Diff of the two buildlogs: -- --- b1/build.log 2025-10-31 20:43:55.201273754 +0000 +++ b2/build.log 2025-10-31 20:45:01.873358267 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 31 08:42:44 -12 2025 -I: pbuilder-time-stamp: 1761943364 +I: Current time: Fri Dec 4 17:06:57 +14 2026 +I: pbuilder-time-stamp: 1796353617 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying ignore_flaky_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2850112/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2833925/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 Dec 4 03:07 /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/2833925/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2833925/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='719751e6babf45c0afa773ad3f148814' - 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='2850112' - PS1='# ' - PS2='> ' + INVOCATION_ID=973ba0b3268840748de01e2d5c9e3116 + 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=2833925 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.nQEyLFwy/pbuilderrc_LMNV --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nQEyLFwy/b1 --logfile b1/build.log barclay_6.0.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.nQEyLFwy/pbuilderrc_ThYa --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nQEyLFwy/b2 --logfile b2/build.log barclay_6.0.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2850112/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2833925/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -376,7 +408,7 @@ Get: 241 http://deb.debian.org/debian forky/main arm64 libjacoco-java all 0.8.12-1 [647 kB] Get: 242 http://deb.debian.org/debian forky/main arm64 libjoptsimple-java all 5.0.4-7 [73.7 kB] Get: 243 http://deb.debian.org/debian forky/main arm64 libmockito-java all 3.3.0-2 [510 kB] -Fetched 256 MB in 1s (236 MB/s) +Fetched 256 MB in 1s (230 MB/s) Preconfiguring packages ... Selecting previously unselected package libpipeline1: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 ... 19971 files and directories currently installed.) @@ -1174,8 +1206,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Oct 31 20:43:18 UTC 2025. -Universal Time is now: Fri Oct 31 20:43:18 UTC 2025. +Local time is now: Fri Dec 4 03:07:31 UTC 2026. +Universal Time is now: Fri Dec 4 03:07:31 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1577,7 +1609,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/barclay-6.0.0+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 > ../barclay_6.0.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2833925/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2833925/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/barclay-6.0.0+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 > ../barclay_6.0.0+dfsg-1_source.changes dpkg-buildpackage: info: source package barclay dpkg-buildpackage: info: source version 6.0.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1599,7 +1635,7 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" Duplicate specification "u=s" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper @@ -1634,8 +1670,8 @@ dh_auto_configure make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+dfsg' jh_linkjars -O--buildsystem=gradle -Duplicate specification "u=s" for option "u" Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" rm -f debian/libbarclay-java.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/barclay-6.0.0+dfsg' @@ -1650,18 +1686,18 @@ 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/barclay-6.0.0+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=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.913 secs. -The client will now receive all logging from the daemon (pid: 2865673). The daemon log file: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/daemon/4.4.1/daemon-2865673.out.log +An attempt to start the daemon took 0.997 secs. +The client will now receive all logging from the daemon (pid: 2852898). The daemon log file: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/daemon/4.4.1/daemon-2852898.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/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@3e623aac -Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@3e623aac -Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@74ca76 +Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2856b1e0 +Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2856b1e0 +Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@798ed014 Starting Build Compiling initialization script '/build/reproducible-path/barclay-6.0.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@10e33f9f +Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@10f38da1 Compiling initialization script '/build/reproducible-path/barclay-6.0.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle'. Settings file not found (/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle) @@ -1680,15 +1716,15 @@ 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/barclay-6.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@7466c1a4 +Creating new cache for annotation-processors, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@62e36ee7 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@74ca76 -Creating new cache for taskHistory, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@755243a5 -Creating new cache for outputFiles, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@520a82cb -:compileJava (Thread[#55,Task worker for ':',5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@798ed014 +Creating new cache for taskHistory, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@278736d1 +Creating new cache for outputFiles, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@25a11574 +:compileJava (Thread[#56,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.004 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@58b03dda +Putting task artifact state for task ':compileJava' into context took 0.006 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1bd9ea3d Loading the Maven rules... Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian @@ -1700,7 +1736,7 @@ Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Passing through org.apache.logging.log4j:log4j-bom:jar:debian -Up-to-date check for task ':compileJava' took 0.725 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 0.775 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. @@ -1708,2698 +1744,35 @@ .map(line -> WordUtils.wrap(line, width)) ^ 1 warning -:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 3.365 secs. -:processResources (Thread[#55,Task worker for ':',5,main]) started. +:compileJava (Thread[#56,Task worker for ':',5,main]) completed. Took 2.909 secs. +:processResources (Thread[#56,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.007 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.01 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#55,Task worker for ':',5,main]) completed. Took 0.032 secs. -:classes (Thread[#57,Task worker for ':' Thread 3,5,main]) started. +:processResources (Thread[#56,Task worker for ':',5,main]) completed. Took 0.037 secs. +:classes (Thread[#56,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#57,Task worker for ':' Thread 3,5,main]) completed. Took 0.0 secs. -:debianMavenPom (Thread[#57,Task worker for ':' Thread 3,5,main]) started. +:classes (Thread[#56,Task worker for ':',5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[#56,Task worker for ':',5,main]) started. :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: +Up-to-date check for task ':debianMavenPom' took 0.004 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/barclay-6.0.0+dfsg/build/debian/barclay.pom -:debianMavenPom (Thread[#57,Task worker for ':' Thread 3,5,main]) completed. Took 0.072 secs. -:jar (Thread[#58,Task worker for ':' Thread 4,5,main]) started. +:debianMavenPom (Thread[#56,Task worker for ':',5,main]) completed. Took 0.081 secs. +:jar (Thread[#58,Task worker for ':' Thread 3,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.013 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.01 secs. It is not up-to-date because: No history is available. -:jar (Thread[#58,Task worker for ':' Thread 4,5,main]) completed. Took 0.09 secs. +:jar (Thread[#58,Task worker for ':' Thread 3,5,main]) completed. Took 0.068 secs. -BUILD SUCCESSFUL in 8s +BUILD SUCCESSFUL in 10s 4 actionable tasks: 4 executed make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+dfsg' jh_build -O--buildsystem=gradle - rm -f debian/libbarclay-java.debhelper.log - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/barclay-6.0.0+dfsg' -# Tests do not work with locales with a different decimal separator -# (for example ',') -LC_ALL=C.UTF-8 dh_auto_test - mkdir -p .gradle/init.d - cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=barclay -Dfile.encoding=UTF-8 --parallel --max-workers=12 test -openjdk version "21.0.9" 2025-10-21 -OpenJDK Runtime Environment (build 21.0.9+10-Debian-1) -OpenJDK 64-Bit Server VM (build 21.0.9+10-Debian-1, mixed mode, sharing) -Initialized native services in: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/native -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/barclay-6.0.0+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 0.788 secs. -The client will now receive all logging from the daemon (pid: 2868415). The daemon log file: /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/daemon/4.4.1/daemon-2868415.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/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@62a4ef64 -Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@62a4ef64 -Creating new cache for fileHashes, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@1518122e -Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@6ac210e9 -Settings evaluated using settings file '/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle'. - Settings file not found (/build/reproducible-path/barclay-6.0.0+dfsg/settings.gradle) - Root project name not defined in settings.gradle, defaulting to 'barclay' instead of the name of the root directory 'barclay-6.0.0+dfsg' -Projects loaded. Root project using build file '/build/reproducible-path/barclay-6.0.0+dfsg/build.gradle'. -Included projects: [root project 'barclay'] - Keep-alive timer started - Adding Debian repository to project 'barclay' -Parallel execution is an incubating feature. -Evaluating root project 'barclay' using build file '/build/reproducible-path/barclay-6.0.0+dfsg/build.gradle'. -Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/barclay-6.0.0+dfsg Command: dpkg-parsechangelog -S Version -Successfully started process 'command 'dpkg-parsechangelog'' - Adding Maven pom generation to project 'barclay' - 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/barclay-6.0.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@3bdb010d -Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@1518122e -Creating new cache for taskHistory, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3411532d -Creating new cache for outputFiles, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7a110e8e -:compileJava (Thread[#56,Task worker for ':',5,main]) started. -:compileJava -Putting task artifact state for task ':compileJava' into context took 0.004 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/barclay-6.0.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@603625e6 - Loading the Maven rules... - Replacing net.sf.jopt-simple:jopt-simple:jar:5.0.3 -> net.sf.jopt-simple:jopt-simple:jar:debian - Replacing com.google.code.gson:gson:jar:2.8.9 -> com.google.code.gson:gson:jar:debian - Passing through com.google.code.gson:gson-parent:jar:debian - Replacing org.freemarker:freemarker:jar:2.3.30 -> org.freemarker:freemarker:jar:debian - Replacing org.apache.commons:commons-lang3:jar:3.4 -> org.apache.commons:commons-lang3:jar:debian - Passing through org.apache.commons:commons-parent:jar:debian - Passing through org.apache:apache:jar:debian - Replacing org.apache.logging.log4j:log4j-api:jar:2.17.1 -> org.apache.logging.log4j:log4j-api:jar:debian - Passing through org.apache.logging.log4j:log4j:jar:debian - Passing through org.apache.logging.log4j:log4j-bom:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 0.32 secs). -:compileJava UP-TO-DATE -:compileJava (Thread[#56,Task worker for ':',5,main]) completed. Took 0.352 secs. -:processResources (Thread[#56,Task worker for ':',5,main]) started. -:processResources -Putting task artifact state for task ':processResources' into context took 0.0 secs. -Skipping task ':processResources' as it is up-to-date (took 0.011 secs). -:processResources UP-TO-DATE -:processResources (Thread[#56,Task worker for ':',5,main]) completed. Took 0.015 secs. -:classes (Thread[#56,Task worker for ':',5,main]) started. -:classes -Skipping task ':classes' as it has no actions. -:classes UP-TO-DATE -:classes (Thread[#56,Task worker for ':',5,main]) completed. Took 0.0 secs. -:compileTestJava (Thread[#56,Task worker for ':',5,main]) started. -:compileTestJava -Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. -Malformed class file [Pair.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. - at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) - at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) - at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) - at org.gradle.api.internal.changedetection.state.ClasspathEntrySnapshotBuilder.visitFileSnapshot(ClasspathEntrySnapshotBuilder.java:62) - at org.gradle.api.internal.changedetection.state.FileTree.visit(FileTree.java:36) - at org.gradle.api.internal.changedetection.state.AbstractClasspathSnapshotBuilder.visitFileTreeSnapshot(AbstractClasspathSnapshotBuilder.java:66) - at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitDirectoryTree(AbstractFileCollectionSnapshotter.java:100) - at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter$FileCollectionVisitorImpl.visitCollection(AbstractFileCollectionSnapshotter.java:82) - at org.gradle.api.internal.file.AbstractFileCollection.visitRootElements(AbstractFileCollection.java:234) - at org.gradle.api.internal.file.CompositeFileCollection.visitRootElements(CompositeFileCollection.java:185) - at org.gradle.api.internal.changedetection.state.AbstractFileCollectionSnapshotter.snapshot(AbstractFileCollectionSnapshotter.java:53) - at org.gradle.api.internal.changedetection.state.DefaultCompileClasspathSnapshotter.snapshot(DefaultCompileClasspathSnapshotter.java:38) - at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.snapshotTaskFiles(CacheBackedTaskHistoryRepository.java:331) - at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.createExecution(CacheBackedTaskHistoryRepository.java:154) - at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository.access$100(CacheBackedTaskHistoryRepository.java:61) - at org.gradle.api.internal.changedetection.state.CacheBackedTaskHistoryRepository$1.getCurrentExecution(CacheBackedTaskHistoryRepository.java:114) - at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.getStates(DefaultTaskArtifactStateRepository.java:201) - at org.gradle.api.internal.changedetection.changes.DefaultTaskArtifactStateRepository$TaskArtifactStateImpl.isUpToDate(DefaultTaskArtifactStateRepository.java:86) - at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:53) - at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54) - at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:60) - at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:97) - at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:87) - at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52) - at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52) - at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54) - at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43) - at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34) - at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248) - at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336) - at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328) - at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199) - at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110) - at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241) - at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230) - at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:123) - at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:79) - at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:104) - at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:98) - at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:626) - at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:581) - at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:98) - at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) - at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) - at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) - at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) - at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) - at java.base/java.lang.Thread.run(Thread.java:1583) - Replacing commons-io:commons-io:jar:2.11.0 -> commons-io:commons-io:jar:debian - Passing through org.testng:testng:jar:debian - Replacing org.mockito:mockito-core:jar:4.6.1 -> org.mockito:mockito-core:jar:debian - Passing through org.beanshell:bsh:jar:debian - Passing through com.beust:jcommander:jar:debian - Passing through net.bytebuddy:byte-buddy:jar:debian - Passing through net.bytebuddy:byte-buddy-parent:jar:debian - Passing through net.bytebuddy:byte-buddy-agent:jar:debian - Passing through org.objenesis:objenesis:jar:debian - Passing through org.objenesis:objenesis-parent:jar:debian - Passing through net.bytebuddy:byte-buddy-dep:jar:debian - Passing through org.ow2.asm:asm:jar:debian - Passing through org.ow2.asm:asm-commons:jar:debian -Up-to-date check for task ':compileTestJava' took 1.109 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. -:compileTestJava (Thread[#56,Task worker for ':',5,main]) completed. Took 3.164 secs. -:processTestResources (Thread[#56,Task worker for ':',5,main]) started. -:processTestResources -Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.016 secs. It is not up-to-date because: - No history is available. -:processTestResources (Thread[#56,Task worker for ':',5,main]) completed. Took 0.057 secs. -:testClasses (Thread[#56,Task worker for ':',5,main]) started. -:testClasses -Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#56,Task worker for ':',5,main]) completed. Took 0.0 secs. -:test (Thread[#56,Task worker for ':',5,main]) started. -:test -Putting task artifact state for task ':test' into context took 0.001 secs. - Replacing org.apache.logging.log4j:log4j-core:jar:2.17.1 -> org.apache.logging.log4j:log4j-core:jar:debian -Up-to-date check for task ':test' took 0.507 secs. It is not up-to-date because: - Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/barclay-6.0.0+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath14172018598252240770txt -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. -Running Test: Test method testCollectionFromExpansionFile[0](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@14169601, [], /tmp/enabledExpansion11457264335553066759.args, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@46244d6e, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@20dde459, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion16334097341377047152.args, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@264679c6, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[2](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@553913dd, [], /tmp/enabledExpansion3403026449448851937.list, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@2c08beb4, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[3](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@50291511, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion9937194823008497400.list, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@5d88b1ff, false)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[4](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@5c911886, [], /tmp/enabledExpansion14763095379112574170.args, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@672a4be7, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[5](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@144c7e66, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion16898928097796813601.args, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@5faf3c32, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[6](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@2126ad8e, [], /tmp/enabledExpansion9032840953001004463.list, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@337309d0, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromExpansionFile[7](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$SuppressedListFileArguments@10fa6539, [APPEND_TO_COLLECTIONS], /tmp/enabledExpansion14600764793923075822.list, [Ljava.lang.String;@31e937e3, [Ljava.lang.String;@5aada723, true)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromListFileMixed[0](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@21b3e0ab, [], [Ljava.lang.String;@695f443a, [Ljava.lang.String;@61535fac, [Ljava.lang.String;@47093656, [Ljava.lang.String;@798120a4)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionFromListFileMixed[1](org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests$EnabledListFileArguments@e4d30b4, [APPEND_TO_COLLECTIONS], [Ljava.lang.String;@695f443a, [Ljava.lang.String;@61535fac, [Ljava.lang.String;@147c928c, [Ljava.lang.String;@7583a265)(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testCollectionThatCannotBeAutoInitialized(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testGetCommandLineWithExpansionFile(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[0]([Ljava.lang.String;@3462447a, [APPEND_TO_COLLECTIONS], [foo, bar, baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[1]([Ljava.lang.String;@3462447a, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[2]([Ljava.lang.String;@5ac10463, [APPEND_TO_COLLECTIONS], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[3]([Ljava.lang.String;@5ac10463, [], [baz, frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[4]([Ljava.lang.String;@183053ee, [APPEND_TO_COLLECTIONS], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[5]([Ljava.lang.String;@183053ee, [], [frob])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[6]([Ljava.lang.String;@7ba361a2, [APPEND_TO_COLLECTIONS], [foo, bar])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testInitializedCollections[7]([Ljava.lang.String;@6e7274ea, [[]], [foo, bar])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testPositionalCollectionFromExpansionFile(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testRejectNonCollectionFileExpansionSuppression(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testUninitializedCollections[0]([Ljava.lang.String;@6dce3682, [], [L1, L2], [S1], [HS1], [P1, P2])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method testUninitializedCollections[1]([Ljava.lang.String;@6dce3682, [APPEND_TO_COLLECTIONS], [L1, L2], [S1], [HS1], [P1, P2])(org.broadinstitute.barclay.argparser.CollectionArgumentUnitTests) -Running Test: Test method passingMutexCheck[0](simple mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@43128b9f, [Ljava.lang.String;@5c7f7c96)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method passingMutexCheck[1](collection mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@69ac22d1, [Ljava.lang.String;@77405c18)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method passingMutexCheck[2](collection multiple mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@20718487, [Ljava.lang.String;@360aea80)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method passingMutexCheck[3](scalar mixed, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@12e82180, [Ljava.lang.String;@49e9348f)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testAbbreviationsAreRejected(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testAdvancedArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgCollectionNotInitialized(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgUsage[0](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@41688c85, [--FROBNICATION_FLAVOR , --SHMIGGLE_TYPE , --arguments-file,-arguments_file , --FROBNICATION_THRESHOLD,-T , --TRUTHINESS ])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgUsage[1](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$FrobnicateArguments@30021b5d, [--deprecatedString, This argument is DEPRECATED, and will be removed in a future])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgUsage[2](org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@333e749, [--collection , --scalar ])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgumentCollection(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgumentNameCollision(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgumentUseClash(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgumentsFile(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArgumentsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testArrayArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBadFieldCausesException(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBadValue(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBetaExperimentalMutex(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBetaFeatureUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testCombinationOfFlags(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testDanglingMutex(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testDefault(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testEnsureClusteringDisabled(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testEnumSet(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testEnumSetNegative(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testExperimentalFeatureUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFailingMutex[0](no args, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@6c88376, [Ljava.lang.String;@218375b2)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFailingMutex[1](1 of group required, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@6110e578, [Ljava.lang.String;@66fee8)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFailingMutex[2](mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@229bb9fb, [Ljava.lang.String;@31b67c0d)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFailingMutex[3](mega mutex, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MutexArguments@6516a08e, [Ljava.lang.String;@bdff365)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFailingMutex[4](collection and scalar mutex mix, org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest$MixedCardinalityMutexArguments@403f7a5e, [Ljava.lang.String;@4ff5768c)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFlagNoArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFlagWithPositionalFollowing(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testFlagsWithArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testGatherArgumentValuesOfType[0]([--childSuperTypeTarget, childSuperTypeTargetValue, --childSubTypeTarget, childSubTypeTargetValue, --parentSuperTypeTarget, parentSuperTypeTargetValue, --parentSubTypeTarget, parentSubTypeTargetValue, --childCollectionSuperTypeTarget, childCollectionSuperTypeTargetValue, --childCollectionSubTypeTarget, childCollectionSubTypeTargetValue, --parentCollectionSuperTypeTarget, parentCollectionSuperTypeTargetValue, --parentCollectionSubTypeTarget, parentCollectionSubTypeTargetValue, --childListSuperTypeTarget, childListSuperTypeTargetValue1, --childListSuperTypeTarget, childListSuperTypeTargetValue2, --childListSuperTypeTarget, childListSuperTypeTargetValue3, --childListSubTypeTarget, childListSubTypeTargetValue1, --childListSubTypeTarget, childListSubTypeTargetValue2, --childListSubTypeTarget, childListSubTypeTargetValue3, --parentListSuperTypeTarget, parentListSuperTypeTargetValue1, --parentListSuperTypeTarget, parentListSuperTypeTargetValue2, --parentListSuperTypeTarget, parentListSuperTypeTargetValue3, --parentListSubTypeTarget, parentListSubTypeTargetValue1, --parentListSubTypeTarget, parentListSubTypeTargetValue2, --parentListSubTypeTarget, parentListSubTypeTargetValue3, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue1, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue2, --childCollectionListSuperTypeTarget, childCollectionListSuperTypeTargetValue3, --childNonTargetArgument, 1, --parentNonTargetArgument, 1, --childCollectionNonTargetArgument, 1, --parentCollectionNonTargetArgument, 1, --childNonTargetListArgument, 1], [Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue1], Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue2], Pair[left=childCollectionListSuperTypeTarget, right=childCollectionListSuperTypeTargetValue3], Pair[left=childCollectionSubTypeTarget, right=childCollectionSubTypeTargetValue], Pair[left=childCollectionSuperTypeTarget, right=childCollectionSuperTypeTargetValue], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue1], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue2], Pair[left=childListSubTypeTarget, right=childListSubTypeTargetValue3], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue1], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue2], Pair[left=childListSuperTypeTarget, right=childListSuperTypeTargetValue3], Pair[left=childSubTypeTarget, right=childSubTypeTargetValue], Pair[left=childSuperTypeTarget, right=childSuperTypeTargetValue], Pair[left=parentCollectionSubTypeTarget, right=parentCollectionSubTypeTargetValue], Pair[left=parentCollectionSuperTypeTarget, right=parentCollectionSuperTypeTargetValue], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue1], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue2], Pair[left=parentListSubTypeTarget, right=parentListSubTypeTargetValue3], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue1], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue2], Pair[left=parentListSuperTypeTarget, right=parentListSuperTypeTargetValue3], Pair[left=parentSubTypeTarget, right=parentSubTypeTargetValue], Pair[left=parentSuperTypeTarget, right=parentSuperTypeTargetValue], Pair[left=uninitializedChildCollectionTarget, right=null], Pair[left=uninitializedChildListTarget, right=null], Pair[left=uninitializedChildTarget, right=null], Pair[left=uninitializedParentCollectionTarget, right=null], Pair[left=uninitializedParentTarget, right=null]])(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testGatherArgumentValuesOfTypeWithParameterizedType(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testGetCommandLine(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testGetCommandLineWithSensitiveArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: USAGE: BooleanFlags [arguments] - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest.testHelp STANDARD_ERROR - USAGE: BooleanFlags [arguments] -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Usage: program [arguments...] - - Usage: program [arguments...] -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Version:null - - Version:null -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Optional Arguments: - - Optional Arguments: -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --antiflag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used - - --antiflag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: in conjunction with argument(s) flag1 - - in conjunction with argument(s) flag1 -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --arguments-file,-arguments_file - - --arguments-file,-arguments_file -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: read one or more arguments files and add them to the command line This argument may be - - read one or more arguments files and add them to the command line This argument may be -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: specified 0 or more times. Default value: null. - - specified 0 or more times. Default value: null. -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used - - --flag1 Undocumented option Default value: false. Possible values: {true, false} Cannot be used -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: in conjunction with argument(s) antiflag1 - - in conjunction with argument(s) antiflag1 -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag2 Undocumented option Default value: true. Possible values: {true, false} - - --flag2 Undocumented option Default value: true. Possible values: {true, false} -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --flag3 Undocumented option Default value: false. Possible values: {true, false} - - --flag3 Undocumented option Default value: false. Possible values: {true, false} -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --help,-h display the help message Default value: false. Possible values: {true, false} - - --help,-h display the help message Default value: false. Possible values: {true, false} -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --version display the version number for this tool Default value: false. Possible values: {true, - - --version display the version number for this tool Default value: false. Possible values: {true, -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: false} - - false} -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Advanced Arguments: - - Advanced Arguments: -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: --show-hidden,-showHidden - - --show-hidden,-showHidden -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: display hidden arguments Default value: false. Possible values: {true, false} - - display hidden arguments Default value: false. Possible values: {true, false} -Test: Test method testHelp(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testHiddenArguments(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testHiddenRequiredArgumentThrowException(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testLongPreamble(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testMissingRequiredCollectionArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testNotEnoughOfListArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOnlyPrintNameOnce(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOptionalOnlyUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[0]([Ljava.lang.String;@3f21aba6)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[1]([Ljava.lang.String;@158c621)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[2]([Ljava.lang.String;@716fad8b)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[3]([Ljava.lang.String;@4c3a21f4)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[4]([Ljava.lang.String;@2a405a3d)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[5]([Ljava.lang.String;@1076731e)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testOutOfRangesArguments[6]([Ljava.lang.String;@5a953510)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testPositionalDeprecated(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testPositive(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testPrivateArgument(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testRequiredAdvancedNotAllowed(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testRequiredOnlyUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testRequiredOptionalWithDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testRequiredOptionalWithoutDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testSetNonNullableArgumentsToNull[0]([Ljava.lang.String;@382b8f0b)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testSetNonNullableArgumentsToNull[1]([Ljava.lang.String;@5fa47e3e)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testSetNonNullableArgumentsToNull[2]([Ljava.lang.String;@67142d99)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testVersionSpecialFlag(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Test: Test method testVersionSpecialFlag(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) produced standard out/err: Version:null - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest.testVersionSpecialFlag STANDARD_ERROR - Version:null -Running Test: Test method testWithBoundariesArgumentsForNoNumeric(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithDoubleBoundariesArgumentsForInteger(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[0]([Ljava.lang.String;@61fd9afa, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[1]([Ljava.lang.String;@22cce131, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[2]([Ljava.lang.String;@418dfb13, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[3]([Ljava.lang.String;@cc730f0, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[4]([Ljava.lang.String;@4feeeb41, null, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[5]([Ljava.lang.String;@2987624e, 1, null, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[6]([Ljava.lang.String;@18d8013c, null, 2.0, null)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[7]([Ljava.lang.String;@2653152b, null, null, somestring)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithinBoundariesArguments[8]([Ljava.lang.String;@59c46fde, 1, 2.0, somestring)(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithoutPositionalWithDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testWithoutPositionalWithoutDefaultUsage(org.broadinstitute.barclay.argparser.CommandLineArgumentParserTest) -Running Test: Test method testBasicPlugin[0]([Ljava.lang.String;@16c9ca3b, 0)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testBasicPlugin[1]([Ljava.lang.String;@381482b5, 1)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testDanglingFilterArguments[0](TestPluginWithRequiredArg, requiredStringArgForPlugin, fakeArgValue)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testDanglingFilterArguments[1](TestPluginWithOptionalArg, optionalStringArgForPlugin, fakeArgValue)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testDefaultIncludePluginClass[0](class org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest$TestPluginBase, true)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testDefaultIncludePluginClass[1](class org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest$TestPluginWithOptionalArg, true)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testDefaultIncludePluginClass[2](class java.lang.Integer, false)(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testEnableNonExistentPlugin(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testNoPluginsSpecified(org.broadinstitute.barclay.argparser.CommandLinePluginUnitTest) -Running Test: Test method testAddToDefaultValuesListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testArgumentCollectionFlat(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testArgumentCollectionNested(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testArgumentCollectionNoReferenceProvidedForOptional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'REFERENCE_SEQUENCE' is required. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testArgumentCollectionNoReferenceProvidedForRequired STANDARD_ERROR - ERROR: Option 'REFERENCE_SEQUENCE' is required. -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: ToolWithRequiredReference [options] - - USAGE: ToolWithRequiredReference [options] -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] - - Usage: program [options...] -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: REFERENCE_SEQUENCE=File A reference is required Required. - - REFERENCE_SEQUENCE=File A reference is required Required. -Test: Test method testArgumentCollectionNoReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testArgumentCollectionWithReferenceProvidedForOptional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testArgumentCollectionWithReferenceProvidedForRequired(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: 'HiMom' is not a valid value for FrobnicationFlavor. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testBadEnumValue STANDARD_ERROR - ERROR: 'HiMom' is not a valid value for FrobnicationFlavor. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testBadEnumValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Problem constructing Integer from the string 'ABC'. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testBadValue STANDARD_ERROR - ERROR: Problem constructing Integer from the string 'ABC'. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testBadValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testBetaExperimentalMutex(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testBetaFeatureUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testClearDefaultValuesFromListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testClearDefaultValuesFromListOptionAndAddNew(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testCollectionThatCannotBeAutoInitialized(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testExperimentalFeatureUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testForIdenticalShortName(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[0](hello, hello)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[1](, )(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[2](hibye, hi bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[3](hibye, hibye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[4](hi
  • bye, hi - bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[5](hibye, hibye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[6](
    , 
-
-)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
-Running Test: Test method testHTMLConverter[7]( string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
-Running Test: Test method testHTMLConverter[8]( string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
-Running Test: Test method testHTMLConverter[9](< a href="http://go.here.org"> string,  string (http://go.here.org))(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest)
-Running Test: Test method testHTMLConverter[10](hi
    • bye, hi -bye)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHTMLConverter[11](Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina).

    Usage example:

        java -jar picard.jar CollectAlignmentSummaryMetrics \
              R=reference_sequence.fasta \
              I=input.bam \
              O=output.txt
    Please see     the AlignmentSummaryMetrics documentation for detailed explanations of each metric.

    Additional information about Illumina's quality filters can be found in the following documents on the Illumina website:
    , Using read outputs from high throughput sequencing (HTS) technologies, this tool provides metrics regarding the quality of read alignments to a reference sequence, as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters (Illumina). -Usage example: - - java -jar picard.jar CollectAlignmentSummaryMetrics \ - R=reference_sequence.fasta \ - I=input.bam \ - O=output.txt -Please see the AlignmentSummaryMetrics documentation (http://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics) for detailed explanations of each metric. - -Additional information about Illumina's quality filters can be found in the following documents on the Illumina website: - - hiseq-x-percent-pf-technical-note (http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf) - - hiseq-x-system-guide (http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseqx/hiseq-x-system-guide-15050091-d.pdf) - - -)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHtmlUnescape[0](<, <)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHtmlUnescape[1](x)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testHtmlUnescape[4]( x y< x , x<y y< x )(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[0](-15)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[1](-5)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[2](-2)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[3](1)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[4](0)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[5](2)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[6](5)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testIgnoringBoundaries[7](10)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testLongPreamble(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'FROBNICATION_FLAVOR' is required. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMissingRequiredArgument STANDARD_ERROR - ERROR: Option 'FROBNICATION_FLAVOR' is required. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testMissingRequiredArgument(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testMutex[0](pass, [Ljava.lang.String;@13c04808, true)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[1](no args, [Ljava.lang.String;@3c7e488, false) STANDARD_ERROR - ERROR: Option 'A' is required unless any of [Y, Z, M, N] are specified. -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] - - USAGE: MutexOptions [options] -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] - - Usage: program [options...] -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[1](no args, [Ljava.lang.String;@3c7e488, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false) STANDARD_ERROR - ERROR: Option 'B' is required unless any of [Y, Z, M, N] are specified. -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] - - USAGE: MutexOptions [options] -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] - - Usage: program [options...] -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[2](1 of group required, [Ljava.lang.String;@4c123a48, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' cannot be used in conjunction with option(s) Y - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false) STANDARD_ERROR - ERROR: Option 'A' cannot be used in conjunction with option(s) Y -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] - - USAGE: MutexOptions [options] -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] - - Usage: program [options...] -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[3](mutex, [Ljava.lang.String;@5e1a1ce8, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false) STANDARD_ERROR - ERROR: Option 'A' cannot be used in conjunction with option(s) Y Z M N -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: MutexOptions [options] - - USAGE: MutexOptions [options] -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: program [options...] - - Usage: program [options...] -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - A=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N - - B=String Undocumented option Required. Cannot be used in conjuction with option(s) Y Z M N -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - M=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z - - N=String Undocumented option Required. Cannot be used in conjuction with option(s) A B Y Z -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Y=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N - - Z=String Undocumented option Required. Cannot be used in conjuction with option(s) A B M N -Test: Test method testMutex[4](mega mutex, [Ljava.lang.String;@416f0a88, false)(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testNonASCIIAccept(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testNonASCIIReject(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testNonAsciiAssertion(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testNonAsciiConverted(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNotEnoughOfListOption STANDARD_ERROR - ERROR: Option 'SHMIGGLE_TYPE' must be specified at least 1 times. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testNotEnoughOfListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: At least 2 positional arguments must be specified. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNotEnoughPositional STANDARD_ERROR - ERROR: At least 2 positional arguments must be specified. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testNotEnoughPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testNullValue STANDARD_ERROR - ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptionsWithNullList [options] - - USAGE: FrobnicateOptionsWithNullList [options] -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Required. - - T=Integer Frobnication threshold setting. Required. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Default value: BAR. This option can be set to 'null' to clear the - - Undocumented option Default value: BAR. This option can be set to 'null' to clear the -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {FOO, BAR, BAZ} - - default value. Possible values: {FOO, BAR, BAZ} -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the - - TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {true, false} - - default value. Possible values: {true, false} -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. - - ERROR: non-null value must be provided for 'FROBNICATION_THRESHOLD'. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptionsWithNullList [options] - - USAGE: FrobnicateOptionsWithNullList [options] -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Required. - - T=Integer Frobnication threshold setting. Required. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Default value: BAR. This option can be set to 'null' to clear the - - Undocumented option Default value: BAR. This option can be set to 'null' to clear the -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {FOO, BAR, BAZ} - - default value. Possible values: {FOO, BAR, BAZ} -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option must be specified no more than 3 -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the - - TRUTHINESS=Boolean Undocumented option Default value: false. This option can be set to 'null' to clear the -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: default value. Possible values: {true, false} - - default value. Possible values: {true, false} -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testNullValue(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testOptionDefinitionCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testOptionUseCaseClash STANDARD_ERROR - ERROR: Option 'FROBNICATION_FLAVOR' cannot be specified more than once. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testOptionUseCaseClash(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testOptionsFile(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'T' cannot be specified more than once. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testOptionsFileWithDisallowedOverride STANDARD_ERROR - ERROR: Option 'T' cannot be specified more than once. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testOptionsFileWithDisallowedOverride(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testPositive(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testPositiveTerminalEqualSign(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testPositiveWithSpaces(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testPositiveWithoutPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testTooManyListOption STANDARD_ERROR - ERROR: Option 'SHMIGGLE_TYPE' cannot be used more than 3 times. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line - - OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file - - options, unrecognized options are ignored. A single-valued option set in an options file -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is - - may be overridden by a subsequent command-line option. A line starting with '#' is -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: considered a comment. Required. - - considered a comment. Required. -Test: Test method testTooManyListOption(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: No more than 2 positional arguments may be specified on the command line. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testTooManyPositional STANDARD_ERROR - ERROR: No more than 2 positional arguments may be specified on the command line. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: FrobnicateOptions [options] - - USAGE: FrobnicateOptions [options] -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: frobnicate [options] input-file output-file - - Usage: frobnicate [options] input-file output-file -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Read input-file, frobnicate it, and write frobnicated results to output-file - - Read input-file, frobnicate it, and write frobnicated results to output-file -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testTooManyPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: ERROR: Invalid argument 'positional'. - - -Gradle suite > Gradle test > org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest.testUnexpectedPositional STANDARD_ERROR - ERROR: Invalid argument 'positional'. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: USAGE: OptionsWithoutPositional [options] - - USAGE: OptionsWithoutPositional [options] -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Usage: framistat [options] - - Usage: framistat [options] -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Compute the plebnick of the freebozzle. - - Compute the plebnick of the freebozzle. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Version: null - - Version: null -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Options: - - Options: -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --help - - --help -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -h Displays options specific to this tool. - - -h Displays options specific to this tool. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --stdhelp - - --stdhelp -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line - - -H Displays options specific to this tool AND options common to all Picard command line -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: tools. - - tools. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: --version Displays program version. - - --version Displays program version. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_THRESHOLD=Integer - - FROBNICATION_THRESHOLD=Integer -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to - - T=Integer Frobnication threshold setting. Default value: 20. This option can be set to 'null' to -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: clear the default value. - - clear the default value. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: FROBNICATION_FLAVOR=FrobnicationFlavor - - FROBNICATION_FLAVOR=FrobnicationFlavor -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: Undocumented option Required. Possible values: {FOO, BAR, BAZ} - - Undocumented option Required. Possible values: {FOO, BAR, BAZ} -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 - - SHMIGGLE_TYPE=String Allowed shmiggle types. Default value: null. This option may be specified between 1 and 3 -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: times. - - times. -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} - - TRUTHINESS=Boolean Undocumented option Required. Possible values: {true, false} -Test: Test method testUnexpectedPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) produced standard out/err: - - -Running Test: Test method testUninitializedCollections(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testUsage(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testUsageWithDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testUsageWithoutPositional(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testUsageWithoutPositionalWithDefault(org.broadinstitute.barclay.argparser.LegacyCommandLineArgumentParserTest) -Running Test: Test method testDefaultValueAsString[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$1@1277e3f9, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@17ad4ba, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@38536f28, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@36e29fec, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@10fdbc34, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@1d8c18b, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@6aa10aea, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@37709b43, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@42f2ec73, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@1fa45907, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@58b2c2b9, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testDefaultValueAsString[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@22b33500, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliasDisplayString[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@66a97b0e, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliasDisplayString[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@12c95e57, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliasDisplayString[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@3684fa0d, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliasDisplayString[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@3aa535c5, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliases[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@6e421836, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliases[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@2868e7e0, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliases[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@1759d097, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetArgumentAliases[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@449f739f, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetLongName[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$13@53c0c488, arg, arg, [arg], arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetLongName[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$14@79f97866, arg, arg, [shortName, arg], shortName/arg)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetLongName[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$15@5a45060, arg, fullName, [fullName], fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetLongName[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$16@5ec507f1, arg, fullName, [shortName, fullName], shortName/fullName)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[0](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$1@fae342, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[1](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$2@717ed153, arg, true, 0)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[2](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$3@55c45a66, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[3](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$4@40719d4b, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[4](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$5@2f36cd5b, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[5](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$6@3570fe16, arg, true, 27)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[6](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$7@41d4757a, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[7](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$8@3778a652, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[8](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$9@41c4993, arg, true, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[9](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$10@207d406f, arg, false, null)(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[10](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$11@2cdc4e9c, arg, true, [stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testIsOptional[11](org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest$12@1de4de57, arg, true, [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[0](required, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[1](optional, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[2](defaultedRequired, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[3](defaultedOptional, [], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[4](required, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[5](optional, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[6](defaultedRequired, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[7](defaultedOptional, [], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[8](required, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[9](optional, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[10](defaultedRequired, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[11](defaultedOptional, [], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[12](optional, [], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[13](defaultedOptional, [], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[14](required, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[15](optional, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[16](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [default, stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[17](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, more stuff], [default, stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[18](required, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[19](optional, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[20](defaultedRequired, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[21](defaultedOptional, [APPEND_TO_COLLECTIONS], [null, stuff, more stuff], [stuff, more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[22](required, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[23](optional, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[24](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[25](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, null, more stuff], [more stuff])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[26](optional, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollections[27](defaultedOptional, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null], [])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollectionsFailures[0](required, [], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollectionsFailures[1](defaultedRequired, [], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollectionsFailures[2](required, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testSetArgumentValuesCollectionsFailures[3](defaultedRequired, [APPEND_TO_COLLECTIONS], [stuff, more stuff, null])(org.broadinstitute.barclay.argparser.NamedArgumentDefinitionUnitTest) -Running Test: Test method testGetCommandLineDisplayString[0]([Ljava.lang.String;@5afc5874, )(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testGetCommandLineDisplayString[1]([Ljava.lang.String;@5af7b77d, arg1)(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testGetCommandLineDisplayString[2]([Ljava.lang.String;@6434568a, arg1 arg2)(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testMaxElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testMinElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testMinElementsGreaterThanMaxElements(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method testNonCollection(org.broadinstitute.barclay.argparser.PositionalArgumentsDefinitionUnitTest) -Running Test: Test method recognizedValues(org.broadinstitute.barclay.argparser.StrictBooleanConverterTest) -Running Test: Test method unrecognizedValues(org.broadinstitute.barclay.argparser.StrictBooleanConverterTest) -Running Test: Test method testBadTaggedArguments[0]([Ljava.lang.String;@7934dd35)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[1]([Ljava.lang.String;@335d5377)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[2]([Ljava.lang.String;@a4d4935)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[3]([Ljava.lang.String;@6e752a15)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[4]([Ljava.lang.String;@1b83a1dd)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[5]([Ljava.lang.String;@1cdc16c8)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[6]([Ljava.lang.String;@5b2a05e5)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[7]([Ljava.lang.String;@9fd3961)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[8]([Ljava.lang.String;@51570e7a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[9]([Ljava.lang.String;@fb876df)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[10]([Ljava.lang.String;@363549a6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[11]([Ljava.lang.String;@3024a40e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[12]([Ljava.lang.String;@35d78c7a)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[13]([Ljava.lang.String;@640c8d5f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[14]([Ljava.lang.String;@58f31442)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[15]([Ljava.lang.String;@430e77de)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[16]([Ljava.lang.String;@25c5c480)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[17]([Ljava.lang.String;@15c9db75)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[18]([Ljava.lang.String;@5f5d241f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[19]([Ljava.lang.String;@6e738510)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[20]([Ljava.lang.String;@34bdb37d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[21]([Ljava.lang.String;@245934fa)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[22]([Ljava.lang.String;@4f752c74)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[23]([Ljava.lang.String;@77c23597)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[24]([Ljava.lang.String;@55607a3d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[25]([Ljava.lang.String;@204c0834)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[26]([Ljava.lang.String;@42ba46e0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[27]([Ljava.lang.String;@63cd676e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[28]([Ljava.lang.String;@c4c97b8)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[29]([Ljava.lang.String;@21231027)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[30]([Ljava.lang.String;@5f817674)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[31]([Ljava.lang.String;@1efe8326)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[32]([Ljava.lang.String;@48ed30b6)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[33]([Ljava.lang.String;@34acdf3f)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[34]([Ljava.lang.String;@63d14700)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[35]([Ljava.lang.String;@1765b7d7)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[36]([Ljava.lang.String;@58828d45)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[37]([Ljava.lang.String;@6a0bddbe)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[38]([Ljava.lang.String;@60748e5b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[39]([Ljava.lang.String;@2fa56385)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[40]([Ljava.lang.String;@4eea74f8)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[41]([Ljava.lang.String;@206b4ac0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[42]([Ljava.lang.String;@6ad5dc5e)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[43]([Ljava.lang.String;@3388a5d9)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[44]([Ljava.lang.String;@257c3bfd)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[45]([Ljava.lang.String;@221148bc)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[46]([Ljava.lang.String;@286ba54b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[47]([Ljava.lang.String;@575e0027)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[48]([Ljava.lang.String;@b164caf)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[49]([Ljava.lang.String;@6f8c2051)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[50]([Ljava.lang.String;@b23729b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[51]([Ljava.lang.String;@5a3e15da)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[52]([Ljava.lang.String;@2f6bb1dc)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[53]([Ljava.lang.String;@20079a44)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[54]([Ljava.lang.String;@6c77d826)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[55]([Ljava.lang.String;@3f38fec7)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[56]([Ljava.lang.String;@68355c19)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[57]([Ljava.lang.String;@2f85cc9d)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[58]([Ljava.lang.String;@65f9a824)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testBadTaggedArguments[59]([Ljava.lang.String;@7dc4f6f3)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGetCommandLineTagged[0]([Ljava.lang.String;@7ad8e2b0, TaggableArguments --tFullName:tumor gcs://my/tumor.bam --tScalar:taggableArgScalar foo --scalarArg 17)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGetCommandLineTagged[1]([Ljava.lang.String;@6c4be093, TaggableArguments --tFullName:tumor,training=true,truth=false tumor.bam --tFullName:normal,training=false,truth=true normal.bam --tScalar:taggableArgScalar foo --scalarArg 17)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[0]([Ljava.lang.String;@6108a858, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4a9f3621, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4c71adda)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[1]([Ljava.lang.String;@6fce12dc, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2adb8cfe, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2833bec7)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[2]([Ljava.lang.String;@31b68d2, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@382427e, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@249e1a93)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[3]([Ljava.lang.String;@33568ff2, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3f500dc5, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@32455f52)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[4]([Ljava.lang.String;@dc0a9ac, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5afc6ba8, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@6ec41d30)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[5]([Ljava.lang.String;@33a5ab48, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@43689a9c, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@e71587)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[6]([Ljava.lang.String;@5e9d4a77, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@a031fdf, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4f20cd74)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[7]([Ljava.lang.String;@9611063, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3d316981, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2c2caebb)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[8]([Ljava.lang.String;@60f34058, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7209e7c4, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2a4ed00c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[9]([Ljava.lang.String;@24ea06f7, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@755255da, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3f920e65)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[10]([Ljava.lang.String;@40301028, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@34765c8d, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@722b421b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[11]([Ljava.lang.String;@4d4391d6, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@3fbfa350, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@78dbab9)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[12]([Ljava.lang.String;@9b7d63f, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@7959d9c9, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@488371c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[13]([Ljava.lang.String;@36e8bc2d, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5242f8b6, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@185e0122)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[14]([Ljava.lang.String;@136cb0bd, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@4daec330, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@24b3d2c0)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[15]([Ljava.lang.String;@6fac077a, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@46e0a17c, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@45e525aa)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[16]([Ljava.lang.String;@11fc1e51, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@625df4d7, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2403724b)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testGoodTaggedArguments[17]([Ljava.lang.String;@52af2b04, [Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@2bb586ab, [[Lorg.broadinstitute.barclay.argparser.TaggedArgumentTest$KeyValuePair;@5bd00c8c)(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testMixedTagCollectionArgument(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testMixedTaggedExpansionFile(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testTaggedScalarArgument(org.broadinstitute.barclay.argparser.TaggedArgumentTest) -Running Test: Test method testNonNullDoesNotThrow(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testNonNullThrows(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testNonNullWithMessageReturn(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testNonNullWithMessageThrows(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[0](hello -hello hello hello hello, hello -hello hello -hello hello, 12)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[1](hello -hello hello hello hello, hello -hello hello -hello hello, 11)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[2](hello -hello hello hello hello, hello -hello -hello -hello -hello, 10)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[3](hello - - - -hello hello hello hello, hello - - - -hello -hello -hello -hello, 10)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[4](hello -hello hello hello hello, hello -hello hello hello -hello, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[5](hello -hello hello hello hello -, hello -hello hello hello -hello -, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[6](hello -hello hello hello hello - -, hello -hello hello hello -hello - -, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[7](, , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[8]( , , 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[9]( -, -, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[10](null, null, 20)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[11](hello, hello, 0)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[12](hello, hello, -1)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[13](a b c d e f g, a -b -c -d -e -f -g, 1)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[14](a b c d e f g, a -b -c -d -e -f -g, 0)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[15](a b c d e f g, a -b -c -d -e -f -g, -1)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Running Test: Test method testWrapParagraph[16](a b c d e f g, a -b -c -d -e -f -g, -1000)(org.broadinstitute.barclay.utils.UtilsUnitTest) -Gradle Test Executor 1 finished executing tests. -Results: SUCCESS (369 tests, 369 successes, 0 failures, 0 skipped) -Finished generating test XML results (0.024 secs) into: /build/reproducible-path/barclay-6.0.0+dfsg/build/test-results/test -Generating HTML test report... -Finished generating test html results (0.028 secs) into: /build/reproducible-path/barclay-6.0.0+dfsg/build/reports/tests/test -:test (Thread[#56,Task worker for ':',5,main]) completed. Took 2.938 secs. - -BUILD SUCCESSFUL in 11s -5 actionable tasks: 3 executed, 2 up-to-date - rm -fr -- /tmp/dh-xdg-rundir-B6qz1uZB -make[1]: Leaving directory '/build/reproducible-path/barclay-6.0.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=gradle dh_prep -O--buildsystem=gradle @@ -4408,8 +1781,8 @@ dh_auto_install --destdir=debian/libbarclay-java/ -O--buildsystem=gradle install -m0755 -d /build/reproducible-path/barclay-6.0.0\+dfsg/debian/libbarclay-java jh_installjavadoc -O--buildsystem=gradle -Duplicate specification "author|A=s" for option "A" -Duplicate specification "author|A=s" for option "A" +Duplicate specification "A" for option "A" +Duplicate specification "A" for option "A" dh_installdocs -O--buildsystem=gradle install -m0755 -d debian/libbarclay-java/usr/share/doc/libbarclay-java install -p -m0644 debian/copyright debian/libbarclay-java/usr/share/doc/libbarclay-java/copyright @@ -4426,14 +1799,14 @@ ln -s barclay-6.0.0.jar debian/libbarclay-java/usr/share/java/barclay.jar jh_classpath -O--buildsystem=gradle jh_manifest -plibbarclay-java --classpath="/usr/share/java/commons-lang3.jar /usr/share/java/freemarker.jar /usr/share/java/gson.jar /usr/share/java/joptsimple.jar /usr/share/java/log4j-api.jar" debian/libbarclay-java/usr/share/java/barclay.jar -Duplicate specification "version|V" for option "V" +Duplicate specification "V:s" for option "V" Duplicate specification "V:s" for option "V" Updating symlinked /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar (via debian/libbarclay-java/usr/share/java/barclay.jar) Reading manifest from /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar Updating manifest in /build/reproducible-path/barclay-6.0.0+dfsg/debian/libbarclay-java/usr/share/java/barclay-6.0.0.jar jh_manifest -O--buildsystem=gradle -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" +Duplicate specification "V:s" for option "V" +Duplicate specification "V:s" for option "V" find debian/libbarclay-java -name '*.jar' Found usr/share/java/barclay-6.0.0.jar Found symlink usr/share/java/barclay.jar @@ -4523,12 +1896,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2833925/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2833925/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/2850112 and its subdirectories -I: Current time: Fri Oct 31 08:43:54 -12 2025 -I: pbuilder-time-stamp: 1761943434 +I: removing directory /srv/workspace/pbuilder/2833925 and its subdirectories +I: Current time: Fri Dec 4 17:08:00 +14 2026 +I: pbuilder-time-stamp: 1796353680