Diff of the two buildlogs: -- --- b1/build.log 2025-09-14 10:36:18.484662115 +0000 +++ b2/build.log 2025-09-14 11:13:50.967406203 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Sep 13 21:54:40 -12 2025 -I: pbuilder-time-stamp: 1757843680 +I: Current time: Sun Oct 18 06:59:21 +14 2026 +I: pbuilder-time-stamp: 1792256361 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -37,53 +37,85 @@ dpkg-source: info: applying 190-newest-vcf.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3929544/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 17 17:00 /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/277090/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6dc8c864674246fd92b64545b4648d17' - 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='3929544' - PS1='# ' - PS2='> ' + INVOCATION_ID=7682b24bb7e4483d9711b45052d0d7ef + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=277090 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.TyQT9Tp0/pbuilderrc_D7Dy --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.TyQT9Tp0/b1 --logfile b1/build.log htsjdk_4.1.3+dfsg-2.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.TyQT9Tp0/pbuilderrc_TMhd --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.TyQT9Tp0/b2 --logfile b2/build.log htsjdk_4.1.3+dfsg-2.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3929544/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -560,7 +592,7 @@ Get: 403 http://deb.debian.org/debian forky/main amd64 libngs-jni amd64 3.2.1+dfsg-5 [27.8 kB] Get: 404 http://deb.debian.org/debian forky/main amd64 libngs-java amd64 3.2.1+dfsg-5 [114 kB] Get: 405 http://deb.debian.org/debian forky/main amd64 scala-library all 2.11.12-6 [9586 kB] -Fetched 354 MB in 6s (58.0 MB/s) +Fetched 354 MB in 30s (11.6 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19917 files and directories currently installed.) @@ -1890,8 +1922,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Sep 14 09:56:06 UTC 2025. -Universal Time is now: Sun Sep 14 09:56:06 UTC 2025. +Local time is now: Sat Oct 17 17:01:42 UTC 2026. +Universal Time is now: Sat Oct 17 17:01:42 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2437,7 +2469,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/htsjdk-4.1.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../htsjdk_4.1.3+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/htsjdk-4.1.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../htsjdk_4.1.3+dfsg-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 4.1.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2453,8 +2489,8 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* -Duplicate specification "u=s" for option "u" -Duplicate specification "u=s" for option "u" +Duplicate specification "unlink|u" for option "u" +Duplicate specification "unlink|u" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper dh_clean -O--buildsystem=gradle @@ -2496,7 +2532,7 @@ dh_auto_build -- jar javadoc 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=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=40 jar javadoc + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=42 jar javadoc openjdk version "21.0.9-ea" 2025-10-21 OpenJDK Runtime Environment (build 21.0.9-ea+5-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.9-ea+5-Debian-1, mixed mode, sharing) @@ -2504,12 +2540,12 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.892 secs. -The client will now receive all logging from the daemon (pid: 3955825). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-3955825.out.log +An attempt to start the daemon took 0.74 secs. +The client will now receive all logging from the daemon (pid: 317219). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-317219.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 40 worker leases. +Using 42 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6aca3204 Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6aca3204 Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb4047e @@ -2535,16 +2571,16 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : -Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2fa98891 +Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@d525399 Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6fb4047e -Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@2dcf961f -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7c7e9a24 -:compileJava (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4b4f0c2b +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1eaf5b96 +:compileJava (Thread[#90,Task worker for ':' Thread 2,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.003 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@1624eb77 +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@2c17989c Loading the Maven rules... Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian @@ -2579,52 +2615,52 @@ Passing through xerces:xercesImpl:jar:debian Passing through jaxen:jaxen:jar:debian Passing through xml-apis:xml-apis-1.4:jar:debian -Up-to-date check for task ':compileJava' took 1.603 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.488 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. -/build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java:59: warning: [removal] runFinalization() in System has been deprecated and marked for removal - System.runFinalization(); - ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/DiskBackedQueue.java:258: warning: [removal] finalize() in Object has been deprecated and marked for removal protected void finalize() throws Throwable { ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/DiskBackedQueue.java:260: warning: [removal] finalize() in Object has been deprecated and marked for removal super.finalize(); // NB: intellij wanted me to do this. Need I? I'm not extending anything ^ +/build/reproducible-path/htsjdk-4.1.3+dfsg/src/main/java/htsjdk/samtools/util/FileAppendStreamLRUCache.java:59: warning: [removal] runFinalization() in System has been deprecated and marked for removal + System.runFinalization(); + ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileJava (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 7.284 secs. -:processResources (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +:compileJava (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 7.275 secs. +:processResources (Thread[#90,Task worker for ':' Thread 2,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.003 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.005 secs. It is not up-to-date because: No history is available. -:processResources (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 0.022 secs. -:classes (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +:processResources (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.022 secs. +:classes (Thread[#90,Task worker for ':' Thread 2,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +:classes (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[#90,Task worker for ':' Thread 2,5,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: No history is available. Generating pom file /build/reproducible-path/htsjdk-4.1.3+dfsg/build/debian/htsjdk.pom -:debianMavenPom (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 0.056 secs. -:jar (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +:debianMavenPom (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.054 secs. +:jar (Thread[#90,Task worker for ':' Thread 2,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.02 secs. It is not up-to-date because: No history is available. -:jar (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 0.301 secs. -:javadoc (Thread[#91,Task worker for ':' Thread 3,5,main]) started. +:jar (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 0.302 secs. +:javadoc (Thread[#90,Task worker for ':' Thread 2,5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. -Up-to-date check for task ':javadoc' took 0.279 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.265 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc @/build/reproducible-path/htsjdk-4.1.3+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc'' @@ -2943,9 +2979,9 @@ * Features content type (see {@link htsjdk.beta.plugin.features} for related formats) ^ 100 warnings -:javadoc (Thread[#91,Task worker for ':' Thread 3,5,main]) completed. Took 8.41 secs. +:javadoc (Thread[#90,Task worker for ':' Thread 2,5,main]) completed. Took 7.657 secs. -BUILD SUCCESSFUL in 20s +BUILD SUCCESSFUL in 19s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' jh_build -O--buildsystem=gradle @@ -2956,7 +2992,7 @@ dh_auto_build -- 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=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=40 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=42 test openjdk version "21.0.9-ea" 2025-10-21 OpenJDK Runtime Environment (build 21.0.9-ea+5-Debian-1) OpenJDK 64-Bit Server VM (build 21.0.9-ea+5-Debian-1, mixed mode, sharing) @@ -2964,17 +3000,17 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.725 secs. -The client will now receive all logging from the daemon (pid: 3956557). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-3956557.out.log +An attempt to start the daemon took 0.735 secs. +The client will now receive all logging from the daemon (pid: 317600). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-317600.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 40 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a9dde96 -Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6a9dde96 -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@411b18e4 +Using 42 worker leases. +Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@308764ae +Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@308764ae +Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@762ef58e Starting Build -Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@6e530580 +Creating new cache for metadata-1.1/results, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@55d661d3 Settings evaluated using settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/htsjdk-4.1.3+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] @@ -2989,15 +3025,15 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : -Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@4dd06dd3 +Creating new cache for annotation-processors, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@57b5da0f Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':testWithDefaultReference', task ':testWithOptimisticVCF4_4', task ':test'] -Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@411b18e4 -Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@6064ed92 -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5ed86dea -:compileJava (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +Creating new cache for resourceHashesCache, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@762ef58e +Creating new cache for taskHistory, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@73cc049 +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@69db3ea3 +:compileJava (Thread[#89,Task worker for ':',5,main]) started. :compileJava -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/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@35ac5c82 +Putting task artifact state for task ':compileJava' into context took 0.007 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@dba9ca8 Loading the Maven rules... Replacing gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 -> gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through javax.xml.bind:jaxb-api:jar:debian @@ -3032,24 +3068,24 @@ Passing through xerces:xercesImpl:jar:debian Passing through jaxen:jaxen:jar:debian Passing through xml-apis:xml-apis-1.4:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 0.618 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.603 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 0.65 secs. -:processResources (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#89,Task worker for ':',5,main]) completed. Took 0.638 secs. +:processResources (Thread[#89,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 0.003 secs). :processResources UP-TO-DATE -:processResources (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 0.007 secs. -:classes (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#89,Task worker for ':',5,main]) completed. Took 0.005 secs. +:classes (Thread[#89,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:compileTestJava (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#89,Task worker for ':',5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[#89,Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. -Malformed class file [Gff3Codec$Gff3Directive.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [BCF2Type.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3147,7 +3183,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [BCF2Type.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [VariantContext$Validation.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3196,7 +3232,7 @@ 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) -Malformed class file [VariantContext$Validation.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [Gff3Codec$Gff3Directive.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) @@ -3245,7 +3281,7 @@ 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) -Malformed class file [SRALazyRecord$LazyField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [ContentDigests$KNOWN_DIGESTS.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3294,7 +3330,7 @@ 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) -Malformed class file [SRALazyRecord$LazyFlag.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3343,7 +3379,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [SRALazyRecord$LazyAttribute.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3392,7 +3428,7 @@ 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) -Malformed class file [SamFlagField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SRALazyRecord$LazyField.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3441,7 +3477,7 @@ at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at java.base/java.lang.Thread.run(Thread.java:1583) -Malformed class file [SERIES.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SRALazyRecord$LazyAttribute.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. at org.gradle.api.internal.changedetection.state.AbiExtractingClasspathResourceHasher.hash(AbiExtractingClasspathResourceHasher.java:60) at org.gradle.api.internal.changedetection.state.ResourceSnapshotterCacheService.hashFile(ResourceSnapshotterCacheService.java:44) at org.gradle.api.internal.changedetection.state.CachingResourceHasher.hash(CachingResourceHasher.java:47) @@ -3490,7 +3526,7 @@ 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) -Malformed class file [ContentDigests$KNOWN_DIGESTS.class] found on compile classpath, which means that this class will cause a compile error if referenced in a source file. Gradle 5.0 will no longer allow malformed classes on compile classpath. +Malformed class file [SRALazyRecord$LazyFlag.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) @@ -3599,10 +3635,13 @@ Passing through org.jsr-305:jsr305:jar:0.x Passing through com.google.errorprone:error_prone_annotations:jar:debian Passing through com.google.errorprone:error_prone_parent:jar:debian -Up-to-date check for task ':compileTestJava' took 1.137 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 1.025 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. +/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal + tagMap.put("XC", new Character('q')); + ^ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:15: warning: [removal] Byte(byte) in Byte has been deprecated and marked for removal {new Byte((byte) 7)}, ^ @@ -3726,36 +3765,33 @@ /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java:122: warning: [removal] Long(long) in Long has been deprecated and marked for removal {new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT)), new SAMBinaryTagAndValue(tag, new Long(BinaryCodec.MAX_UINT-1)), false, false}, ^ -/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/java/htsjdk/samtools/SAMTextWriterTest.java:88: warning: [removal] Character(char) in Character has been deprecated and marked for removal - tagMap.put("XC", new Character('q')); - ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 42 warnings -:compileTestJava (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 6.304 secs. -:processTestResources (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:compileTestJava (Thread[#89,Task worker for ':',5,main]) completed. Took 6.508 secs. +:processTestResources (Thread[#89,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 0.447 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.397 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 1.133 secs. -:testClasses (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:processTestResources (Thread[#89,Task worker for ':',5,main]) completed. Took 1.031 secs. +:testClasses (Thread[#89,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 0.0 secs. -:testWithDefaultReference (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:testClasses (Thread[#89,Task worker for ':',5,main]) completed. Took 0.001 secs. +:testWithDefaultReference (Thread[#89,Task worker for ':',5,main]) started. :testWithDefaultReference -Putting task artifact state for task ':testWithDefaultReference' into context took 0.001 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.165 secs. It is not up-to-date because: +Putting task artifact state for task ':testWithDefaultReference' into context took 0.0 secs. +Up-to-date check for task ':testWithDefaultReference' took 0.162 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath16351283806608736175txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' +Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath6686568186597507475txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. Gradle Test Executor 1 STANDARD_ERROR - INFO 2025-09-13 21:57:02 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-10-18 07:02:35 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 1ms @@ -3764,7 +3800,7 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms @@ -3791,22 +3827,22 @@ testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms @@ -3824,7 +3860,7 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequence runtime: 1ms + testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms @@ -3845,10 +3881,10 @@ testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 3ms + testLastCompleteContigRead runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 2ms + testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 1ms @@ -3860,13 +3896,13 @@ testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 8ms + testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 7ms + testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms @@ -3884,7 +3920,7 @@ testFirstOfChr1 runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 6ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms @@ -3896,19 +3932,19 @@ testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 9ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 9ms + testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms @@ -3968,7 +4004,7 @@ testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 1ms + testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -4001,7 +4037,7 @@ testReset runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 9ms + testReset runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 9ms @@ -4012,6 +4048,22 @@ Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms +Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR + WARNING 2026-10-18 07:02:41 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@7e2a3605, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-10-18 07:02:41 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR + WARNING 2026-10-18 07:02:41 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 200 tests + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR + WARNING 2026-10-18 07:02:41 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR + WARNING 2026-10-18 07:02:41 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 Time so far: 0 @@ -5020,7 +5072,6 @@ Testing query chr21_random:4076206-6101050 ... Testing query chr20:5126731-9990106 ... Testing query chr4:3133535-3261569 ... -Finished 200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMFileReaderTest.testGetIndexTypeOK STANDARD_OUT chrM length= 16571 Aligned= 23 Unaligned= 0 @@ -5071,14 +5122,14 @@ NoCoordinateCount= 279 Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.14339477513598198821.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.13878415657438090660.bai - #BAMIndexWriterTest diff /tmp/javaBai.14339477513598198821.bai /tmp/cBai.13878415657438090660.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.17910346252940684769.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.2350405833434141182.bai + #BAMIndexWriterTest diff /tmp/javaBai.17910346252940684769.bai /tmp/cBai.2350405833434141182.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.18318884922900596292.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.4594692912330161381java.bai - #BAMIndexWriterTest diff /tmp/javaBai.4594692912330161381java.bai.txt /tmp/cBai.18318884922900596292.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.3429011087397462097.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.16552565921366120397java.bai + #BAMIndexWriterTest diff /tmp/javaBai.16552565921366120397java.bai.txt /tmp/cBai.3429011087397462097.bai.txt Finished 400 tests Finished 600 tests Finished 800 tests @@ -5090,33 +5141,21 @@ Finished 2000 tests Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 3ms to write + 2ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 2ms to write + 1ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT - Creating file /tmp/BCOST.10893930139390246677.gz + Creating file /tmp/BCOST.4990962850034215570.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.3377891727424262956.gz + Creating file /tmp/testCustomDeflater.1856477917080799507.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.15318918050134118774.gz - -Gradle suite > Gradle test > htsjdk.beta.io.bundle.BundleJSONTest.testAcceptSingleBundleJSONAsCollection[0]({ - "schema":{ - "schemaName":"htsbundle", - "schemaVersion":"0.1.0", - }, - "primary":"ALIGNED_READS", - "ALIGNED_READS":{"path":"file://myreads.bam","format":"BAM"} -}, ALIGNED_READS, [IOPathResource (file://myreads.bam): ALIGNED_READS/BAM]) STANDARD_ERROR - SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". - SLF4J: Defaulting to no-operation (NOP) logger implementation - SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. + Creating file /tmp/BCOST.18354892196193866286.gz Finished 2200 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testAllEncodingStrategyCombinations[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED @@ -5124,10 +5163,10 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) STANDARD_ERROR - WARNING 2025-09-13 21:58:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:58:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:58:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:58:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:03:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:03:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:03:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:03:35 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) SKIPPED @@ -5136,18 +5175,18 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[3](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) STANDARD_ERROR - WARNING 2025-09-13 21:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 21:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED @@ -5158,415 +5197,414 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[7](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_3_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2025-09-13 21:59:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2025-09-13 21:59:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 21:59:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2025-09-13 21:59:57 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-09-13 21:59:57 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2025-09-13 21:59:57 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-09-13 21:59:57 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-10-18 07:04:51 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-10-18 07:04:51 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-10-18 07:04:51 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-10-18 07:04:51 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:00:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2025-09-13 22:00:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:00:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:04:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:04:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2025-09-13 22:00:04 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-09-13 22:00:04 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2025-09-13 22:00:04 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-09-13 22:00:04 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-10-18 07:04:56 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-10-18 07:04:56 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-10-18 07:04:56 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-10-18 07:04:56 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR - WARNING 2025-09-13 22:00:04 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:00:04 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2025-09-13 22:00:04 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:00:04 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. -Finished 2400 tests + WARNING 2026-10-18 07:04:56 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:04:56 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-10-18 07:04:56 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:04:56 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR - INFO 2025-09-13 22:04:26 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2025-09-13 22:04:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:04:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-10-18 07:09:14 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2026-10-18 07:09:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:09:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 2400 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2025-09-13 22:04:26 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:04:26 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2025-09-13 22:04:26 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:04:26 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-10-18 07:09:15 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:09:15 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-10-18 07:09:15 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:09:15 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Gradle is still running, please be patient... -Finished 2600 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6a34239, [Ljava.lang.String;@4c8a37c0) STANDARD_ERROR - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c8c9a80, [Ljava.lang.String;@4fd61d47) STANDARD_ERROR - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@14f14dc9, [Ljava.lang.String;@68318264) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3860c5fd, [Ljava.lang.String;@4581f3a2) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@44a43808, [Ljava.lang.String;@ab03af0) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@754e9a1, [Ljava.lang.String;@37a0f6eb) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c594de8, [Ljava.lang.String;@56e27df9) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41e4ca2, [Ljava.lang.String;@1e18147a) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2abec53a, [Ljava.lang.String;@4e3b7af4) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b17a5cf, [Ljava.lang.String;@65dbd552) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@fe4eb6f, [Ljava.lang.String;@70f8b8df) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3905d898, [Ljava.lang.String;@1cc0117f) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@208d3b57, [Ljava.lang.String;@4ed3fdcb) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@518f69ec, [Ljava.lang.String;@1d72962e) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5da87388, [Ljava.lang.String;@11c1bf) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@276ee9fb, [Ljava.lang.String;@d07ad7) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5fc9e292, [Ljava.lang.String;@78cc818a) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1146e71d, [Ljava.lang.String;@1acb9270) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@bd3311b, [Ljava.lang.String;@4dc76caf) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@751d9ebc, [Ljava.lang.String;@7a9459c0) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69b0dba2, [Ljava.lang.String;@2c6ad3de) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7af3b003) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3bad8296) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@218dde5a) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@71322f22) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@151f53bd) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@25bf7391) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@73e4bc77) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4381dfab) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@ab50a5e, [Ljava.lang.String;@225b4af) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21844294, [Ljava.lang.String;@380f3ceb) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f362440, [Ljava.lang.String;@7949d7ae) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@76a27468, [Ljava.lang.String;@3aaf77a9) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@959cb8b, [Ljava.lang.String;@72326cc) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6cf5b01f, [Ljava.lang.String;@2a5da57) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b80ab39, [Ljava.lang.String;@7ccd5a5d) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@394205ea, [Ljava.lang.String;@57e00e82) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bffdd00, [Ljava.lang.String;@ef531c7) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4481d9c9, [Ljava.lang.String;@64da3cb8) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@32357027, [Ljava.lang.String;@3795818d) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30a8e4cb, [Ljava.lang.String;@1da009c) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e3d98d4, [Ljava.lang.String;@32316c58) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7203d080, [Ljava.lang.String;@3664320c) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@24ff49eb, [Ljava.lang.String;@40af6b84) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@383331b3, [Ljava.lang.String;@72d92a9f) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1cf2ffdb, [Ljava.lang.String;@7e99a391) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@39c16526) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@31f85e23) STANDARD_ERROR + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1d21dd13) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@28bcd8bd) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1d3f3162) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 2600 tests + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2632cee1) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@73adfb08) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@144d0bbd) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@7e39c886, [Ljava.lang.String;@7a6cec0c) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@469dcc7d, [Ljava.lang.String;@70f2837) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69b516ca, [Ljava.lang.String;@2c84c49f) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@25ce90cf, [Ljava.lang.String;@4cc88e1a) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ce4d92, [Ljava.lang.String;@77587c64) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6616d3e7, [Ljava.lang.String;@2f3da3bf) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2493ebba, [Ljava.lang.String;@3b324783) STANDARD_ERROR - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b96e978, [Ljava.lang.String;@55dfc0f3) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44a910b8, [Ljava.lang.String;@260cd141) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@332d5edd, [Ljava.lang.String;@18526425) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@232eaa4f, [Ljava.lang.String;@742195b2) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45eea553, [Ljava.lang.String;@216a9a5b) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@147b200c, [Ljava.lang.String;@550704da) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@180ac1be, [Ljava.lang.String;@38cf3abd) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@76cbdfb0, [Ljava.lang.String;@5d931841) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4164d362, [Ljava.lang.String;@42785ab6) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@390369b1, [Ljava.lang.String;@441d243f) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1f71508b) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@2539fad3) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@17ec35d5) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@5af0e69f) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@60bdeeb8) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@3db076b6) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@14ceb7d5) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@519b4aac) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@457dc78a) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1d9fc646) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@22320fb4) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@4c885cf9) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@75adc504) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@695f4729) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1a6bd570) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6cb6b189) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3625ce01) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@2292d44c) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3bb04009) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7a0df376) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@52601f2b) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@232b17a) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@122ccc05) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4c820cdc) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@272be1ba) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@66a88540) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@3f872ac7) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@de20adc) STANDARD_ERROR - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@71b0adec) STANDARD_ERROR - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@534c5c5) STANDARD_ERROR - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.15556829021755436606.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@199347b7) STANDARD_ERROR - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@4adda351, 5) STANDARD_ERROR - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@19df79f2, [Ljava.lang.String;@6cee9e4c) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4ecc371f, [Ljava.lang.String;@61fe98de) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33842c17, [Ljava.lang.String;@f094619) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8e2b1ce, [Ljava.lang.String;@5038cff) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38f56fd, [Ljava.lang.String;@2d23b41c) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1f3a5eb1, [Ljava.lang.String;@5904585d) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2cd1b643, [Ljava.lang.String;@6a1d8878) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d8c9275, [Ljava.lang.String;@2e33c387) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6933ba21, [Ljava.lang.String;@3921d591) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4cca9dc4, [Ljava.lang.String;@2ca36040) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22ea73ad, [Ljava.lang.String;@3e99658) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54ac2b3, [Ljava.lang.String;@151f53bd) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b17dad5, [Ljava.lang.String;@4dc4c328) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4468d86a, [Ljava.lang.String;@7eb2cdc1) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@eafcfe9, [Ljava.lang.String;@1b88b071) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@132c8747, [Ljava.lang.String;@f15078d) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7a6a259f, [Ljava.lang.String;@73e4bc77) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@20201d24) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@243b5b08) STANDARD_ERROR + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@ca9c212) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@23ce9892) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@615633e8) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7e39c886) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5487bd19) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@6616d3e7) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@46b48e72) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@232eaa4f) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2fe2134b) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@129f4233) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@11d4f990) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@65d90249) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5878d31d) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1624c761) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@4ad09394) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@47757e7a) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@21c594a5) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@3029ed69) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@166fd68d) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@18621f4d) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@779b730d) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@c8d61aa) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@6186e64b) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@70f4c90f) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@6395acd7) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5b258b42) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@69574e13) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@7298beec) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.15028250098786186867.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4140f6d3) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2ed33a8b, 5) STANDARD_ERROR + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 2800 tests + WARNING 2026-10-18 07:14:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2025-09-13 22:10:08 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-10-18 07:14:50 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testForNPE STANDARD_ERROR - INFO 2025-09-13 22:10:08 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2026-10-18 07:14:50 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMNoReferenceRequired STANDARD_ERROR - INFO 2025-09-13 22:10:08 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2026-10-18 07:14:50 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR - INFO 2025-09-13 22:10:08 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2026-10-18 07:14:50 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 1, Read name 20FUKAAXX100202:3:27:11237:128368, Mate Alignment start (9999703) must be <= reference sequence length (200) on reference 20 @@ -6221,16 +6259,17 @@ Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 +Finished 2800 tests Finished 3000 tests -Finished 3200 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2025-09-13 22:10:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2025-09-13 22:10:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:14:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:14:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 3200 tests Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -6284,7 +6323,9 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.10954210106564990080.tmp + +Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.16281696764593721309.tmp Finished 3400 tests Finished 3600 tests Finished 3800 tests @@ -6294,470 +6335,152 @@ Finished 4600 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-09-13 22:10:23 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-10-18 07:15:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-09-13 22:10:23 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-10-18 07:15:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 4800 tests Finished 5000 tests -Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2025-09-13 22:10:24 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec - -Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR - WARNING 2025-09-13 22:10:24 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec -Finished 5200 tests - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5238638a, [Ljava.lang.String;@4d5ac860) STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7ef75f73, [Ljava.lang.String;@2c897ae2) STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@142bb6f7) STANDARD_ERROR - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@1cb3d229) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@7a6518cd) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@58561b8e) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2e08e31a) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@255f03c6) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@16037712) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@72cbdb2e) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@578b2cba, [Ljava.lang.String;@4a960c1) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5acb70f2, [Ljava.lang.String;@2e06340e) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b9226a2, [Ljava.lang.String;@39118633) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a44790b, [Ljava.lang.String;@18fab48b) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44a40e07, [Ljava.lang.String;@6cd17e46) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@366022e7, [Ljava.lang.String;@233001e4) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@454a3cbf, [Ljava.lang.String;@5666bfd9) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@32294389, [Ljava.lang.String;@3061a019) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@276cc717, [Ljava.lang.String;@4513a313) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d1012be, [Ljava.lang.String;@1facb69f) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69c39c28, [Ljava.lang.String;@3ebc1534) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@676f4965, [Ljava.lang.String;@2afa036a) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d94a6e0, [Ljava.lang.String;@35697e06) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6856558c, [Ljava.lang.String;@5ea2f12b) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3439adb, [Ljava.lang.String;@6b8d1fcd) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33bc656, [Ljava.lang.String;@2abf9575) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a504880, [Ljava.lang.String;@26ae0264) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Finished 5200 tests -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:15:10 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR + WARNING 2026-10-18 07:15:11 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@78b17b96) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@2ade8903) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@3ecef42) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@3b3339f9) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6d32aa0e) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@2331595a, [Ljava.lang.String;@4af53f39) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15f26560, [Ljava.lang.String;@4d2d72f8) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3ddd122d, [Ljava.lang.String;@42e19521) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f2e1f9c, [Ljava.lang.String;@437d74f0) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33ae52b3, [Ljava.lang.String;@79ca946e) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@785064e0, [Ljava.lang.String;@2dcb8b41) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@11f83ef3, [Ljava.lang.String;@63201068) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77e417d0, [Ljava.lang.String;@7fab86fd) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b5a4f46, [Ljava.lang.String;@4d336687) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d367102, [Ljava.lang.String;@6213f913) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@132a0584, [Ljava.lang.String;@151b8475) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30c07d3d, [Ljava.lang.String;@428a54b3) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a2c21d0, [Ljava.lang.String;@38edac76) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4db76180, [Ljava.lang.String;@58247ac1) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6bc23dc, [Ljava.lang.String;@2b5827b9) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43e93a90, [Ljava.lang.String;@636ed6a8) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@461d06da, [Ljava.lang.String;@68990e09) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@21f5137b) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@4da34a80) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@7faf7c58) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@76aff666) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7df5f1b4) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@4ee7bdf6) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@6208d5a) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.13499262165486615683.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@b3117f8) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@50572d8f) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7ab446e9) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1b58d944) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@69f65307) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@69decd4a) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@750ca2f8) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@14b1293d) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@e2bb6d4) STANDARD_ERROR - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2672d88d) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR + WARNING 2026-10-18 07:15:11 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 5400 tests - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@341ac3e4, 5) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:10:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@225f5ba5, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@26663661], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767bfc7c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b9600b8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15eaea63, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cb4519c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@28a84d5d], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767bfc7c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b9600b8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15eaea63, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cb4519c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@28a84d5d], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767bfc7c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1b9600b8, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@15eaea63, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cb4519c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@28a84d5d], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:10:27 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 5600 tests +some stuff +Gradle suite > Gradle test > htsjdk.samtools.util.HtsgetRequestUnitTest.testPOSTjsonBody STANDARD_ERROR + SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". + SLF4J: Defaulting to no-operation (NOP) logger implementation + SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +Finished 5800 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file7664254458791433226.bad -Finished 5800 tests + Could not delete file file323090231213693529.bad +Finished 6000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 22 milliseconds - Queried for the same 100-length mapping 225272161 times in 10 seconds. + Time to construct a tree with 50000 nodes: 23 milliseconds + Queried for the same 100-length mapping 223574849 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6000 tests + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6200 tests +Finished 6400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) -Finished 6200 tests + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6400 tests + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -6915,13 +6638,13 @@ Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058 + .) STANDARD_OUT Diagnosing chrX:48774611-48775058 + . (len 448) chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 -Finished 6600 tests Finished 6800 tests +Finished 7000 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:10:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 7000 tests + INFO 2026-10-18 07:15:25 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 7200 tests +Finished 7400 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 @@ -6943,102 +6666,103 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - b d + b e c a -Finished 7400 tests +Finished 7600 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-10-18 07:16:00 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD VN:1.0 SO:FALSE ) STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-10-18 07:16:00 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-10-18 07:16:00 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-10-18 07:16:00 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD VN:1.0 SO:cOoRdinate ) STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-10-18 07:16:00 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2025-09-13 22:11:04 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2025-09-13 22:11:04 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-10-18 07:16:00 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-10-18 07:16:00 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null +Finished 7800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.3063904447446879545..cram - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2025-09-13 22:11:04 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.16381069649482255888..cram + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-10-18 07:16:01 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension2664216500084078880.cram + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension2461561875498056432.cram Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR - Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.11036973922736548474.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.10569988391763085696.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension10063872087162320650.cram - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2025-09-13 22:11:04 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension2676055135705856333.cram + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-10-18 07:16:01 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension8018564233859867213 + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension3863028772103591719 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension9804656738838932148.png + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension16277400366248568005.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://27e33ff1-49cf-4144-8362-d418c91c4c6d/work/testMakeWriterPathsam + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://e7fe66b3-dda5-448c-8377-f561981a8c78/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://445effdf-6a0b-49a5-a2ac-4c33120fa5f9/work/testMakeWriterPathbam + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8d6afecb-894d-4c9b-b423-0cbc9318682a/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://6ce1cac3-f64f-41f4-bbd0-dbf8ee7e0d05/work/testMakeWriterPathcram + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://1e0bd034-7dcf-44ef-8f2e-30d9129bd1e7/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d575f974-4050-45df-b62d-65a54713836c/work/testMakeWriterPathsam + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c76035f0-713f-4fc4-a516-144ae63cef2a/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://29113137-8b81-470b-b56c-f0e75b424077/work/testMakeWriterPathbam + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://fd926c99-85fe-43d3-9f9a-26a2bd273365/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR - INFO 2025-09-13 22:11:04 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://9db92ea0-6edc-4459-995d-290e17ec6760/work/testMakeWriterPathcram + INFO 2026-10-18 07:16:01 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://7c3dd691-4811-4b8d-b3a5-114e1567b825/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 -Finished 7600 tests -Finished 7800 tests +Finished 8000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2025-09-13 22:11:18 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-10-18 07:16:13 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. +Finished 8200 tests Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest STANDARD_ERROR ngs-java: DLL download was disabled @@ -7074,162 +6798,167 @@ Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReference[0](SRR2096940, CM000681.1, 95001, 95050, AGATGATTCAGTCTCACCAAGAACACTGAAAGTCACATGGCTACCAGCAT) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReferenceMt[0](SRR353866, [AAAB01001871.1:1-50 = TGACGCGCATGAATGGATTAACGAGATTCCCTCTGTCCCTATCTACTATC, AAAB01001871.1:901-950 = ACCAAGCGTACGATTGTTCACCCTTTCAAGGGAACGTGAGCTGGGTTTAG, AAAB01008987.1:1-50 = TTTTGGACGATGTTTTTGGTGAACAGAAAACGAGCTCAATCATCCAGAGC, AAAB01008859.1:1-50 = CAAAACGATGCCACAGATCAGAAGTTAATTAACGCACATTCTCCACCCAC]) SKIPPED -Finished 8000 tests Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2025-09-13 22:11:19 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2025-09-13 22:11:19 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2026-10-18 07:16:13 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2026-10-18 07:16:13 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2025-09-13 22:11:21 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2025-09-13 22:11:21 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2025-09-13 22:11:21 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2025-09-13 22:11:21 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-10-18 07:16:14 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-10-18 07:16:14 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-10-18 07:16:14 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-10-18 07:16:14 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2025-09-13 22:11:21 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-10-18 07:16:14 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2025-09-13 22:11:21 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... - INFO 2025-09-13 22:11:21 SamReaderFactoryTest Finished queries in 80ms + INFO 2026-10-18 07:16:15 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2026-10-18 07:16:15 SamReaderFactoryTest Finished queries in 59ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2025-09-13 22:11:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:16:15 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR - WARNING 2025-09-13 22:11:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:16:15 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR - WARNING 2025-09-13 22:11:21 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:16:15 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 8200 tests + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 8400 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2025-09-13 22:11:21 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-10-18 07:16:15 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - INFO 2025-09-13 22:11:21 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:11:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-10-18 07:16:15 ReferenceSource Default reference file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa exists, so going to use that. + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-09-13 22:11:21 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-10-18 07:16:15 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-10-18 07:16:15 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR - WARNING 2025-09-13 22:11:21 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-09-13 22:11:21 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. -Finished 8400 tests + WARNING 2026-10-18 07:16:15 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-10-18 07:16:15 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED +Finished 8600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED +Finished 8800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED -Finished 8600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:22 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:16:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR - WARNING 2025-09-13 22:11:22 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2025-09-13 22:11:22 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-10-18 07:16:15 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-10-18 07:16:15 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir @@ -7252,7 +6981,6 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir -Finished 8800 tests Finished 9000 tests Finished 9200 tests Finished 9400 tests @@ -7262,120 +6990,133 @@ Finished 10200 tests Finished 10400 tests Finished 10600 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[20](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:11:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 10800 tests - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[273](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[274](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[275](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[276](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[277](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[278](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[279](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[280](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[281](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[282](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[283](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[336](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[337](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[338](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[339](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[340](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[341](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[342](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[343](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[344](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[345](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[346](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:12:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 11000 tests Finished 11200 tests +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[344](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[345](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[346](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[347](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[348](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[349](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[350](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[351](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[352](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[353](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[354](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:16:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:16:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[469](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[470](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[471](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[472](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[473](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[474](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[475](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[476](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[477](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[478](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[479](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:17:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[481](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:17:27 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. +Finished 11400 tests +Finished 11600 tests + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR + WARNING 2026-10-18 07:17:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR + WARNING 2026-10-18 07:17:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR + WARNING 2026-10-18 07:17:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 11800 tests +Finished 12000 tests + Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.lambda$demonstrateTestWriteToPipeDoesNotHang_1$0(VariantContextWriterBuilderUnitTest.java:497) @@ -7395,14 +7136,9 @@ at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) -Finished 11400 tests -Finished 11600 tests -Finished 11800 tests -Finished 12000 tests Finished 12200 tests Finished 12400 tests Finished 12600 tests - Gradle is still running, please be patient... Finished 12800 tests Finished 13000 tests Finished 13200 tests @@ -7446,61 +7182,355 @@ Finished 20800 tests Finished 21000 tests Finished 21200 tests +Finished 21400 tests +Finished 21600 tests +Finished 21800 tests -Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2025-09-13 22:18:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream - -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@47c42861, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2025-09-13 22:18:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2025-09-13 22:18:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@55b0b918, [Ljava.lang.String;@7ba80ff2) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4560a6da, [Ljava.lang.String;@63f23ccc) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2025-09-13 22:18:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2025-09-13 22:18:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7adb31fa) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@e534b67) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@1a35aba4) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3711ffb8) STANDARD_ERROR + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7f2dddcb) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7b4f3572) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@24d4a0a2) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2ed29a40) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@8c09c3e, [Ljava.lang.String;@393fc47) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5a9913d, [Ljava.lang.String;@3146d241) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37f3352d, [Ljava.lang.String;@38fa4671) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c47b3dd, [Ljava.lang.String;@6e85029f) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@57f4d209, [Ljava.lang.String;@3b8eca9) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8a2ad16, [Ljava.lang.String;@2dd28d57) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6babb03b, [Ljava.lang.String;@67858acd) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@46f70263, [Ljava.lang.String;@606ec220) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c02385b, [Ljava.lang.String;@5f1ad63) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7a509fe6, [Ljava.lang.String;@49e7cb9a) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@275bb2b2, [Ljava.lang.String;@59c2e3b8) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17ca64a, [Ljava.lang.String;@439501dc) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@375be3c, [Ljava.lang.String;@1c25f146) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@48c13697, [Ljava.lang.String;@b3f95c8) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9c46616, [Ljava.lang.String;@143712fd) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62a482b9, [Ljava.lang.String;@73700805) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@e673d53, [Ljava.lang.String;@14552b20) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:18:49 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@4abde57c) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@415cd4bf) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 22000 tests -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2025-09-13 22:18:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:18:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Finished 21400 tests -Finished 21600 tests -some stuffFinished 21800 tests +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@6a3a8f17) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@61d03e25) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7ed7494f) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@40ff3593, [Ljava.lang.String;@45cc5cfa) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d34a8a8, [Ljava.lang.String;@33311ebe) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@75dad899, [Ljava.lang.String;@6b99f3ce) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1614919c, [Ljava.lang.String;@601c6fe5) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@426a4b7e, [Ljava.lang.String;@2291d19b) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@265b5eac, [Ljava.lang.String;@58ce8469) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@47441aad, [Ljava.lang.String;@587c89bd) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b2db7bd, [Ljava.lang.String;@700ea0e0) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2a182bd9, [Ljava.lang.String;@405d8654) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53969470, [Ljava.lang.String;@adda83d) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1be771f5, [Ljava.lang.String;@282b0c20) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1dbaa21e, [Ljava.lang.String;@5a00620a) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2858ecc2, [Ljava.lang.String;@3a3d2d08) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42dbbe46, [Ljava.lang.String;@6da09ee1) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@369ec663, [Ljava.lang.String;@5a78c252) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c6b1b0e, [Ljava.lang.String;@75593673) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@fcd4321, [Ljava.lang.String;@37528276) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@5985f151) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@1084d290) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@6577f074) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@44215670) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@490681a5) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@34197b29) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@1f95b00d) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.2807531466826141617.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5e384937) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4a4d276a) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7252d38b) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@896dc81) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1c950071) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@708c2e9a) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@effaa79) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@345572ce) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6a70cf6f) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6aedf128) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@f38f9f9, 5) STANDARD_ERROR + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:18:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@79ed3ce7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@23dc7abf], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:18:19 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED -Finished 22000 tests +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:18:19 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2025-09-13 22:18:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27a501a9, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4e15eb4b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2b799176, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75d1bf1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@153319ab], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:18:19 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2025-09-13 22:18:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27a501a9, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4e15eb4b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2b799176, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75d1bf1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@153319ab], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:18:19 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2025-09-13 22:18:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@27a501a9, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4e15eb4b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2b799176, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75d1bf1d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@153319ab], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:18:19 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 22200 tests Finished 22400 tests Finished 22600 tests @@ -7573,16 +7603,16 @@ Finished 36000 tests Gradle Test Executor 1 finished executing tests. Results: SUCCESS (35867 tests, 35832 successes, 0 failures, 35 skipped) -Finished generating test XML results (0.275 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.174 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.229 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 22 mins 2.235 secs. -:testWithOptimisticVCF4_4 (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +Finished generating test html results (0.212 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[#89,Task worker for ':',5,main]) completed. Took 15 mins 47.169 secs. +:testWithOptimisticVCF4_4 (Thread[#89,Task worker for ':',5,main]) started. :testWithOptimisticVCF4_4 Putting task artifact state for task ':testWithOptimisticVCF4_4' into context took 0.0 secs. -Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.03 secs. It is not up-to-date because: +Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.028 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath18353031131662035701txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' +Starting process 'Gradle Test Executor 2'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath2153024813107732470txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 2' Successfully started process 'Gradle Test Executor 2' Gradle Test Executor 2 started executing tests. Gradle Test Executor 2 finished executing tests. @@ -7590,13 +7620,13 @@ Finished generating test XML results (0.0 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithOptimisticVCF4_4 Generating HTML test report... Finished generating test html results (0.002 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithOptimisticVCF4_4 -:testWithOptimisticVCF4_4 (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 1.564 secs. -:test (Thread[#89,Task worker for ':' Thread 2,5,main]) started. +:testWithOptimisticVCF4_4 (Thread[#89,Task worker for ':',5,main]) completed. Took 1.312 secs. +:test (Thread[#89,Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.037 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.034 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath15418555335023883683txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' +Starting process 'Gradle Test Executor 3'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath11461387149882372541txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' Successfully started process 'Gradle Test Executor 3' Gradle Test Executor 3 started executing tests. @@ -7613,37 +7643,37 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms @@ -7667,7 +7697,7 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequence runtime: 1ms + testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms @@ -7682,25 +7712,25 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequenceExtended runtime: 0ms + testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 4ms + testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 2ms + testLastCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 1ms + testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 9ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testLastCompleteContigRead runtime: 9ms @@ -7724,34 +7754,34 @@ testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstOfChr1 runtime: 1ms + testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 6ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 8ms + testNextElementOfIterator runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 8ms + testNextElementOfIterator runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testNextElementOfIterator runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms @@ -7820,7 +7850,7 @@ testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadThroughEndOfContig runtime: 1ms + testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -7832,13 +7862,13 @@ testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 1ms + testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testReset runtime: 9ms @@ -7850,11 +7880,27 @@ testReset runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms +Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR + WARNING 2026-10-18 07:18:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@33a45bdd, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-10-18 07:18:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR + WARNING 2026-10-18 07:18:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 200 tests + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR + WARNING 2026-10-18 07:18:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR + WARNING 2026-10-18 07:18:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 Time so far: 0 @@ -8863,7 +8909,6 @@ Testing query chr21_random:4076206-6101050 ... Testing query chr20:5126731-9990106 ... Testing query chr4:3133535-3261569 ... -Finished 200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMFileReaderTest.testGetIndexTypeOK STANDARD_OUT chrM length= 16571 Aligned= 23 Unaligned= 0 @@ -8914,14 +8959,14 @@ NoCoordinateCount= 279 Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.11071587284964412262.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.14763157995056733319.bai - #BAMIndexWriterTest diff /tmp/javaBai.11071587284964412262.bai /tmp/cBai.14763157995056733319.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.17382073188060983514.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.1151351108655329170.bai + #BAMIndexWriterTest diff /tmp/javaBai.17382073188060983514.bai /tmp/cBai.1151351108655329170.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.4889458326475058541.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.5846940512446914549java.bai - #BAMIndexWriterTest diff /tmp/javaBai.5846940512446914549java.bai.txt /tmp/cBai.4889458326475058541.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.8262631253018917623.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.10355016905300394721java.bai + #BAMIndexWriterTest diff /tmp/javaBai.10355016905300394721java.bai.txt /tmp/cBai.8262631253018917623.bai.txt Finished 400 tests Finished 600 tests Finished 800 tests @@ -8933,33 +8978,21 @@ Finished 2000 tests Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 4ms to write + 738ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 2ms to write + 582ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT - Creating file /tmp/BCOST.15282474486059117761.gz + Creating file /tmp/BCOST.10542873978088160682.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.16366229193089772198.gz + Creating file /tmp/testCustomDeflater.16456547627381603931.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.9518887780595500917.gz - -Gradle suite > Gradle test > htsjdk.beta.io.bundle.BundleJSONTest.testAcceptSingleBundleJSONAsCollection[0]({ - "schema":{ - "schemaName":"htsbundle", - "schemaVersion":"0.1.0", - }, - "primary":"ALIGNED_READS", - "ALIGNED_READS":{"path":"file://myreads.bam","format":"BAM"} -}, ALIGNED_READS, [IOPathResource (file://myreads.bam): ALIGNED_READS/BAM]) STANDARD_ERROR - SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". - SLF4J: Defaulting to no-operation (NOP) logger implementation - SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. + Creating file /tmp/BCOST.4696451836639316702.gz Finished 2200 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testAllEncodingStrategyCombinations[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED @@ -8967,10 +9000,10 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[0](src/test/resources/htsjdk/samtools/cram/NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) STANDARD_ERROR - WARNING 2025-09-13 22:20:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:20:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:20:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:20:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:20:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:20:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:20:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:20:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[1](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10m-10m100.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, false, false) SKIPPED @@ -8979,18 +9012,18 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[3](src/test/resources/htsjdk/samtools/cram/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram, src/test/resources/htsjdk/samtools/reference/human_g1k_v37.20.21.fasta.gz, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) STANDARD_ERROR - WARNING 2025-09-13 22:21:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED @@ -9001,405 +9034,404 @@ Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[7](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest_3_containers_aligned_to_pos_1.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, true, false) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2025-09-13 22:21:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2025-09-13 22:21:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2025-09-13 22:21:37 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-09-13 22:21:37 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2025-09-13 22:21:37 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-09-13 22:21:37 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-10-18 07:21:49 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-10-18 07:21:49 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-10-18 07:21:49 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-10-18 07:21:49 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:21:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2025-09-13 22:21:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:21:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:21:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:21:54 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2025-09-13 22:21:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-09-13 22:21:42 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2025-09-13 22:21:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-09-13 22:21:42 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-10-18 07:21:54 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-10-18 07:21:54 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-10-18 07:21:54 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-10-18 07:21:54 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR - WARNING 2025-09-13 22:21:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:21:42 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2025-09-13 22:21:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:21:42 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. -Finished 2400 tests + WARNING 2026-10-18 07:21:54 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:21:54 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-10-18 07:21:54 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:21:54 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR - WARNING 2025-09-13 22:26:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:26:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:26:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:26:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 2400 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2025-09-13 22:26:09 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:26:09 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2025-09-13 22:26:09 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-09-13 22:26:09 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - Gradle is still running, please be patient... -Finished 2600 tests + WARNING 2026-10-18 07:26:40 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:26:40 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-10-18 07:26:40 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-10-18 07:26:40 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4a60b8a0, [Ljava.lang.String;@34ad0dcf) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@753c04d3, [Ljava.lang.String;@409ecbba) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@16ae0050, [Ljava.lang.String;@4c5628d1) STANDARD_ERROR + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@66e5d241, [Ljava.lang.String;@7188b6c7) STANDARD_ERROR + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@230d0db6, [Ljava.lang.String;@425bf102) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1ffb8e6f, [Ljava.lang.String;@311c83e0) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42d6c26b, [Ljava.lang.String;@66917075) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27ec4e09, [Ljava.lang.String;@78b3aded) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d582ae7, [Ljava.lang.String;@68a56f60) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5078bddd, [Ljava.lang.String;@239a7e78) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@764a3aa, [Ljava.lang.String;@4b3134ee) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7333019a, [Ljava.lang.String;@68cdab3) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@685aef40, [Ljava.lang.String;@7bdcd21d) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@46ef6aee, [Ljava.lang.String;@4d9b013d) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f9bc427, [Ljava.lang.String;@5af763c2) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4bbccd51, [Ljava.lang.String;@f83042a) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2459f0e5, [Ljava.lang.String;@7d84337a) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2d964e8a, [Ljava.lang.String;@4883db3) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5160331e, [Ljava.lang.String;@271f3bb) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4a032c11, [Ljava.lang.String;@5dbaa773) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72ce4a8c, [Ljava.lang.String;@6be466a) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@54bbf0c5) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@52e92ccb) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@7e9fbf8f) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5d5ab3ed) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@4b8c38b3) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@58e527d2) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@70d8238) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@13b8b8e2) STANDARD_ERROR - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@164de017, [Ljava.lang.String;@576ee3bd) STANDARD_ERROR + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5eb0c337, [Ljava.lang.String;@638811e2) STANDARD_ERROR + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c7996df, [Ljava.lang.String;@2531a12b) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@320cfda1, [Ljava.lang.String;@18cf638e) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35256631, [Ljava.lang.String;@48b54956) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@163e9c84, [Ljava.lang.String;@3b1d728) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@ab50a5e, [Ljava.lang.String;@225b4af) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21844294, [Ljava.lang.String;@380f3ceb) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f362440, [Ljava.lang.String;@7949d7ae) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@76a27468, [Ljava.lang.String;@3aaf77a9) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@959cb8b, [Ljava.lang.String;@72326cc) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6cf5b01f, [Ljava.lang.String;@2a5da57) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b80ab39, [Ljava.lang.String;@7ccd5a5d) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@394205ea, [Ljava.lang.String;@57e00e82) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bffdd00, [Ljava.lang.String;@ef531c7) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4481d9c9, [Ljava.lang.String;@64da3cb8) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@32357027, [Ljava.lang.String;@3795818d) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@344cce26) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@7e99a391) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@62cc811c) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7d089f97) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2fe48931) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 2600 tests + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@17c645c5) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@33f82695) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3503af73) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@6011e29b, [Ljava.lang.String;@20dbc13d) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@28a4d455, [Ljava.lang.String;@5c773af1) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5bcd19f5, [Ljava.lang.String;@3e60df08) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@ad46d47, [Ljava.lang.String;@7671983a) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39e01512, [Ljava.lang.String;@584ab297) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@551cc1c0, [Ljava.lang.String;@6d1d74e3) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33fb47a8, [Ljava.lang.String;@6182412b) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1a02de0d, [Ljava.lang.String;@226f2eba) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c7649b8, [Ljava.lang.String;@241ce1d6) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49b7c8f1, [Ljava.lang.String;@2aa68be5) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@22351426, [Ljava.lang.String;@270c28fe) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@51d53b73, [Ljava.lang.String;@1d158548) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68c2f235, [Ljava.lang.String;@4a22d1cb) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@c3cf49e, [Ljava.lang.String;@85dbab4) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@c53cf44, [Ljava.lang.String;@127c6cc1) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@304fbb4f, [Ljava.lang.String;@372e1136) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5f6b1817, [Ljava.lang.String;@5c7f9460) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@44e7de10) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@3cae399e) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@623b0ec3) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@b4771c2) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@721d4c6f) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@5744cb7) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@5ae57651) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@68abc5eb) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@5e65be96) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7ee8d0ec) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@634573f4) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@4f55284c) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@47e0b6c4) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@7073eb41) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4580776) STANDARD_ERROR - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@60c6d416) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@47454e40) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@469bf71a) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@77cf7221) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@134c065f) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@3e102a26) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@175e43c3) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@72d87e3b) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@30e5c510) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@3a06a150) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@75cc7eaf) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@58333a34) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7cd416fe) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@587895aa) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@37bd979e) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.5669798338431281524.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@41279ab1) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1e08fb80, 5) STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@6b3762cd, [Ljava.lang.String;@1de3c910) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@303c19ab, [Ljava.lang.String;@68be0c35) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@b0eb849, [Ljava.lang.String;@71007ed5) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45375f62, [Ljava.lang.String;@3648e2ff) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2ae421de, [Ljava.lang.String;@538fca53) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7af3b003, [Ljava.lang.String;@17ebe631) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2dd8eb31, [Ljava.lang.String;@19df79f2) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54763444, [Ljava.lang.String;@4ecc371f) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@64eaab2e, [Ljava.lang.String;@33842c17) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27256d27, [Ljava.lang.String;@8e2b1ce) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@218dde5a, [Ljava.lang.String;@38f56fd) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@15e10345, [Ljava.lang.String;@1f3a5eb1) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41b947ba, [Ljava.lang.String;@2cd1b643) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5da7fddc, [Ljava.lang.String;@3d8c9275) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@11eeaad, [Ljava.lang.String;@6933ba21) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@344e63bd, [Ljava.lang.String;@4cca9dc4) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62d7c0b5, [Ljava.lang.String;@22ea73ad) STANDARD_ERROR + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@3e7a9f05) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@f15078d) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@278698f7) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1f55f869) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSequence[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2a5424ce) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@2de28111) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@63238fdb) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@62f9ecf6) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@1a366ccb) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingSingleInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4b65594a) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1d77be27) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@216a9a5b) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@7c6a1ac9) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@441d243f) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5e98294a) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@cd93c3e) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@62e4b4a) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@298fd878) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1c27f463) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@7939fcbb) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@729a4de8) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@1c9b54fc) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2753ab39) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@1525a10) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@1327ad96) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@a64b2d0) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@df81452) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5c42f97c) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@1d1f33f7) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@26714f55) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.11801059961338635676.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@7831dc5) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@3bb04009, 5) STANDARD_ERROR + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 2800 tests + WARNING 2026-10-18 07:31:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:10 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2025-09-13 22:32:20 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-10-18 07:31:10 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be <= reference sequence length (200) on reference 20 @@ -10056,16 +10088,17 @@ Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 351, Read name 20GAVAAXX100126:8:6:11303:64367, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 +Finished 2800 tests Finished 3000 tests -Finished 3200 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2025-09-13 22:32:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2025-09-13 22:32:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:31:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:31:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Finished 3200 tests Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -10118,12 +10151,8 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir - -Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.spillToDiskTest STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.4132939994472620134.tmp - -Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.6126776387325240744.tmp Finished 3400 tests Finished 3600 tests Finished 3800 tests @@ -10133,470 +10162,152 @@ Finished 4600 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-09-13 22:32:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-10-18 07:31:31 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-09-13 22:32:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-10-18 07:31:31 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 4800 tests Finished 5000 tests -Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2025-09-13 22:32:36 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec - -Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR - WARNING 2025-09-13 22:32:36 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec -Finished 5200 tests - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@395646a4, [Ljava.lang.String;@6a0fc86c) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@549bc953, [Ljava.lang.String;@48ee803b) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@5188e235) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@40f5282a) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@6573655d) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@116826c5) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@23634f8e) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@74736909) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@3ed07bb9) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2b494c4e) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@e02d270, [Ljava.lang.String;@30146dd0) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e3c0104, [Ljava.lang.String;@3e3ce24d) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1c98d4dd, [Ljava.lang.String;@22be1c0c) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5dc573ed, [Ljava.lang.String;@7f4397ff) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@649d5d89, [Ljava.lang.String;@6bbcd973) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@31091bf3, [Ljava.lang.String;@177f9728) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@673716e6, [Ljava.lang.String;@79e9a20e) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@512fd260, [Ljava.lang.String;@62731d7) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@34e15a3c, [Ljava.lang.String;@6a8cc4b2) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21119c8a, [Ljava.lang.String;@16b455df) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53391703, [Ljava.lang.String;@53c8c971) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35cbce22, [Ljava.lang.String;@a18fe26) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@499fdb03, [Ljava.lang.String;@3f05c44f) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53e157d9, [Ljava.lang.String;@33775b03) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36d0fcd0, [Ljava.lang.String;@50791a12) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@114da359, [Ljava.lang.String;@538db8f) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7f7df4f1, [Ljava.lang.String;@7f3f9b14) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Finished 5200 tests -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-10-18 07:31:33 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR + WARNING 2026-10-18 07:31:33 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@65010ea8) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@6b341204) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@b226c97) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@875377a) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@24873a71) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@dfa5c9, [Ljava.lang.String;@393473ff) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5059b3f, [Ljava.lang.String;@6393f9d4) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2fe55a44, [Ljava.lang.String;@13bc1e7d) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6a6af4b0, [Ljava.lang.String;@5e042d83) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3214bdc8, [Ljava.lang.String;@10301f63) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@310cae9e, [Ljava.lang.String;@6b517d57) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@75e61671, [Ljava.lang.String;@6361a931) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1fc9e7ff, [Ljava.lang.String;@289a9e00) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5de757e0, [Ljava.lang.String;@195c304c) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5e143c81, [Ljava.lang.String;@2a3121c0) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39c9ef79, [Ljava.lang.String;@21bca541) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d685647, [Ljava.lang.String;@6d21f35) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7aa2211a, [Ljava.lang.String;@3e624f6f) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@52029c2, [Ljava.lang.String;@6dad5561) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3bfac208, [Ljava.lang.String;@4e958f4c) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6267f843, [Ljava.lang.String;@4609a9d4) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@328b2fd2, [Ljava.lang.String;@5b204576) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@fdeba3a) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@c1d8f8d) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@37f6df01) STANDARD_ERROR - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6fe3a7d1) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7de2acd7) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@5377d864) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@6037c48c) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.8720238236455740557.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4fdd5cdd) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@54c5fa02) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5a02f2fb) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@636c79c5) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@269d87b1) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@737ce5a3) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@4db5801f) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@27eedbb7) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@60903790) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@740d66f0) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombRiceIntegerEncodingTest.testToString STANDARD_ERROR + WARNING 2026-10-18 07:31:33 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 5400 tests - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@773ce7d4, 5) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:32:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7e6ed556, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@422a64f6], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4d8e8a48, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22232ed1, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1dfbf950, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22144316, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72ef9447], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4d8e8a48, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22232ed1, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1dfbf950, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22144316, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72ef9447], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) - -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4d8e8a48, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22232ed1, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1dfbf950, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@22144316, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@72ef9447], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-09-13 22:32:39 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 5600 tests +some stuff +Gradle suite > Gradle test > htsjdk.samtools.util.HtsgetRequestUnitTest.testPOSTjsonBody STANDARD_ERROR + SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". + SLF4J: Defaulting to no-operation (NOP) logger implementation + SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. +Finished 5800 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file11889269791624786191.bad -Finished 5800 tests + Could not delete file file4467788049327850888.bad +Finished 6000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 23 milliseconds - Queried for the same 100-length mapping 224816260 times in 10 seconds. + Time to construct a tree with 50000 nodes: 22 milliseconds + Queried for the same 100-length mapping 224977581 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6000 tests + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6200 tests +Finished 6400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) -Finished 6200 tests + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 6400 tests + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) +Finished 6600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[282](chr6:32071709-32071869 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[283](chr6:32072183-32072358 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[284](chr6:32104446-32104606 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[285](chr6:32104920-32105095 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[286](chr7:101995561-101995739 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[288](chr7:142179850-142180013 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[292](chr15:19335778-19336302 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[293](chr17:33364376-33364428 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[294](chr17:33546162-33546214 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[295](chr17:33706667-33706736 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[0](chr3:50911035-50911051 + .) STANDARD_OUT Diagnosing chr3:50911035-50911051 + . (len 17) @@ -10754,13 +10465,13 @@ Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testDiagnosticLiftover[36](chrX:48774611-48775058 + .) STANDARD_OUT Diagnosing chrX:48774611-48775058 + . (len 448) chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 -Finished 6600 tests Finished 6800 tests +Finished 7000 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-09-13 22:32:54 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) -Finished 7000 tests + INFO 2026-10-18 07:31:47 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 7200 tests +Finished 7400 tests Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 @@ -10787,249 +10498,256 @@ d e c -Finished 7400 tests +Finished 7600 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-10-18 07:32:15 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD VN:1.0 SO:FALSE ) STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-10-18 07:32:15 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-10-18 07:32:15 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-10-18 07:32:15 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD VN:1.0 SO:cOoRdinate ) STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-10-18 07:32:15 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2025-09-13 22:33:19 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2025-09-13 22:33:19 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-10-18 07:32:15 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-10-18 07:32:15 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null +Finished 7800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.8881742280781245005..cram - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.12257031751750547366..cram + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension6513892041873589968.cram + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension4472171222655937511.cram Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[0](sam) STANDARD_ERROR Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter[1](bam) STANDARD_ERROR - Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.3511833322132472258.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.18098205306303595062.bam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForCramExtensionNoReference STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension13771906889658887100.cram - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension15646240277007696219.cram + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension6195710019873291380 + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension17650847812938023838 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension1614911451568373567.png + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension10564952030285578354.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://cc7dbcdc-58c4-4e16-be5b-9bfeab51c15d/work/testMakeWriterPathsam + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://aee34a6f-1484-408c-bc4e-f7b6012e05f0/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[1](bam) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ab88ac61-6a5a-45fa-9a0b-fc7e0afa92d0/work/testMakeWriterPathbam + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d4c4b5c7-0f76-4529-83eb-86ce75f03c1d/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[2](cram) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://59e625e1-a40c-41d2-92a2-bbb8103b642b/work/testMakeWriterPathcram + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://faf8ad40-da81-4ca7-a756-0fe859b9a05a/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[0](sam) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://eefdf02e-75a4-487c-be0a-f9db35d70ed0/work/testMakeWriterPathsam + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://95920085-b95d-453b-8fa1-f1085778b691/work/testMakeWriterPathsam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathsam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[1](bam) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d2a628e4-8f19-44a2-9d65-3e692f2a17de/work/testMakeWriterPathbam + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://84c11337-5030-453a-91c4-c578b480e146/work/testMakeWriterPathbam Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPathAndReferencePath[2](cram) STANDARD_ERROR - INFO 2025-09-13 22:33:19 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://baf2ffdf-4f04-406f-a8b9-f5bdba96bfaf/work/testMakeWriterPathcram + INFO 2026-10-18 07:32:15 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://3833b518-136e-479e-817c-a2ed1b1b8754/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 -Finished 7600 tests -Finished 7800 tests + Gradle is still running, please be patient... +Finished 8000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2025-09-13 22:33:32 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-10-18 07:32:27 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. +Finished 8200 tests Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2025-09-13 22:33:32 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2025-09-13 22:33:32 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam -Finished 8000 tests + WARNING 2026-10-18 07:32:27 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2026-10-18 07:32:27 SamFiles The index file /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2025-09-13 22:33:33 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2025-09-13 22:33:33 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2025-09-13 22:33:33 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2025-09-13 22:33:33 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-10-18 07:32:28 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-10-18 07:32:28 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-10-18 07:32:28 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-10-18 07:32:28 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2025-09-13 22:33:33 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-10-18 07:32:28 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2025-09-13 22:33:33 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... - INFO 2025-09-13 22:33:33 SamReaderFactoryTest Finished queries in 53ms + INFO 2026-10-18 07:32:29 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2026-10-18 07:32:29 SamReaderFactoryTest Finished queries in 62ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2025-09-13 22:33:33 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:32:29 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromSeekableStream STANDARD_ERROR - WARNING 2025-09-13 22:33:33 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:32:29 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromURL STANDARD_ERROR - WARNING 2025-09-13 22:33:33 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-10-18 07:32:29 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[0](cram/test.cram, cram/auxf.fa, 0:12-13, Jim) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Finished 8200 tests + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 8400 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:33:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:32:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-09-13 22:33:34 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-10-18 07:32:29 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-10-18 07:32:29 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-09-13 22:33:34 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. -Finished 8400 tests + WARNING 2026-10-18 07:32:29 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-10-18 07:32:29 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED + +Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED +Finished 8600 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlockReadStreamTest.testSliceBlocksReadStreamsRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED +Finished 8800 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. -Finished 8600 tests + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[7]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], false, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:32:29 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.testValidateReferenceMD5Fails STANDARD_ERROR - WARNING 2025-09-13 22:33:34 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2025-09-13 22:33:34 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-10-18 07:32:29 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-10-18 07:32:29 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir @@ -11052,7 +10770,6 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir -Finished 8800 tests Finished 9000 tests Finished 9200 tests Finished 9400 tests @@ -11064,117 +10781,130 @@ Finished 10600 tests Finished 10800 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[225](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-09-13 22:34:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[244](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[245](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[246](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[247](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[248](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[249](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[250](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[251](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[252](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[253](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[254](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[82](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-10-18 07:33:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 11000 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[475](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[476](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[477](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[478](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[479](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[480](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[481](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[482](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[483](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[484](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[485](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-09-13 22:34:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[172](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[173](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[174](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[175](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[176](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[177](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[178](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[179](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[180](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[181](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[182](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[266](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[267](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[268](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[269](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[270](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[271](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[272](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[273](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[274](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[275](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[276](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:33:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 11200 tests +Finished 11400 tests +Finished 11600 tests + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR + WARNING 2026-10-18 07:34:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR + WARNING 2026-10-18 07:34:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + +Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR + WARNING 2026-10-18 07:34:03 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Finished 11800 tests +Finished 12000 tests Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops @@ -11195,10 +10925,6 @@ at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642) at java.base/java.lang.Thread.run(Thread.java:1583) -Finished 11400 tests -Finished 11600 tests -Finished 11800 tests -Finished 12000 tests Finished 12200 tests Finished 12400 tests Finished 12600 tests @@ -11244,62 +10970,356 @@ Finished 20600 tests Finished 20800 tests Finished 21000 tests +Finished 21200 tests +Finished 21400 tests +Finished 21600 tests +Finished 21800 tests -Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2025-09-13 22:35:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream - -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@503b2ce4, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2025-09-13 22:35:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2025-09-13 22:35:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[1](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d63f712, [Ljava.lang.String;@2fa3e148) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@10c29a01, [Ljava.lang.String;@6d53ad98) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2025-09-13 22:35:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2025-09-13 22:35:53 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Finished 21200 tests +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2928b955) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2b01d5c) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@99ba76e) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4029ef43) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2b243ae5) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2485afff) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@13554361) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@7de9d8af) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@3c8284c4, [Ljava.lang.String;@4fa6e78c) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@25824f1b, [Ljava.lang.String;@48e8af9c) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5e5d6939, [Ljava.lang.String;@20fb0820) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@bc969ce, [Ljava.lang.String;@2bd1de1c) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39f51d30, [Ljava.lang.String;@1b213634) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@74a3e172, [Ljava.lang.String;@2ebb1fdd) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1b9c3869, [Ljava.lang.String;@5b9a7b) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@60d5e7fc, [Ljava.lang.String;@5c161698) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e37d68a, [Ljava.lang.String;@2eaeaecf) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@681e12a, [Ljava.lang.String;@3668a00a) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@8012366, [Ljava.lang.String;@7f08fe4a) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3f8697e, [Ljava.lang.String;@1ae905bb) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79fb0192, [Ljava.lang.String;@2fdbe86f) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d234841, [Ljava.lang.String;@1cdf5e38) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2b1eee88, [Ljava.lang.String;@47841fa7) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5978a865, [Ljava.lang.String;@5e92958a) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@469ad53b, [Ljava.lang.String;@58c367c1) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@36c3ad13) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@159ccbb0) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@6331cc23) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@5c1063b4) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4a689a58) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@635779a1, [Ljava.lang.String;@69908628) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@d6f83a, [Ljava.lang.String;@3711ffb8) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Finished 22000 tests -Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-09-13 22:35:55 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 -Finished 21400 tests -Finished 21600 tests -some stuffFinished 21800 tests +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e4a78a, [Ljava.lang.String;@ee8ad71) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@35ed479e, [Ljava.lang.String;@17d494fe) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72ad5fe0, [Ljava.lang.String;@62969057) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@21d79a61, [Ljava.lang.String;@27ae8fcb) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@39e174be, [Ljava.lang.String;@8e7601b) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@10dd9dca, [Ljava.lang.String;@52365c8b) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@40529b0b, [Ljava.lang.String;@33dc0e27) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5fad7a86, [Ljava.lang.String;@5c5c3418) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@284d6b65, [Ljava.lang.String;@4108d55c) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d1b9d9, [Ljava.lang.String;@103f0e14) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@28738401, [Ljava.lang.String;@7e7a1bc8) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@152321ba, [Ljava.lang.String;@500416e7) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@33ae460d, [Ljava.lang.String;@2ed29a40) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@cf9c79a, [Ljava.lang.String;@5956308f) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5b5a1c1f, [Ljava.lang.String;@1c93436f) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6e83bd0) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@37f3352d) STANDARD_ERROR + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2230fca1) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6ff720fd) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4b9866fe) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@73700805) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@e673d53) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.8063734986078179549.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@51e57171) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@640f0095) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@29054498) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@68bb1e44) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@11a870a6) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@31669358) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@c81972e) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@fa6a4ba) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@4ecf49c7) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@26842354) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@65ddea32, 5) STANDARD_ERROR + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-10-18 07:36:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsIsAvailable SKIPPED +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1c68bca0, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@451922bb], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:36:29 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testSamtoolsVersion SKIPPED -Finished 22000 tests +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:36:29 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2025-09-13 22:36:00 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@580d3666, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1c6b1b0e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75593673, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5cffd090, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cc41670], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:36:29 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2025-09-13 22:36:00 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@580d3666, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1c6b1b0e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75593673, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5cffd090, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cc41670], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:36:29 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2025-09-13 22:36:00 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@580d3666, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1c6b1b0e, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75593673, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5cffd090, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3cc41670], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-10-18 07:36:29 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 22200 tests Finished 22400 tests Finished 22600 tests @@ -11372,12 +11392,12 @@ Finished 36000 tests Gradle Test Executor 3 finished executing tests. Results: SUCCESS (35850 tests, 35831 successes, 0 failures, 19 skipped) -Finished generating test XML results (0.105 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/test +Finished generating test XML results (0.083 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.125 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/test -:test (Thread[#89,Task worker for ':' Thread 2,5,main]) completed. Took 16 mins 57.134 secs. +Finished generating test html results (0.142 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/test +:test (Thread[#89,Task worker for ':',5,main]) completed. Took 18 mins 8.631 secs. -BUILD SUCCESSFUL in 39m 13s +BUILD SUCCESSFUL in 34m 9s 7 actionable tasks: 5 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' create-stamp debian/debhelper-build-stamp @@ -11391,8 +11411,8 @@ install -m0755 -d debian/libhtsjdk-java/usr/share/libhtsjdk-java cp --reflink=auto -a ./scripts/explain_sam_flags.py debian/libhtsjdk-java/usr/share/libhtsjdk-java/ jh_installjavadoc -O--buildsystem=gradle -Duplicate specification "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" Installing javadoc from build/docs/javadoc into package libhtsjdk-java-doc install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java cp -r build/docs/javadoc debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/ @@ -11406,10 +11426,10 @@ install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc-base/ install -p -m0644 debian/libhtsjdk-java-doc.doc-base.javadoc debian/libhtsjdk-java-doc/usr/share/doc-base/libhtsjdk-java-doc.libhtsjdk-java-doc dh_installchangelogs -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java - install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian install -m0755 -d debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc install -p -m0644 debian/.debhelper/generated/libhtsjdk-java-doc/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/changelog.Debian + install -m0755 -d debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java + install -p -m0644 debian/.debhelper/generated/libhtsjdk-java/dh_installchangelogs.dch.trimmed debian/libhtsjdk-java/usr/share/doc/libhtsjdk-java/changelog.Debian dh_installsystemduser -O--buildsystem=gradle dh_lintian -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java-doc/usr/share/lintian/overrides @@ -11480,10 +11500,10 @@ rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar dh_link -plibhtsjdk-java /usr/share/javahtsjdk.jar usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar - rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar - ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-4.1.3.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar + rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar + ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/4.1.3/htsjdk-4.1.3.jar install -m0755 -d debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian rm -f debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar ln -s ../../../../../../java/htsjdk.jar debian/libhtsjdk-java/usr/share/maven-repo/com/github/samtools/htsjdk/debian/htsjdk-debian.jar @@ -11491,1004 +11511,1004 @@ Using 1735551212 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar using File::StripNondeterminism::handlers::jar Using 1735551212 as canonical time - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NamedFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/IOUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsContentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsBundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InvertFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.Strategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/search.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFEncoderV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/DeflaterFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkUnsupportedOperationException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Log.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMEncoderV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/NamedFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IOUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/Upgradeable.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.SequenceListsDifferException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ListMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/InternalAPI.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/annotations/BetaAPI.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/AsyncWriterPool.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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+ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeIOException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFormatException.html using File::StripNondeterminism::handlers::javadoc - 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Insertion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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+ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html using 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamIndexes.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/LocusComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Iso8601Date.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequest.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetRequestField.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetClass.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetResponse.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java cd debian/libhtsjdk-java-doc @@ -12503,8 +12523,8 @@ find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -12533,8 +12553,8 @@ dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. -dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.3+dfsg-2_all.deb'. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_4.1.3+dfsg-2_all.deb'. +dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_4.1.3+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../htsjdk_4.1.3+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../htsjdk_4.1.3+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -12542,12 +12562,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/277090/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/277090/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/3929544 and its subdirectories -I: Current time: Sat Sep 13 22:36:18 -12 2025 -I: pbuilder-time-stamp: 1757846178 +I: removing directory /srv/workspace/pbuilder/277090 and its subdirectories +I: Current time: Sun Oct 18 07:36:50 +14 2026 +I: pbuilder-time-stamp: 1792258610