Diff of the two buildlogs: -- --- b1/build.log 2024-12-15 13:42:34.584206027 +0000 +++ b2/build.log 2024-12-15 14:25:44.286493712 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 15 01:09:12 -12 2024 -I: pbuilder-time-stamp: 1734268152 +I: Current time: Sun Jan 18 10:05:39 +14 2026 +I: pbuilder-time-stamp: 1768680339 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -41,52 +41,84 @@ 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/2839298/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/354657/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Jan 17 20:05 /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/354657/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/354657/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='arm64' - 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a94f73d3e6364779b9862874b960c37d' - 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='2839298' - PS1='# ' - PS2='> ' + INVOCATION_ID=bc3de39f48bd42218f83e2cbf91a9bf7 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=354657 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.2NtSTkCJ/pbuilderrc_i0UL --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2NtSTkCJ/b1 --logfile b1/build.log htsjdk_4.1.0+dfsg-2.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' - http_proxy='http://192.168.101.4:3128' + 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.2NtSTkCJ/pbuilderrc_1RfC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2NtSTkCJ/b2 --logfile b2/build.log htsjdk_4.1.0+dfsg-2.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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2839298/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/354657/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -565,7 +597,7 @@ Get: 405 http://deb.debian.org/debian unstable/main arm64 libngs-jni arm64 3.0.9+dfsg-7+b1 [25.8 kB] Get: 406 http://deb.debian.org/debian unstable/main arm64 libngs-java arm64 3.0.9+dfsg-7+b1 [112 kB] Get: 407 http://deb.debian.org/debian unstable/main arm64 scala-library all 2.11.12-5 [9588 kB] -Fetched 346 MB in 2s (188 MB/s) +Fetched 346 MB in 2s (167 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20082 files and directories currently installed.) @@ -1906,8 +1938,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 15 13:10:06 UTC 2024. -Universal Time is now: Sun Dec 15 13:10:06 UTC 2024. +Local time is now: Sat Jan 17 20:07:30 UTC 2026. +Universal Time is now: Sat Jan 17 20:07:30 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2446,7 +2478,11 @@ 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-2_source.changes +I: user script /srv/workspace/pbuilder/354657/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/354657/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-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 4.1.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2462,7 +2498,7 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" Duplicate specification "u=s" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper @@ -2485,7 +2521,7 @@ dh_autoreconf -O--buildsystem=gradle dh_auto_configure -O--buildsystem=gradle jh_linkjars -O--buildsystem=gradle -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" Duplicate specification "unlink|u" for option "u" debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/htsjdk-4.1.0+dfsg' @@ -2500,18 +2536,18 @@ 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-21-openjdk-arm64/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 1.069 secs. -The client will now receive all logging from the daemon (pid: 2857569). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-2857569.out.log +An attempt to start the daemon took 2.277 secs. +The client will now receive all logging from the daemon (pid: 403772). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-403772.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@6447a887 -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@6447a887 -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@63776227 +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@222132c4 +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@222132c4 +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@1b0871ac 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@79a2ad7c +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@597fc60c 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. @@ -2531,17 +2567,17 @@ 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@1e420e6b +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@10a8bcf9 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@63776227 -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@4f81aa3d -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@2ba72708 -:compileJava (Thread[#58,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@1b0871ac +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@14b76fb9 +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c93a7ac +:compileJava (Thread[#55,Task worker for ':',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@70dbd4fe +Putting task artifact state for task ':compileJava' into context took 0.025 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@73f0eed7 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 @@ -2564,7 +2600,7 @@ 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 1.634 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 4.004 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. @@ -2582,39 +2618,39 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileJava (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 10.699 secs. -:processResources (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 24.982 secs. +:processResources (Thread[#55,Task worker for ':',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 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.015 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.044 secs. -:classes (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:processResources (Thread[#55,Task worker for ':',5,main]) completed. Took 0.075 secs. +:classes (Thread[#55,Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. -:classes (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:classes (Thread[#55,Task worker for ':',5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[#55,Task worker for ':',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[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.081 secs. -:jar (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:debianMavenPom (Thread[#55,Task worker for ':',5,main]) completed. Took 0.183 secs. +:jar (Thread[#55,Task worker for ':',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 0.035 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.069 secs. It is not up-to-date because: No history is available. -:jar (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.37 secs. -:javadoc (Thread[#58,Task worker for ':' Thread 3,5,main]) started. +:jar (Thread[#55,Task worker for ':',5,main]) completed. Took 0.575 secs. +:javadoc (Thread[#55,Task worker for ':',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 0.169 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.388 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc @/build/reproducible-path/htsjdk-4.1.0+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc'' @@ -2933,9 +2969,9 @@ /** Formats date & time */ ^ 100 warnings -:javadoc (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 10.808 secs. +:javadoc (Thread[#55,Task worker for ':',5,main]) completed. Took 27.678 secs. -BUILD SUCCESSFUL in 27s +BUILD SUCCESSFUL in 1m 5s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg' jh_build -O--buildsystem=gradle @@ -2954,17 +2990,17 @@ 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-21-openjdk-arm64/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 1.156 secs. -The client will now receive all logging from the daemon (pid: 2865699). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-2865699.out.log +An attempt to start the daemon took 2.38 secs. +The client will now receive all logging from the daemon (pid: 416143). The daemon log file: /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/daemon/4.4.1/daemon-416143.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@784241e0 -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@784241e0 -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@66f4f993 +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@fb44848 +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@fb44848 +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@63c1bb73 Starting Build -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@8909652 +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@630488ad Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.0+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.0+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] @@ -2979,16 +3015,16 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' 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@171f341e +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@3bc3fcbc Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':testWithDefaultReference', task ':testWithOptimisticVCF4_4', task ':test'] -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@66f4f993 -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@20016a52 -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1c89ef85 +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@63c1bb73 +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@14b0edfe +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5cad2778 :compileJava (Thread[#55,Task worker for ':',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@6e6fe503 +Putting task artifact state for task ':compileJava' into context took 0.009 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@243dd2ee 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 @@ -3011,23 +3047,23 @@ 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 0.83 secs). +Skipping task ':compileJava' as it is up-to-date (took 2.426 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 0.908 secs. -:processResources (Thread[#55,Task worker for ':',5,main]) started. +:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 2.548 secs. +:processResources (Thread[#56,Task worker for ':' Thread 2,5,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 0.004 secs). +Skipping task ':processResources' as it is up-to-date (took 0.023 secs). :processResources UP-TO-DATE -:processResources (Thread[#55,Task worker for ':',5,main]) completed. Took 0.009 secs. -:classes (Thread[#55,Task worker for ':',5,main]) started. +:processResources (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 0.064 secs. +:classes (Thread[#56,Task worker for ':' Thread 2,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#55,Task worker for ':',5,main]) completed. Took 0.001 secs. -:compileTestJava (Thread[#55,Task worker for ':',5,main]) started. +:classes (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. +:compileTestJava (Thread[#56,Task worker for ':' Thread 2,5,main]) started. :compileTestJava executing task ':compileTestJava' ... Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. @@ -3581,7 +3617,7 @@ 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 1.743 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 3.993 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. @@ -3716,31 +3752,31 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 42 warnings -:compileTestJava (Thread[#55,Task worker for ':',5,main]) completed. Took 9.709 secs. -:processTestResources (Thread[#55,Task worker for ':',5,main]) started. +:compileTestJava (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 23.204 secs. +:processTestResources (Thread[#56,Task worker for ':' Thread 2,5,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 0.489 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.668 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#55,Task worker for ':',5,main]) completed. Took 1.141 secs. -:testClasses (Thread[#55,Task worker for ':',5,main]) started. +:processTestResources (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 1.457 secs. +:testClasses (Thread[#56,Task worker for ':' Thread 2,5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#55,Task worker for ':',5,main]) completed. Took 0.001 secs. -:testWithDefaultReference (Thread[#55,Task worker for ':',5,main]) started. +:testClasses (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. +:testWithDefaultReference (Thread[#56,Task worker for ':' Thread 2,5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... Putting task artifact state for task ':testWithDefaultReference' into context took 0.001 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.26 secs. It is not up-to-date because: +Up-to-date check for task ':testWithDefaultReference' took 0.463 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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath12181565097525055729txt -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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath17362424986227316684txt -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 2024-12-15 01:11:12 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 2026-01-18 10:10:19 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa Finished 200 tests Finished 400 tests Finished 600 tests @@ -3751,128 +3787,128 @@ Finished 1600 tests Finished 1800 tests Finished 2000 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[62](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[63](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[64](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[65](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[66](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[67](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[68](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[69](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[70](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[71](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[72](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2200 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[247](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:12:15 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[116](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[117](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[118](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[119](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[120](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[121](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[122](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[123](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[124](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[125](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[126](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[138](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[139](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[140](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[141](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[142](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[143](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[144](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[145](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[146](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[147](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[148](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:10:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2400 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[339](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[340](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[341](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[342](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[343](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[344](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[345](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[346](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[347](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[348](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[349](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:12:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[328](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:11:00 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2024-12-15 01:12:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:12:36 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 2024-12-15 01:12:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:12:36 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 2024-12-15 01:12:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:12:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Finished 3000 tests @@ -3958,7 +3994,7 @@ testFirstCompleteContigRead runtime: 0ms 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 @@ -3985,13 +4021,13 @@ 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: 0ms + testFirstElementOfIterator runtime: 1ms 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: 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 @@ -4003,7 +4039,7 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testFirstSequence runtime: 0ms + testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[2](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms @@ -4033,25 +4069,25 @@ testLastCompleteContigRead runtime: 4ms 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: 3ms + testLastCompleteContigRead runtime: 4ms 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 + testLastCompleteContigRead runtime: 2ms 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: 7ms + testLastCompleteContigRead runtime: 8ms 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: 8ms + testLastCompleteContigRead runtime: 7ms 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: 8ms + testLastCompleteContigRead runtime: 7ms 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: 2ms + testLastCompleteContigRead runtime: 4ms 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 @@ -4069,7 +4105,7 @@ testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstOfChr1 runtime: 0ms + testFirstOfChr1 runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[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 testNextElementOfIterator runtime: 1ms @@ -4084,7 +4120,7 @@ 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: 9ms + 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: 7ms @@ -4096,7 +4132,7 @@ testNextElementOfIterator runtime: 2ms 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: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms @@ -4157,7 +4193,7 @@ 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: 0ms + testReadStartingInCenterOfMiddleLine runtime: 1ms 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 @@ -4169,52 +4205,52 @@ testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testReadThroughEndOfContig runtime: 0ms + testReadThroughEndOfContig runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR 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: 3ms + testReset runtime: 2ms 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 + testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[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 - testReset runtime: 1ms + testReset runtime: 3ms 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: 4ms 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: 7ms + testReset runtime: 16ms 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: 7ms + testReset runtime: 13ms 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: 6ms + testReset runtime: 11ms 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 + testReset runtime: 3ms 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: 2ms + testReset runtime: 4ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2024-12-15 01:13:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:13:32 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@2a2545c, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2024-12-15 01:13:15 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@42135722, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-01-18 10:13:32 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.testReadLines STANDARD_ERROR - WARNING 2024-12-15 01:13:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:13:32 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.voidTestLineEndingLength STANDARD_ERROR - WARNING 2024-12-15 01:13:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:13:32 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.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2024-12-15 01:13:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:13:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 @@ -5275,443 +5311,443 @@ Finished 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.14290237342454119962.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.12548589419423560444.bai - #BAMIndexWriterTest diff /tmp/javaBai.14290237342454119962.bai /tmp/cBai.12548589419423560444.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.12767239232143267130.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.7853336517203097512.bai + #BAMIndexWriterTest diff /tmp/javaBai.12767239232143267130.bai /tmp/cBai.7853336517203097512.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.16542413050534312795.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.4542035446507123743java.bai - #BAMIndexWriterTest diff /tmp/javaBai.4542035446507123743java.bai.txt /tmp/cBai.16542413050534312795.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.12018682308838766778.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.1522640304767661043java.bai + #BAMIndexWriterTest diff /tmp/javaBai.1522640304767661043java.bai.txt /tmp/cBai.12018682308838766778.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 0ms to write + 1ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 1ms to write + 0ms 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.324736082008535758.gz + Creating file /tmp/BCOST.5698897126075578211.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.5546914679512270020.gz + Creating file /tmp/testCustomDeflater.13463150092085772355.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.2611127818151922817.gz + Creating file /tmp/BCOST.15228828181510725111.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2024-12-15 01:14:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:14:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2024-12-15 01:14:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:14:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2024-12-15 01:14:16 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-12-15 01:14:16 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2024-12-15 01:14:16 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-12-15 01:14:16 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-01-18 10:14:34 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-01-18 10:14:34 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-01-18 10:14:34 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-01-18 10:14:34 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 2024-12-15 01:14:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:14:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:40 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 2024-12-15 01:14:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:14:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2024-12-15 01:14:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:14:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 13600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2024-12-15 01:14:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:14:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:14:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:14:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2024-12-15 01:14:21 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-12-15 01:14:21 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2024-12-15 01:14:21 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-12-15 01:14:21 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-01-18 10:14:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-01-18 10:14:42 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-01-18 10:14:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-01-18 10:14:42 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 2024-12-15 01:14:21 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:14:21 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2024-12-15 01:14:21 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:14:21 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-01-18 10:14:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:14:42 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-01-18 10:14:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:14:42 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 2024-12-15 01:18:17 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 2024-12-15 01:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-01-18 10:19:38 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 2026-01-18 10:19:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:19:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2024-12-15 01:18:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:18:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2024-12-15 01:18:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:18:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-01-18 10:19:38 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:19:38 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-01-18 10:19:38 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:19:38 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Gradle is still running, please be patient... Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@556a9b5, [Ljava.lang.String;@1fe7d04c) STANDARD_ERROR - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2aeabd81, [Ljava.lang.String;@6d77a626) STANDARD_ERROR - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:37 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;@56484ba4, [Ljava.lang.String;@62524f46) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@52e3c1b3, [Ljava.lang.String;@5ec7fdbf) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 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 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@99f3006, [Ljava.lang.String;@4725030f) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@51d1ecd0, [Ljava.lang.String;@774e7851) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3bab498b, [Ljava.lang.String;@66f76aa3) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@198798b2, [Ljava.lang.String;@77c0063c) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c446820, [Ljava.lang.String;@5b9878cc) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@568ba236, [Ljava.lang.String;@7ca9d340) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49a510bd, [Ljava.lang.String;@1d709228) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@37943ec5, [Ljava.lang.String;@3e949296) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@750118c3, [Ljava.lang.String;@47c4d274) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@55ad8885, [Ljava.lang.String;@581d7e5e) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9d53605, [Ljava.lang.String;@135ee019) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@4a850f6d, [Ljava.lang.String;@6145ddd9) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3acab11b, [Ljava.lang.String;@3b0bb5c4) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@13e93d2a, [Ljava.lang.String;@781cbae4) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@16b9d184, [Ljava.lang.String;@753e9071) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@21596931, [Ljava.lang.String;@702163a7) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4a5b7d9f, [Ljava.lang.String;@59e7dc2c) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 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;@3cc51b2c) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@21ea9b74) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@51b21865) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@5c4d7ae1) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@278bc335) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@6f3b44dd) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@7b958d90) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@4776b7b2) STANDARD_ERROR - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 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;@2892476e, [Ljava.lang.String;@e16755f) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 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;@2ba2b31c, [Ljava.lang.String;@63256cf2) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e7647a7, [Ljava.lang.String;@7031b24a) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@2b83c97c, [Ljava.lang.String;@3b6cb389) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15406118, [Ljava.lang.String;@2e284819) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@7ca6054a, [Ljava.lang.String;@6cda7d96) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6bccae52, [Ljava.lang.String;@716e3c6d) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@65e4ab43, [Ljava.lang.String;@5171a62f) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e9d5497, [Ljava.lang.String;@3200a207) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@7aec40a2, [Ljava.lang.String;@10bff4df) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d3a58ce, [Ljava.lang.String;@3d32cf8c) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@589f41c6, [Ljava.lang.String;@9334ede) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5caa60b, [Ljava.lang.String;@3fe84d91) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@6c33e794, [Ljava.lang.String;@6bac0e6) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@571cd2be, [Ljava.lang.String;@48dbc5b9) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@266d86e1, [Ljava.lang.String;@617cea92) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@11622e83, [Ljava.lang.String;@7b542996) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:04 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;@227d1eb3) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 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;@552fe353) STANDARD_ERROR + WARNING 2026-01-18 10:27:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:04 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;@55542dfd) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@44618d1) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@3a69c4f3) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@760c3781) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@31b09f5e) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@67c76d83) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@185c8063, [Ljava.lang.String;@2bab6f23) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@4d0fd571, [Ljava.lang.String;@167a9519) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d92cfe4, [Ljava.lang.String;@eb46ae5) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@61b7c4de, [Ljava.lang.String;@6f07f235) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@712c6267, [Ljava.lang.String;@3cd5c535) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@5053112, [Ljava.lang.String;@2ab89616) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62d8e3fb, [Ljava.lang.String;@3bb7896f) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@28f4ff26, [Ljava.lang.String;@306e937c) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@dff0a0f, [Ljava.lang.String;@582591ac) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@6508a87b, [Ljava.lang.String;@122aca4b) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77c7171d, [Ljava.lang.String;@d005246) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@28aca08c, [Ljava.lang.String;@6e50e50f) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f3246d1, [Ljava.lang.String;@5d74e003) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@5814246f, [Ljava.lang.String;@178d196) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27d4361c, [Ljava.lang.String;@65e42ff3) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@6752535a, [Ljava.lang.String;@706d00fc) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@dc8740e, [Ljava.lang.String;@6989a6d8) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:39 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;@5480a7a1) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@279cfd5b) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@3321ceb1) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@566fda6e) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@63207cde) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@1d1494eb) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@30690450) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@46ae0ae7) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@5c61111) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@3c7ecb2d) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@41efd7f5) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@38f863d0) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@7b5995d7) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@77a49955) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@4e78fbfc) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@3ce351d6) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@6efd2bb6) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@2f48374d) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@60d1bca8) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@7767c5ee) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@699d8069) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@32e906fd) STANDARD_ERROR - WARNING 2024-12-15 01:24:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:39 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;@128d65d) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@3e4e4666) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@13aa5770, [Ljava.lang.String;@4d26fdde) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@5290d1b6, [Ljava.lang.String;@2b45dbcf) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78446161, [Ljava.lang.String;@76b183bb) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@5c653c1f, [Ljava.lang.String;@61eeba3) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@220e48e1, [Ljava.lang.String;@70675c1b) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@3b9bd8d9, [Ljava.lang.String;@44616398) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7740dcb5, [Ljava.lang.String;@2188c5d6) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@7c7c164, [Ljava.lang.String;@748bb384) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4c5342f2, [Ljava.lang.String;@6e824092) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@7a0ca38d, [Ljava.lang.String;@61d7009d) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@47c33258, [Ljava.lang.String;@289fd586) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@4a9b0528, [Ljava.lang.String;@5e3ed17a) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@23f1b384, [Ljava.lang.String;@74ff6091) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@6d9e89c2, [Ljava.lang.String;@5e99489c) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4f3303ad, [Ljava.lang.String;@eb77706) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@3a89a1a4, [Ljava.lang.String;@6a503a57) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2765feb9, [Ljava.lang.String;@62c0a75d) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:05 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;@2502b675) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@5e9175b4) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@4ce5cfdb) STANDARD_ERROR + WARNING 2026-01-18 10:27:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:05 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;@4db49646) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@16d761bb) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@3f053010) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@7ac0cf4c) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@1af7c4c0) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@2e0f4d9) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@6f183244) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@24171a4c) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@7567c965) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@6454e7fa) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@42fb26d3) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@280b84ef) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@30465608) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@5898b2d0) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@2bc4bed8) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@8937120) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@3c855716) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@78c34822) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@7633e318) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@41ce2732) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@52ddc1cc) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests -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;@796ededd) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@3ea0132) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@7587994b) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@32b8294c) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@3ccbe219) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@5780c7d1) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.10283851576548787306.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4a7f22ad) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:40 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;@66a2f730, 5) STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:40 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;@8775bfa) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@34a938cf) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@634218f1) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@72374c44) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@601baf3a) STANDARD_ERROR + WARNING 2026-01-18 10:27:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:06 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;@4c0ee65) STANDARD_ERROR + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.3780534431820323550.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2e9a18ef) STANDARD_ERROR + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:07 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;@257c4fc5, 5) STANDARD_ERROR + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:24:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2024-12-15 01:24:41 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-01-18 10:27:08 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 2024-12-15 01:24:41 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 2026-01-18 10:27:08 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 2024-12-15 01:24:41 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 2026-01-18 10:27:08 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 2024-12-15 01:24:41 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 2026-01-18 10:27:08 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 @@ -6370,12 +6406,12 @@ Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2024-12-15 01:24:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2024-12-15 01:24:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:24:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -6430,7 +6466,9 @@ Resetting tmpdir Finished 14600 tests Resetting tmpdir - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.5408511931586956462.tmp + +Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.4763045128257843974.tmp Finished 14800 tests Finished 15000 tests Finished 15200 tests @@ -6439,492 +6477,492 @@ Finished 15800 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 2024-12-15 01:25:00 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:27:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2024-12-15 01:25:00 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:27:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 16000 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 2024-12-15 01:25:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 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 2024-12-15 01:25:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 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 2024-12-15 01:25:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 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 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 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 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:34 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 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:25:03 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:35 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:27:35 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2024-12-15 01:25:03 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-01-18 10:27:35 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 2024-12-15 01:25:03 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-01-18 10:27:35 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 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;@75685826, [Ljava.lang.String;@18d7b07e) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@305fbc12, [Ljava.lang.String;@2e37e272) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@2302dabc, [Ljava.lang.String;@38dd8d8e) STANDARD_ERROR + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6e2a5b99, [Ljava.lang.String;@6965c904) STANDARD_ERROR + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 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 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:35 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 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:35 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;@56686915) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@33de91cb) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@168d7033) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@1a20eb23) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@542860fb) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@577a433b) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@55e22b88) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@192c77db) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@2f7fc201, [Ljava.lang.String;@6696410a) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:04 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;@42693295, [Ljava.lang.String;@326af60f) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2873d8bd, [Ljava.lang.String;@6e12c5c6) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@714bc2ed, [Ljava.lang.String;@1a830868) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@cf71df3, [Ljava.lang.String;@6e1b818a) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@379a4b32, [Ljava.lang.String;@489f8593) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@713d538f, [Ljava.lang.String;@39c3f954) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@15c3646a, [Ljava.lang.String;@c756690) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d2522f4, [Ljava.lang.String;@9163c4f) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@c9e7933, [Ljava.lang.String;@7297dfc4) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1732f11d, [Ljava.lang.String;@c41f1e4) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 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;@54235149, [Ljava.lang.String;@75b0d388) STANDARD_ERROR - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f188770, [Ljava.lang.String;@27d13705) STANDARD_ERROR - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 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;@4ae05673, [Ljava.lang.String;@2ac4cdbe) STANDARD_ERROR - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4a90fcc1, [Ljava.lang.String;@5c74fa7e) STANDARD_ERROR - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 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;@17d22d48, [Ljava.lang.String;@7b3de3ec) STANDARD_ERROR - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c82d43e, [Ljava.lang.String;@7dcf9004) STANDARD_ERROR - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 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;@37984653) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@18085cce) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@35f7d196) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@39e784a6) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@522552e) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@6ad754ea) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@1a78995e) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@2343fa12) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@425ed469, [Ljava.lang.String;@323c9d7) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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;@508d3e24, [Ljava.lang.String;@5bada683) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a84b60d, [Ljava.lang.String;@7a5cf5a5) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@3ecd542a, [Ljava.lang.String;@501ba54a) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@289881f6, [Ljava.lang.String;@47dc3b6) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@5922d5f6, [Ljava.lang.String;@3eb92ca4) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b645ff2, [Ljava.lang.String;@1f7932bc) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@7597f4bc, [Ljava.lang.String;@145e5ff6) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@434c62eb, [Ljava.lang.String;@13756780) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@7d823d4, [Ljava.lang.String;@1e748f14) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8a06d1, [Ljava.lang.String;@2e5f40d) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@58585daf, [Ljava.lang.String;@3b95506a) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68f4913b, [Ljava.lang.String;@2ef56d66) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@729fe839, [Ljava.lang.String;@5c7f51b7) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3169e91b, [Ljava.lang.String;@702b6886) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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;@ab54f79, [Ljava.lang.String;@31ab646a) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@73a8c8b5, [Ljava.lang.String;@58986484) STANDARD_ERROR + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 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 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:36 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 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 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 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 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 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@719bede6) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@3ccf0a60) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@6ef8771c) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@2a57b239) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@764ed79a) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@ea7611e, [Ljava.lang.String;@257d11e2) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@3e95fca, [Ljava.lang.String;@f104865) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@167c03f2, [Ljava.lang.String;@3187229c) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@5863ac47, [Ljava.lang.String;@2ff05d86) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e2b96af, [Ljava.lang.String;@c7c67d6) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@1734a2d1, [Ljava.lang.String;@6e3d046d) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3fb4e3f6, [Ljava.lang.String;@42f7a213) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@40129bb4, [Ljava.lang.String;@17a6caa9) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@75b5e4e, [Ljava.lang.String;@77ab7154) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@53246f2b, [Ljava.lang.String;@501ccd2b) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@241bff01, [Ljava.lang.String;@24f49862) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@53b3204e, [Ljava.lang.String;@37d5aa9f) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6247b47d, [Ljava.lang.String;@2a3aa586) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@116bee6b, [Ljava.lang.String;@3644e598) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8252aa, [Ljava.lang.String;@5903e21d) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@528e495e, [Ljava.lang.String;@5c44fdfc) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@71b4564e, [Ljava.lang.String;@3db3abcf) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@c76f6d8) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@67417f89) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@79e344ec) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@1d436d5d) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@287a5dab) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@729f811b) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@6490ddd1) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.8888002367975408114.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@6feda4df) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:06 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;@2a7170d5) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@5547fc1c) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@375cc331) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@1f83546c) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@7250af0e) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@734f4205) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@498f1f9e) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@769cda85) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 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;@14ee895d) STANDARD_ERROR - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:37 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;@13d8ddc0) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@5cbb5050) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@691d707) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@2f54bf7b) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@1f6d3057) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@4fac83c1, [Ljava.lang.String;@c638c10) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@6e800fe1, [Ljava.lang.String;@54654c48) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2807b838, [Ljava.lang.String;@31e1b61f) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@477c5d5d, [Ljava.lang.String;@6130984d) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d66ba0b, [Ljava.lang.String;@3119dc4a) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@33a07ce, [Ljava.lang.String;@4951ab3a) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3b4f0e75, [Ljava.lang.String;@4e01518d) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@57668d72, [Ljava.lang.String;@16147339) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@131fae6b, [Ljava.lang.String;@5bb4d6cd) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@4ad8aa4c, [Ljava.lang.String;@17bcfc7e) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fc9deb9, [Ljava.lang.String;@13f80a2e) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@25aa66ed, [Ljava.lang.String;@61555767) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1785552f, [Ljava.lang.String;@3abd4a24) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@496c615, [Ljava.lang.String;@66b8159c) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6cbe30cb, [Ljava.lang.String;@3b78a3ca) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@430309f1, [Ljava.lang.String;@13f20000) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29624f2e, [Ljava.lang.String;@3bae6d33) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@3898998f) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@57251cab) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@4a51424d) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@2d5415c9) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@458fe5b7) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@39809541) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@1ca58d64) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.10784150113206417882.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@32739d9c) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:38 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;@651a6dde) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@97c1d45) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@436e6e2c) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@7db5116b) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@41d5660a) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@4cded2ef) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@5bfbeeaf) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@65a92dc) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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;@ea044be) STANDARD_ERROR + WARNING 2026-01-18 10:27:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:38 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 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:07 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;@cf08a26, 5) STANDARD_ERROR - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:25:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:39 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;@7fa415c3, 5) STANDARD_ERROR + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:27:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@573aee12, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@528ffd02], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:25:07 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@711ef665, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@749709a3], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:27:39 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16400 tests 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 2024-12-15 01:25:07 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2026-01-18 10:27:39 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@2e9f25c2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@30983ce6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39305a77, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@51254437, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1f78e69c], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:25:07 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@2bd1919c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@60def7d4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6bc7e4fa, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@780ae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d4aa6e8], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:27:39 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@2e9f25c2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@30983ce6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39305a77, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@51254437, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1f78e69c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:25:07 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@2bd1919c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@60def7d4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6bc7e4fa, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@780ae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d4aa6e8], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:27:39 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@2e9f25c2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@30983ce6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39305a77, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@51254437, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1f78e69c], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:25:07 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@2bd1919c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@60def7d4, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6bc7e4fa, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@780ae84d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d4aa6e8], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:27:39 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16600 tests some stuffFinished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file5406984601552799040.bad + Could not delete file file9599540241861702890.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 21 milliseconds - Queried for the same 100-length mapping 171282181 times in 10 seconds. + Time to construct a tree with 50000 nodes: 39 milliseconds + Queried for the same 100-length mapping 206229268 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:27:54 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 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-01-18 10:27:54 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.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -7086,7 +7124,7 @@ Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:25:21 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:27:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT @@ -7119,93 +7157,93 @@ Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2024-12-15 01:26:04 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-01-18 10:28:32 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2024-12-15 01:26:04 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2024-12-15 01:26:04 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-01-18 10:28:32 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.13456568571593378906..cram - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2024-12-15 01:26:04 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 2026-01-18 10:28:32 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.18133870133593516493..cram + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension1292407892639685948.cram + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension17650686855499348064.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.1745401788205194406.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.2216389333901787471.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 2024-12-15 01:26:04 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension2790392737713871056.cram - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2024-12-15 01:26:04 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 2026-01-18 10:28:32 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension542763594178331832.cram + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-01-18 10:28:32 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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension2940560703424015663 + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension9185589448523606889 Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension8237248941385125627.png + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension5601724447663543210.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://e9c30920-e676-4328-886b-402a7bb98a08/work/testMakeWriterPathsam + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://07b3bd3a-4db5-47e4-8734-7c0ffdaf1b20/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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ba5440ef-2618-404a-a57c-bd67af8f6197/work/testMakeWriterPathbam + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f94aedff-4fd8-4f64-9728-e3f186e51689/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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://5b6f3e38-7456-4a64-943c-12c0b677a7da/work/testMakeWriterPathcram + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://dc4ecc86-b089-432a-992c-45e5c0c0fb9f/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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://b94c6cc6-bed8-4f76-9510-1ab9821c13d4/work/testMakeWriterPathsam + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://305249ae-41ce-4afa-a70c-6fd1b74fc3dd/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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://cd09fb74-1aaa-495f-aa1b-58477fdf6bdf/work/testMakeWriterPathbam + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://e7cc18ab-10ef-4c8f-894f-3ad850fcfade/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 2024-12-15 01:26:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://47b538d3-157d-407b-b484-19dcb671037b/work/testMakeWriterPathcram + INFO 2026-01-18 10:28:32 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2d5b02c7-bb54-49aa-a222-e8ac2e562b62/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 19200 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 2024-12-15 01:26:18 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-01-18 10:28:44 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 @@ -7244,103 +7282,103 @@ 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 2024-12-15 01:26:20 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 2024-12-15 01:26:20 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 2026-01-18 10:28:46 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 2026-01-18 10:28:46 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 Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2024-12-15 01:26:21 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2024-12-15 01:26:21 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2024-12-15 01:26:21 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2024-12-15 01:26:21 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-01-18 10:28:47 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-01-18 10:28:47 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-01-18 10:28:47 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-01-18 10:28:47 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 2024-12-15 01:26:21 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-01-18 10:28:47 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 2024-12-15 01:26:21 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 2024-12-15 01:26:21 SamReaderFactoryTest Finished queries in 52ms + INFO 2026-01-18 10:28:47 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 2026-01-18 10:28:47 SamReaderFactoryTest Finished queries in 49ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2024-12-15 01:26:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2024-12-15 01:26:21 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-01-18 10:28:47 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 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2024-12-15 01:26:21 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 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-01-18 10:28:47 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 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:28:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2024-12-15 01:26:21 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-12-15 01:26:21 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-01-18 10:28:47 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-01-18 10:28:47 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 2024-12-15 01:26:21 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-12-15 01:26:21 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-01-18 10:28:47 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-01-18 10:28:47 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -7355,54 +7393,54 @@ Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:21 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 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 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 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 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:28:48 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 2024-12-15 01:26:22 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2024-12-15 01:26:22 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-01-18 10:28:48 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-01-18 10:28:48 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 @@ -7506,17 +7544,17 @@ Finished 35800 tests Gradle Test Executor 1 finished executing tests. Results: SUCCESS (35817 tests, 35791 successes, 0 failures, 26 skipped) -Finished generating test XML results (0.385 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.248 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.435 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[#55,Task worker for ':',5,main]) completed. Took 15 mins 15.797 secs. -:testWithOptimisticVCF4_4 (Thread[#55,Task worker for ':',5,main]) started. +Finished generating test html results (0.276 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 18 mins 36.349 secs. +:testWithOptimisticVCF4_4 (Thread[#56,Task worker for ':' Thread 2,5,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 0.086 secs. It is not up-to-date because: +Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.066 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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath10440878316225347537txt -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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath3371872420234673085txt -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. @@ -7524,14 +7562,14 @@ 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 (0.002 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/testWithOptimisticVCF4_4 -:testWithOptimisticVCF4_4 (Thread[#55,Task worker for ':',5,main]) completed. Took 3.111 secs. -:test (Thread[#55,Task worker for ':',5,main]) started. +:testWithOptimisticVCF4_4 (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 1.735 secs. +:test (Thread[#56,Task worker for ':' Thread 2,5,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 0.116 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.057 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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17564831823081791777txt -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-21-openjdk-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath4698128477398200911txt -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. Finished 200 tests @@ -7544,128 +7582,129 @@ Finished 1600 tests Finished 1800 tests Finished 2000 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[59](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[60](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[61](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[62](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[63](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[64](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[65](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[66](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[67](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[68](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[69](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:26:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + Gradle is still running, please be patient... Finished 2200 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[158](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:26:53 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[229](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[230](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[231](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[232](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[233](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[234](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[235](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[236](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[237](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[238](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[239](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[249](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[250](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[251](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[252](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[253](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[254](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[255](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[256](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[257](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[258](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[259](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-01-18 10:30:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:30:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2400 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[386](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[387](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[388](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[389](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[390](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[391](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[392](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[393](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[394](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[395](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[396](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:27:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[393](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:30:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2024-12-15 01:27:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:30:14 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 2024-12-15 01:27:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:30:14 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 2024-12-15 01:27:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:30:14 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Finished 3000 tests @@ -7748,7 +7787,7 @@ testFirstCompleteContigRead runtime: 0ms 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: 0ms @@ -7757,7 +7796,7 @@ 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: 1ms + testFirstCompleteContigRead runtime: 0ms 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: 0ms @@ -7781,7 +7820,7 @@ 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: 0ms + testFirstElementOfIterator runtime: 1ms 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 @@ -7790,7 +7829,7 @@ 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: 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 @@ -7802,10 +7841,10 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[3](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testFirstSequence runtime: 0ms + testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequence runtime: 1ms + testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/reproducible-path/htsjdk-4.1.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms @@ -7829,7 +7868,7 @@ testLastCompleteContigRead runtime: 4ms 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: 2ms + testLastCompleteContigRead runtime: 1ms 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 @@ -7841,7 +7880,7 @@ testLastCompleteContigRead runtime: 7ms 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: 8ms + testLastCompleteContigRead runtime: 7ms 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: 3ms @@ -7865,22 +7904,22 @@ testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[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 - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 4ms 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: 1ms + testNextElementOfIterator runtime: 3ms 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: 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: 2ms + 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: 10ms + 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: 10ms + testNextElementOfIterator runtime: 7ms 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 @@ -7935,7 +7974,7 @@ 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 @@ -7977,37 +8016,37 @@ 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: 2ms + 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: 18ms + 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: 14ms + 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: 11ms + testReset runtime: 8ms 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: 3ms 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 2024-12-15 01:28:37 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:31:02 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@3686d198, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2024-12-15 01:28:37 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@1f8decfd, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-01-18 10:31:02 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 2024-12-15 01:28:37 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:31:02 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.voidTestLineEndingLength STANDARD_ERROR - WARNING 2024-12-15 01:28:37 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:31:02 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 2024-12-15 01:28:37 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:31:02 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 @@ -9068,433 +9107,433 @@ Finished 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.9829526739297746143.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.11067755514143833034.bai - #BAMIndexWriterTest diff /tmp/javaBai.9829526739297746143.bai /tmp/cBai.11067755514143833034.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.2632015091370955124.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.16220749046666721025.bai + #BAMIndexWriterTest diff /tmp/javaBai.2632015091370955124.bai /tmp/cBai.16220749046666721025.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.939802318188633690.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.17149239855151918396java.bai - #BAMIndexWriterTest diff /tmp/javaBai.17149239855151918396java.bai.txt /tmp/cBai.939802318188633690.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.960441014410408538.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.10905639616318484023java.bai + #BAMIndexWriterTest diff /tmp/javaBai.10905639616318484023java.bai.txt /tmp/cBai.960441014410408538.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 0ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 0ms to write + 1ms 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.7995931544203122112.gz + Creating file /tmp/BCOST.17428608805201114868.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.13734993447770314007.gz + Creating file /tmp/testCustomDeflater.4394092529155792094.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.2499755085095588692.gz + Creating file /tmp/BCOST.1378482641406600416.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2024-12-15 01:29:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:29:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2024-12-15 01:29:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:29:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2024-12-15 01:29:51 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-12-15 01:29:51 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2024-12-15 01:29:51 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2024-12-15 01:29:51 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-01-18 10:32:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-01-18 10:32:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-01-18 10:32:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-01-18 10:32:09 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 2024-12-15 01:29:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:29:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:13 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 2024-12-15 01:29:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:29:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2024-12-15 01:29:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:29:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 13600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2024-12-15 01:30:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:30:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:32:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:32:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2024-12-15 01:30:01 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-12-15 01:30:01 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2024-12-15 01:30:01 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2024-12-15 01:30:01 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-01-18 10:32:17 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-01-18 10:32:17 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-01-18 10:32:17 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-01-18 10:32:17 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 2024-12-15 01:30:01 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:30:01 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2024-12-15 01:30:01 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:30:01 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - Gradle is still running, please be patient... + WARNING 2026-01-18 10:32:17 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:32:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-01-18 10:32:17 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:32:17 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 2024-12-15 01:34:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:34:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:37:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:37:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2024-12-15 01:34:05 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:34:05 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2024-12-15 01:34:05 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2024-12-15 01:34:05 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-01-18 10:37:59 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:37:59 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-01-18 10:38:00 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-01-18 10:38:00 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + Gradle is still running, please be patient... Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@47870c9f, [Ljava.lang.String;@6698f348) STANDARD_ERROR - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d3daf26, [Ljava.lang.String;@97b1d04) STANDARD_ERROR - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:35 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;@5d7656d5, [Ljava.lang.String;@dab6b6d) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@23757bd, [Ljava.lang.String;@16cb5a3c) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 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 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@613d7e46, [Ljava.lang.String;@59dd6b0d) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@2b6fe83f, [Ljava.lang.String;@243f54f9) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15830738, [Ljava.lang.String;@4769a572) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@6516496, [Ljava.lang.String;@4b382f3e) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@121e6d7, [Ljava.lang.String;@3b132b5c) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@44183213, [Ljava.lang.String;@1f7b9bd1) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@d89acb, [Ljava.lang.String;@2bbead3c) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@47b0e2ed, [Ljava.lang.String;@7f2d3458) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41006f64, [Ljava.lang.String;@4a6ccb7e) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@6e483f9, [Ljava.lang.String;@54bbec7e) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5878600, [Ljava.lang.String;@3df35fd7) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@7d20d3de, [Ljava.lang.String;@7761dc43) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27447584, [Ljava.lang.String;@7e1193e6) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@215979f7, [Ljava.lang.String;@7788528f) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@701a831, [Ljava.lang.String;@47dc329) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@52e7a297, [Ljava.lang.String;@35ebd4d1) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@40f1204e, [Ljava.lang.String;@57cb060e) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 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;@428d613a) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@52632653) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@73134490) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@1c2bc461) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@35039a55) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@674a56f5) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@36466c8f) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@7704bab9) STANDARD_ERROR - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 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;@36f4e3f7, [Ljava.lang.String;@bb19de3) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:35 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;@bc02746, [Ljava.lang.String;@4abfe39d) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@eade245, [Ljava.lang.String;@3e96f44) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@6438cb98, [Ljava.lang.String;@70733d91) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7571c54, [Ljava.lang.String;@1ce07c8) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@553e2689, [Ljava.lang.String;@245daad9) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@67bf2354, [Ljava.lang.String;@6d00438a) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@3c44d41f, [Ljava.lang.String;@413b94a0) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@164110, [Ljava.lang.String;@61a1b8b4) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 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;@4dad24cc, [Ljava.lang.String;@7a0067be) STANDARD_ERROR + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d6a210f, [Ljava.lang.String;@193824df) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@234dc07f, [Ljava.lang.String;@6206eff3) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@721aa981, [Ljava.lang.String;@440d2a20) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@53945bc3, [Ljava.lang.String;@2881deb5) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@b29579e, [Ljava.lang.String;@46dea65) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@764e0b7f, [Ljava.lang.String;@42dea9b6) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ede5f43, [Ljava.lang.String;@20193967) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@dc80f3d) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@609c31f9) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@2c21feac) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@49f50018) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@6a4959fb) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@45a33ffa) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@4929f62b) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@3543b191) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@36627a5e, [Ljava.lang.String;@475d89d1) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@47c5be74, [Ljava.lang.String;@60dd16f3) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b0897e4, [Ljava.lang.String;@16a19ba1) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@62e5d674, [Ljava.lang.String;@1d0aab0f) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@561eacad, [Ljava.lang.String;@153e8e81) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@48157265, [Ljava.lang.String;@109d2029) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@50139d48, [Ljava.lang.String;@625cf580) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@4e0e06e5, [Ljava.lang.String;@7395255d) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@601a254c, [Ljava.lang.String;@4affc4da) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@46815f9, [Ljava.lang.String;@42806585) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2629454e, [Ljava.lang.String;@20414848) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@491af409, [Ljava.lang.String;@43f566fb) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6727efe1, [Ljava.lang.String;@746fc3c8) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@fdad83c, [Ljava.lang.String;@5e3d3db7) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@31cde20e, [Ljava.lang.String;@8b66464) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@3cb08899, [Ljava.lang.String;@2e0f021) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79afca2a, [Ljava.lang.String;@39703334) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:37 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;@1e76210d) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@42283708) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@29cef845) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@51141f8b) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@4088d3a4) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@4b0658b) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@38b0235a) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@52e76386) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@584f342b) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@18cd2f48) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@65aa2b51) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@1005da9f) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@6dc3a9d4) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@ebc1675) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@c61dc4f) STANDARD_ERROR - WARNING 2024-12-15 01:40:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:37 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;@c61ae32) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@12201953) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@40543b0a) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@16409cff) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@7c6297a) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@6a4e07b1) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@6ca1b030) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@ad2daca) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@2dc4bde7) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@78a64479, [Ljava.lang.String;@71d8ca28) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:36 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;@432a50e4, [Ljava.lang.String;@77358512) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@59c71606, [Ljava.lang.String;@258145b1) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@2df1f539, [Ljava.lang.String;@b261602) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4176859a, [Ljava.lang.String;@51cccc2c) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@2450dd5a, [Ljava.lang.String;@7afb4765) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6086dece, [Ljava.lang.String;@309003bd) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@4dabde6, [Ljava.lang.String;@9980bd) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@737a247b, [Ljava.lang.String;@5d2d853d) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@1742655f, [Ljava.lang.String;@53264873) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@25b6d50f, [Ljava.lang.String;@50eaaba1) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@32f984fc, [Ljava.lang.String;@75faefc1) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b22e07a, [Ljava.lang.String;@5a237467) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@95bd743, [Ljava.lang.String;@5cbf4b0b) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@638aa8e0, [Ljava.lang.String;@48375c51) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 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;@4eb34df3, [Ljava.lang.String;@77d5f7d7) STANDARD_ERROR + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@653b8788, [Ljava.lang.String;@476c7ce3) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:37 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;@7fd2e52e) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@2c753ce4) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@1c11261c) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@5ed976a5) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@8e004f) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@4dbaa359) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@35c94116) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@175c345a) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@7387d44b) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@74c40456) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@5b9e6369) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@4886d09) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@10fa300) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@658c617e) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@177c1cf2) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@59da655e) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@6831bcd1) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@5b5fd317) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@2216228c) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@287f64e) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@5e370b90) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@29f0854b) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@4058674b) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 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;@570bc577) STANDARD_ERROR + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests -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;@147fba34) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@13698a44) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@4c16f924) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@484ac187) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@317f06ba) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@3ae326ba) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.12474830132109913754.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5de4e00d) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:38 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;@731515ec, 5) STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:38 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;@4c1c8ab7) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 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;@45bf6af2) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 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;@13327677) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 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;@5c982222) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 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;@546f4cc2) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 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;@2ba1f7a2) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.15633415755553600847.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@2be98b0b) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:38 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;@3be7795, 5) STANDARD_ERROR + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2024-12-15 01:40:39 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-01-18 10:46:39 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 @@ -10155,12 +10194,12 @@ Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2024-12-15 01:40:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2024-12-15 01:40:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:46:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:46:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -10215,7 +10254,9 @@ Resetting tmpdir Finished 14600 tests Resetting tmpdir - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.9962533156212848175.tmp + +Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.10883124534464834733.tmp Finished 14800 tests Finished 15000 tests Finished 15200 tests @@ -10224,493 +10265,492 @@ Finished 15800 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 2024-12-15 01:40:57 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-01-18 10:46:59 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 2024-12-15 01:40:57 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream - Gradle is still running, please be patient... + WARNING 2026-01-18 10:46:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 16000 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:01 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:01 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:01 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 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 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2024-12-15 01:40:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-01-18 10:47:02 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2024-12-15 01:40:59 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-01-18 10:47:02 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 2024-12-15 01:40:59 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-01-18 10:47:02 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:02 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;@73f2092a, [Ljava.lang.String;@40b40ec5) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3ebd0fa, [Ljava.lang.String;@20104b9) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 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;@29690359, [Ljava.lang.String;@7e907dec) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6cca6c3c, [Ljava.lang.String;@480f8bd2) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@36d1329a) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@4db00a1e) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@24ae7997) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@64dcb014) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@394a96e3) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@20085f5b) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@4af99a89) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@644e19d1) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@15096180, [Ljava.lang.String;@7a8f06ee) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:40:59 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;@5b639200, [Ljava.lang.String;@7b2664b9) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6a18dcea, [Ljava.lang.String;@456297b6) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 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;@19a3618d, [Ljava.lang.String;@7867d56f) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7473f9e2, [Ljava.lang.String;@61dd5309) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 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;@18086a1d, [Ljava.lang.String;@236129f5) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@55f9e7e1, [Ljava.lang.String;@c9ca32c) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 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;@16b6fe4, [Ljava.lang.String;@4010cba3) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17692023, [Ljava.lang.String;@44668699) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 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;@2c66c01d, [Ljava.lang.String;@168198ec) STANDARD_ERROR - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:40:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@196e9482, [Ljava.lang.String;@64dd536d) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 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;@11cd10f5, [Ljava.lang.String;@7483db5c) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@631d15b1, [Ljava.lang.String;@4120d816) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 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;@5eab9fb4, [Ljava.lang.String;@1a0d5d37) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38b799c5, [Ljava.lang.String;@5a73ed0f) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 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;@4efa1600, [Ljava.lang.String;@1a6c8e96) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@24af574a, [Ljava.lang.String;@71289caa) STANDARD_ERROR - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 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;@45dc9c3f) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@198749bd) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@3b25eb2d) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@4da765e8) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@2cb8da26) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@3b3c5042) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@f49bb0b) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@348f164a) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@4cae21d4, [Ljava.lang.String;@6fb6fc2b) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 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;@471448aa, [Ljava.lang.String;@1f50319b) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@737a4042, [Ljava.lang.String;@3004a52a) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@15083716, [Ljava.lang.String;@10c689fe) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1f0d2d28, [Ljava.lang.String;@522d64f3) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@4bc80adf, [Ljava.lang.String;@587c4ca8) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8c6454a, [Ljava.lang.String;@9cbc61b) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@72ef43c8, [Ljava.lang.String;@173b1397) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@732832e0, [Ljava.lang.String;@2ab8402d) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@205fca5, [Ljava.lang.String;@19a11171) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@19f8a071, [Ljava.lang.String;@3368c826) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@126cfb0b, [Ljava.lang.String;@1a215731) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7e508f51, [Ljava.lang.String;@2b486a36) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@4db3ce80, [Ljava.lang.String;@4925d744) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@c1e4ac9, [Ljava.lang.String;@754f7401) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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;@40b14a9d, [Ljava.lang.String;@102d4261) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45105447, [Ljava.lang.String;@41f2a604) STANDARD_ERROR + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 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 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 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 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 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 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 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 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@43b8420) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@7fbb71f9) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@7886c0b2) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@2bb12c3c) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@2d9135d7) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@33cd2e75, [Ljava.lang.String;@292efcad) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@590da26, [Ljava.lang.String;@7389f63b) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26dbe946, [Ljava.lang.String;@766db890) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@4789182b, [Ljava.lang.String;@75850c26) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@65ad8391, [Ljava.lang.String;@4be28297) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@18cd5b2c, [Ljava.lang.String;@24246ef8) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17d36cbc, [Ljava.lang.String;@6f933331) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@2ebe7043, [Ljava.lang.String;@68aebecd) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3b28fad, [Ljava.lang.String;@64a01433) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@4b111abe, [Ljava.lang.String;@2d29028a) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@345e8f16, [Ljava.lang.String;@6d84cc73) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@5f7c0573, [Ljava.lang.String;@24cfb74f) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@57382753, [Ljava.lang.String;@3128bd63) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@43cae66d, [Ljava.lang.String;@9597320) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43cc7aa4, [Ljava.lang.String;@40e164f6) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@4e6c6ed1, [Ljava.lang.String;@2dde02fc) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@364b0048, [Ljava.lang.String;@c6934b4) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@400d34aa) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@511e301) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@f5eb760) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@53071174) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@34f81ebd) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@1f4519c) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@19afbb9e) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.7623439422773739001.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@21c9b9fc) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:01 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;@412073b5) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@52d2e99f) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@2956208) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@2608b579) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@471b4c39) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@1732afe3) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@54612351) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@3dfd87b6) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 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;@429fff88) STANDARD_ERROR - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:04 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;@7cd3f25f) STANDARD_ERROR + WARNING 2026-01-18 10:47:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:04 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;@2bd2eba9) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@48d6c121) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@2a745803) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@6c58b2d0) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@18305308, [Ljava.lang.String;@10b85a11) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@444d15b3, [Ljava.lang.String;@45e49446) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44c8ccff, [Ljava.lang.String;@14bea204) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@292a2be8, [Ljava.lang.String;@5745b79b) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15efeaac, [Ljava.lang.String;@2ace02c4) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@7b00470c, [Ljava.lang.String;@105d94f6) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@162411e2, [Ljava.lang.String;@5e7ec950) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@436c72cb, [Ljava.lang.String;@7a057a50) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3538b7d0, [Ljava.lang.String;@6377a8b7) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@a1ac31d, [Ljava.lang.String;@1368f95a) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d6c7aff, [Ljava.lang.String;@51627713) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@63752df5, [Ljava.lang.String;@66930735) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7da6c26a, [Ljava.lang.String;@5bc4ceeb) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@75154d1a, [Ljava.lang.String;@134dd07) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b815f22, [Ljava.lang.String;@7e36cd16) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@57043ed6, [Ljava.lang.String;@4c309477) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22c104af, [Ljava.lang.String;@da753e8) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@279b27f8) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@293c4566) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@5220347e) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@14d562de) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@5b86a71c) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@347fd2ef) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@4832ede2) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.3740891686131953806.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3bf4548f) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 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;@3697f81e) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@6bfda1cb) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@6749be75) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@62bcd5e8) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@2d532edc) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@18a29dab) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@55af6d9f) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@746b184d) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@6ec770ee) STANDARD_ERROR + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:02 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;@2268da69, 5) STANDARD_ERROR - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:41:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:05 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;@43dcdff, 5) STANDARD_ERROR + WARNING 2026-01-18 10:47:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:47:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:47:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6ee31c31, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1baff634], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:41:02 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@223339fc, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15903cca], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:47:06 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16400 tests 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 2024-12-15 01:41:02 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2026-01-18 10:47:06 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@19120dab, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72cf8c96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49da779f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2ecf197f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39908a99], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:41:02 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@4d780876, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7d9ff708, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@233f5c5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22596b90, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@64cbe061], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:47:06 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@19120dab, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72cf8c96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49da779f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2ecf197f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39908a99], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:41:02 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@4d780876, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7d9ff708, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@233f5c5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22596b90, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@64cbe061], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:47:06 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@19120dab, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72cf8c96, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@49da779f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2ecf197f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@39908a99], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2024-12-15 01:41:02 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@4d780876, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7d9ff708, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@233f5c5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22596b90, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@64cbe061], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-01-18 10:47:06 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16600 tests some stuffFinished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file16074626162088750198.bad + Could not delete file file16524742906900257143.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 24 milliseconds - Queried for the same 100-length mapping 206167639 times in 10 seconds. + Time to construct a tree with 50000 nodes: 25 milliseconds + Queried for the same 100-length mapping 206984533 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-01-18 10:47:19 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 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-01-18 10:47:19 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.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -10872,7 +10912,7 @@ Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2024-12-15 01:41:15 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-01-18 10:47:19 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT @@ -10895,199 +10935,199 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - b d + b + a e c - a Finished 18600 tests Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2024-12-15 01:41:53 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-01-18 10:47:58 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 2024-12-15 01:41:53 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-01-18 10:47:58 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 2024-12-15 01:41:53 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-01-18 10:47:58 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 2024-12-15 01:41:53 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-01-18 10:47:58 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 2024-12-15 01:41:53 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-01-18 10:47:58 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2024-12-15 01:41:53 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2024-12-15 01:41:53 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-01-18 10:47:58 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-01-18 10:47:58 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 2024-12-15 01:41:54 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.8060466078503204020..cram - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.10073291372361085291..cram + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension13580925168350997785.cram + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension3048456244007632657.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.13636277394222749293.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.11493274257131660238.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 2024-12-15 01:41:54 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension8542243013460757936.cram - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension15344282678789258309.cram + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension10236617211953254653 + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension17762506282066358084 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension15783109508993167261.png + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension16800566871712595647.png Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8c999f96-6645-43d6-bc7e-d3f09c27ee92/work/testMakeWriterPathsam + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://3640219e-e9ae-4d1e-80e7-7638ed120fb3/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 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://18df8a2c-303a-4a39-b620-a5ca4c68c095/work/testMakeWriterPathbam + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://0147b7ec-0b0f-4542-9c3b-659434c74489/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 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ed651d94-d952-491b-8d9c-5da0d67078c1/work/testMakeWriterPathcram + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f7c8f152-94cf-4bf9-8de9-09cbf78b5cda/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 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://a2d0c9c1-80cf-4e14-a8cf-c4a4cd8d9ae6/work/testMakeWriterPathsam + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://0b0eb5f2-c865-4566-ba1e-e3628616b7e8/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 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4eb4c3c1-fb84-4ef3-9f29-3a3281d64d00/work/testMakeWriterPathbam + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://fb0cd4ca-40ea-4c47-a7ff-0179663e8fad/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 2024-12-15 01:41:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://91125e7e-3218-4719-94ec-f1d707f77f91/work/testMakeWriterPathcram + INFO 2026-01-18 10:47:58 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://de26112e-c344-48cb-bbf1-64c6e90f8bff/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 19200 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 2024-12-15 01:42:06 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-01-18 10:48:11 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Finished 19400 tests 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 2024-12-15 01:42:06 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 2024-12-15 01:42:06 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 2026-01-18 10:48:11 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 2026-01-18 10:48:11 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 Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2024-12-15 01:42:07 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2024-12-15 01:42:07 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2024-12-15 01:42:07 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2024-12-15 01:42:07 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-01-18 10:48:12 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-01-18 10:48:12 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-01-18 10:48:12 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-01-18 10:48:12 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 2024-12-15 01:42:07 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-01-18 10:48:12 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 2024-12-15 01:42:08 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 2024-12-15 01:42:08 SamReaderFactoryTest Finished queries in 53ms + INFO 2026-01-18 10:48:13 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 2026-01-18 10:48:13 SamReaderFactoryTest Finished queries in 44ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2024-12-15 01:42:08 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2024-12-15 01:42:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-01-18 10:48:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2024-12-15 01:42:08 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-12-15 01:42:08 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-01-18 10:48:13 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2024-12-15 01:42:08 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-01-18 10:48:13 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-01-18 10:48:13 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -11102,54 +11142,54 @@ Finished 20000 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:13 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 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 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 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2024-12-15 01:42:08 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-01-18 10:48:14 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 2024-12-15 01:42:08 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2024-12-15 01:42:08 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-01-18 10:48:14 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-01-18 10:48:14 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 @@ -11253,12 +11293,12 @@ Finished 35800 tests Gradle Test Executor 3 finished executing tests. Results: SUCCESS (35800 tests, 35790 successes, 0 failures, 10 skipped) -Finished generating test XML results (0.133 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test +Finished generating test XML results (0.105 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.188 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test -:test (Thread[#55,Task worker for ':',5,main]) completed. Took 15 mins 43.072 secs. +Finished generating test html results (0.185 secs) into: /build/reproducible-path/htsjdk-4.1.0+dfsg/build/reports/tests/test +:test (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 19 mins 26.888 secs. -BUILD SUCCESSFUL in 31m 19s +BUILD SUCCESSFUL in 38m 47s 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 @@ -11272,7 +11312,7 @@ install -m0755 -d debian/libhtsjdk-java/usr/share/libhtsjdk-java cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/ jh_installjavadoc -O--buildsystem=gradle -Duplicate specification "A" for option "A" +Duplicate specification "author|A=s" for option "A" Duplicate specification "A" for option "A" Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java @@ -11287,10 +11327,10 @@ 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/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 + 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 dh_installsystemduser -O--buildsystem=gradle dh_lintian -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides @@ -11308,14 +11348,14 @@ make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.0+dfsg' jh_classpath -O--buildsystem=gradle jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/mjson.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar -Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" Updating symlinked /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) Reading manifest from /build/reproducible-path/htsjdk-4.1.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.0.jar 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 Duplicate specification "V:s" for option "V" -Duplicate specification "version|V" for option "V" +Duplicate specification "V:s" for option "V" find debian/libhtsjdk-java -name '*.jar' Found usr/share/java/htsjdk-4.1.0.jar Found symlink usr/share/java/htsjdk.jar @@ -11419,7 +11459,51 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.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/RANS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/c 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/samtools/c 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/VariantContextWriterBuilder.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 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/Options.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/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/IntGenotypeFieldAccessors.DPAccessor.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/IntGenotypeFieldAccessors.Accessor.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/BCF2FieldWriterManager.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/BCF2FieldWriter.SiteWriter.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/BCF2FieldWriter.IGFGenotypesWriter.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.GenotypesWriter.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/BCF2FieldWriter.FTGenotypesWriter.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/BCF2FieldEncoder.StringOrCharacter.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/BCF2FieldEncoder.GenericInts.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/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/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/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/VCFTextTransformer.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-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/VCFSampleHeaderLine.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/VCFReader.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/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.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/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/li 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/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 @@ -11467,102 +11551,55 @@ 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/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/varia 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/package-tree.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/SignatureStream.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/OutputStreamResource.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/BundleResourceType.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/BundleResource.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/BundleBuilder.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/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/package-summary.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/VCFDecoder.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/VariantsCodecUtils.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/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/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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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_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/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/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/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/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/VCFCodecV3_3.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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/varian 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/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.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/BAMFileSpan.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/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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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/apps/TimeChannel.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/package-summary.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/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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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/liftover/LiftOver.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/package-summary.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/StringHeader.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/MetricBase.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/example/package-tree.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/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/seekablestream/package-tree.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/SeekableStreamFactory.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/SeekablePathStream.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/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/libhts 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/varia 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/MutableIndex.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/IndexFactory.IndexBalanceApproach.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/IndexCreator.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/DynamicIndexCreator.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/Block.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/AbstractIndex.BlockStats.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/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/linear/LinearIndex.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/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/interval/IntervalTreeIndex.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/Interval.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/package-summary.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/TabixIndexCreator.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/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/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + 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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.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/TextCigarCodec.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/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.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/SRAFileReader.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/SQTagUtil.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/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using Fi 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/SamReader.Indexing.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/SamReader.html using File::StripNondeterminism::handlers::javadoc @@ -11611,7 +11648,56 @@ 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/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaultram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Default 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/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.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/BAMFileSpan.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/BAMFileReader.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/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.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/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/samtools/apps/TimeChannel.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/package-summary.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/SRAUnalignmentIterator.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/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/ReferenceCache.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/liftover/LiftOver.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/package-summary.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/StringHeader.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/MetricBase.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/example/package-tree.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/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/seekablestream/package-tree.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/SeekableStreamFactory.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/SeekablePathStream.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/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/libhtsram/io/package-tree.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/LTF8.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 @@ -11648,100 +11734,7 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.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/FeatureReader.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/FeatureCodec.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/tribble/CloseableTribbleIterator.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/AbstractFeatureReader.ComponentMethods.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/AbstractFeatureCodec.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/package-summary.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/package-tree.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 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/gff/package-tree.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/SequenceRegion.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/Gff3FeatureImpl.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/gff/Gff3Constants.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/gff/Gff3Codec.DecodeDepth.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/Gff3BaseData.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/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/URLHelper.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/TabixUtils.TIntv.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/TabixUtils.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/ParsingUtils.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/MathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.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/HTTPHelper.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/popgen/package-tree.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/HardyWeinbergCalculation.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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNon 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/VariantContextWriterBuilder.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 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/Options.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/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/IntGenotypeFieldAccessors.DPAccessor.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/IntGenotypeFieldAccessors.Accessor.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/BCF2FieldWriterManager.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/BCF2FieldWriter.SiteWriter.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/BCF2FieldWriter.IGFGenotypesWriter.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.GenotypesWriter.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/BCF2FieldWriter.FTGenotypesWriter.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/BCF2FieldEncoder.StringOrCharacter.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/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.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/BCF2FieldEncoder.html 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/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/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/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/VCFTextTransformer.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-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/VCFSampleHeaderLine.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/VCFReader.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/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.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/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/li 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/help-doc.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/search.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 @@ -11792,103 +11785,190 @@ 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/package-summary.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/ReadsFormats.html using File::S 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/AggregateFilter.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/util/package-tree.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/WholeGenomeReferenceSequenceMask.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/TrimmingUtil.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/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.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/StringLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.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/SortingCollection.Codec.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/SolexaQualityConverter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.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/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordWithOrdinal.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.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/SamLocusIterator.RecordAndOffset.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/AbstractLocusInfo.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- 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/FeatureReader.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/FeatureCodec.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/tribble/CloseableTribbleIterator.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/AbstractFeatureReader.ComponentMethods.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/AbstractFeatureCodec.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/package-summary.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/package-tree.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 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/gff/package-tree.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/SequenceRegion.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/Gff3FeatureImpl.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/gff/Gff3Constants.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/gff/Gff3Codec.DecodeDepth.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/Gff3BaseData.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/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/URLHelper.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/TabixUtils.TIntv.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/TabixUtils.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/ParsingUtils.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/MathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.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/HTTPHelper.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/popgen/package-tree.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/HardyWeinbergCalculation.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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNon 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/package-tree.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/SignatureStream.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/OutputStreamResource.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/BundleResourceType.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/BundleResource.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/BundleBuilder.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/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/package-summary.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/VCFDecoder.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/VariantsCodecUtils.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/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/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/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_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/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/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/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/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_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/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/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/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_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/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/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/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/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/VCFCodecV3_3.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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/varianbhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.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/VCFIDHeaderLine.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/VCFHeaderLineType.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/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.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/VCFFormatHeaderLine.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/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.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/VCFConstants.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/VCFCompoundHeaderLine.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/VCFAltHeaderLine.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/AbstractVCFCodec.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/package-summary.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/TribbleException.UnableToReadIndexFile.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 + 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.MalformedFeatureFile.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.InvalidDecodeLine.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/TribbleException.FeatureFileDoesntExist.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/TribbleException.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/TabixFeatureReader.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/NamedFeature.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 +nt/variantcontext/VariantContextUtils.JexlVCMatchExp.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/VariantContextComparator.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 @@ -11924,79 +12004,39 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.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/package-summary.html using File::StripNondeterminism::handlers::javadoc -ts/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/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/VCFCodecV3_2.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/hapref/fasta/FASTACodecV1_0.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/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/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/SAMDecoder.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/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/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/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/SAMCodecV1_0.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/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/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/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/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/package-summary.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/CRAMEncoder.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/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/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc -jdk-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/SeekableFileStream.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/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/reference/package-tree.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/SamLocusAndReferenceIterator.SAMLocusAndReference.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/ReferenceSequenceFileWalker.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/ReferenceSequenceFile.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/IndexedFastaSequenceFile.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/FastaSequenceIndexCreator.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/FastaSequenceFile.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/FastaReferenceWriter.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/fastq/package-tree.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/FastqWriterFactory.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/FastqRecord.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/FastqReader.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/FastqConstants.FastqExtensions.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/AsyncFastqWriter.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 +tripNondeterminism::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/ReadsEncoder.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/ReadsDecoder.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/ReadsBundle.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/HtsQueryRule.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/HtsQuery.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/HtsInterval.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/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/ReadsResolver.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/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/HaploidReferenceResolver.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/package-summary.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/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/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/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/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/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/package-summary.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 @@ -12041,7 +12081,42 @@ 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/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/EncodSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Encodjdk-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/SeekableFileStream.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/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/reference/package-tree.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/SamLocusAndReferenceIterator.SAMLocusAndReference.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/ReferenceSequenceFileWalker.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/ReferenceSequenceFile.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/IndexedFastaSequenceFile.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/FastaSequenceIndexCreator.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/FastaSequenceFile.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/FastaReferenceWriter.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/fastq/package-tree.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/FastqWriterFactory.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/FastqRecord.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/FastqReader.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/FastqConstants.FastqExtensions.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/AsyncFastqWriter.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 +SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.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 @@ -12076,129 +12151,6 @@ 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/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc -bhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.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/VCFIDHeaderLine.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/VCFHeaderLineType.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/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.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/VCFFormatHeaderLine.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/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.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/VCFConstants.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/VCFCompoundHeaderLine.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/VCFAltHeaderLine.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/AbstractVCFCodec.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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using 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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/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.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/FileExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using 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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/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.MultiMap.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 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.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-determinism::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/IndexToTable.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 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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.Exon2.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/bed/FullBEDFeature.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/BEDCodec.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/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 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/TabixReader.Iterator.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/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/PositionalBufferedStream.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/LongLineBufferedReader.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/LineIteratorImpl.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/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/index/package-tree.html using File::StripNondeterminism::handlers::javadoc le::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.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 @@ -12235,75 +12187,41 @@ 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/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc -tripNondeterminism::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/ReadsEncoder.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/ReadsDecoder.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/ReadsBundle.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/HtsQueryRule.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/HtsQuery.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/HtsInterval.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/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/ReadsResolver.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/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/HaploidReferenceResolver.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/package-summary.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/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/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/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/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 -oc/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/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingInputStream.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/Log.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Locus.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocationAware.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/ListMap.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/Lazy.LazyInitializer.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/Iterables.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableOnceIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IterableAdapter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.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/IntervalTreeMap.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/IntervalTree.RevIterator.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/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.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/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.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/IntervalList.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/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.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 +determinism::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/IndexToTable.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/CountRecords.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/package-summary.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/bed/package-tree.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.Exon2.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/bed/FullBEDFeature.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/BEDCodec.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/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 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/TabixReader.Iterator.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/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/PositionalBufferedStream.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/LongLineBufferedReader.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/LineIteratorImpl.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/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/index/package-tree.html using File::StripNondeterminism::handlers::javadoc java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.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/package-summary.html using File::StripNondeterminism::handlers::javadoc @@ -12329,6 +12247,92 @@ Normalizing debian/libhtsjdk-java-doc/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/util/zip/DeflaterFactory.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/AggregateFilter.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/util/package-tree.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/WholeGenomeReferenceSequenceMask.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/TrimmingUtil.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/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.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/StringLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.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/SortingCollection.Codec.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/SolexaQualityConverter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.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/SequenceUtil.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/PositionalOutputStream.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 + 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/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/dts/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/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/VCFCodecV3_2.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/hapref/fasta/FASTACodecV1_0.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/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/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/SAMDecoder.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/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/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/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/SAMCodecV1_0.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/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/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/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/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/package-summary.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/CRAMEncoder.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/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/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc ingDescriptor.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/DataSeries.html using File::StripNondeterminism::handlers::javadoc @@ -12369,6 +12373,42 @@ 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/FailsVendorReadQualityFilter.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 +oc/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/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Md5CalculatingInputStream.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/Log.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.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/IntervalTreeMap.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/IntervalTree.RevIterator.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/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.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/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.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/IntervalList.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/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.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 dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java cd debian/libhtsjdk-java-doc @@ -12393,20 +12433,20 @@ 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/DEBIAN - cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums @@ -12422,12 +12462,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/354657/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/354657/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/2839298 and its subdirectories -I: Current time: Sun Dec 15 01:42:33 -12 2024 -I: pbuilder-time-stamp: 1734270153 +I: removing directory /srv/workspace/pbuilder/354657 and its subdirectories +I: Current time: Sun Jan 18 10:48:43 +14 2026 +I: pbuilder-time-stamp: 1768682923