +Finished 9200 tests Finished 9400 tests Finished 9600 tests Finished 9800 tests Finished 10000 tests -Finished 10200 tests -Finished 10400 tests -Finished 10600 tests -Finished 10800 tests -Finished 11000 tests -Finished 11200 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[6](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-04-30 06:38:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[23](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[24](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[25](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[26](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[27](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[28](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[29](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[30](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[31](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[32](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[33](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:38:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 11400 tests +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[233](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[234](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[235](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[236](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[237](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[238](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[239](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[240](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[241](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[242](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[243](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[277](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[278](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[279](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[280](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[281](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[282](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[283](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[284](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[285](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[286](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[287](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2025-06-03 15:28:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 10200 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[320](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[321](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[322](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[323](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[324](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[325](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[326](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[327](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[328](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[329](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[330](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-04-30 06:39:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 11600 tests -Finished 11800 tests -Finished 12000 tests +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[511](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2025-06-03 15:29:57 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. +Finished 10400 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2024-04-30 06:40:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:29:58 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2024-04-30 06:40:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2025-06-03 15:29:58 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2024-04-30 06:40:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Finished 12200 tests -Finished 12400 tests + WARNING 2025-06-03 15:29:58 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 10600 tests +Finished 10800 tests Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops @@ -11488,6 +11516,14 @@ at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:840) +Finished 11000 tests +Finished 11200 tests +Finished 11400 tests +Finished 11600 tests +Finished 11800 tests +Finished 12000 tests +Finished 12200 tests +Finished 12400 tests Finished 12600 tests Finished 12800 tests Finished 13000 tests @@ -11603,20 +11639,20 @@ Finished 35000 tests Finished 35200 tests Finished 35400 tests -Finished 35600 tests -Finished 35800 tests -Gradle Test Executor 3 finished executing tests. WARNING: A terminally deprecated method in java.lang.System has been called +Gradle Test Executor 3 finished executing tests. WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release +Finished 35600 tests +Finished 35800 tests Results: SUCCESS (35800 tests, 35790 successes, 0 failures, 10 skipped) -Finished generating test XML results (0.062 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test +Finished generating test XML results (0.274 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.122 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test -:test (Thread[Task worker for ':' Thread 6,5,main]) completed. Took 11 mins 55.361 secs. +Finished generating test html results (0.182 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test +:test (Thread[Task worker for ':' Thread 3,5,main]) completed. Took 11 mins 45.223 secs. -BUILD SUCCESSFUL in 24m 50s +BUILD SUCCESSFUL in 23m 55s 7 actionable tasks: 5 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg' create-stamp debian/debhelper-build-stamp @@ -11643,10 +11679,10 @@ install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc-base/ install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc dh_installchangelogs -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc - install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian + install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc + install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian dh_installsystemduser -O--buildsystem=gradle dh_lintian -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides @@ -11669,8 +11705,8 @@ Updating manifest in /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar jh_manifest -O--buildsystem=gradle find debian/libhtsjdk-java -name '*.jar' - Found symlink usr/share/java/htsjdk.jar Found usr/share/java/htsjdk-4.1.0.jar + Found symlink usr/share/java/htsjdk.jar Reading manifest from debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar No update of debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar required. find debian/libhtsjdk-java-doc -name '*.jar' @@ -11724,1005 +11760,1005 @@ Using 1707687699 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar using File::StripNondeterminism::handlers::jar Using 1707687699 as canonical time - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Bases.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huff Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsContentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/IOUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.PairOrientation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::han Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cra Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/u Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::S Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.Strategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Chunk.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordDuplicateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.ht Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SamRecordFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/JavascriptSamRecordFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InvertFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/OverclippedReadFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/ReadNameFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SamRecordFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.LazyInitializer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequest.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequestField.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetClass.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetErrorResponse.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-d Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism:: Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SolexaQualityConverter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.OverlapIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iterables.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.ValuesIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Lazy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeIOException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.SequenceListsDifferException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTreeMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.LogLevel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.InvalidDateException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CodeUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ListMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-javaoc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc +ml using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc +Gff3Constants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc -ipNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png -va/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-dom/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc +tripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc -api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPClient.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc -bhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc +oc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc -Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NamedFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc +using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamConstants.html using 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc +handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc -/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc -dlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc -debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc -ism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locatable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekableIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc +c/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle - cd debian/libhtsjdk-java-doc cd debian/libhtsjdk-java + cd debian/libhtsjdk-java-doc chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.0+dfsg' @@ -12734,8 +12770,8 @@ find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -12744,19 +12780,19 @@ install -m0755 -d debian/libhtsjdk-java/DEBIAN install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN dh_gencontrol -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java/DEBIAN - echo misc:Depends= >> debian/libhtsjdk-java.substvars - echo misc:Pre-Depends= >> debian/libhtsjdk-java.substvars - dpkg-gencontrol -plibhtsjdk-java -ldebian/changelog -Tdebian/libhtsjdk-java.substvars -cdebian/control -Pdebian/libhtsjdk-java install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN echo misc:Depends= >> debian/libhtsjdk-java-doc.substvars echo misc:Pre-Depends= >> debian/libhtsjdk-java-doc.substvars dpkg-gencontrol -plibhtsjdk-java-doc -ldebian/changelog -Tdebian/libhtsjdk-java-doc.substvars -cdebian/control -Pdebian/libhtsjdk-java-doc + install -m0755 -d debian/libhtsjdk-java/DEBIAN + echo misc:Depends= >> debian/libhtsjdk-java.substvars + echo misc:Pre-Depends= >> debian/libhtsjdk-java.substvars + dpkg-gencontrol -plibhtsjdk-java -ldebian/changelog -Tdebian/libhtsjdk-java.substvars -cdebian/control -Pdebian/libhtsjdk-java chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control dh_md5sums -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN install -m0755 -d debian/libhtsjdk-java/DEBIAN + install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums @@ -12764,8 +12800,8 @@ dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. -dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb'. dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.0+dfsg-1_all.deb'. +dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../htsjdk_4.1.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../htsjdk_4.1.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -12773,12 +12809,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/787020/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1256643 and its subdirectories -I: Current time: Tue Apr 30 06:41:18 -12 2024 -I: pbuilder-time-stamp: 1714502478 +I: removing directory /srv/workspace/pbuilder/787020 and its subdirectories +I: Current time: Tue Jun 3 15:31:52 +14 2025 +I: pbuilder-time-stamp: 1748914312