Diff of the two buildlogs: -- --- b1/build.log 2025-08-23 14:06:06.231861023 +0000 +++ b2/build.log 2025-08-23 14:45:11.158712683 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 23 01:32:39 -12 2025 -I: pbuilder-time-stamp: 1755955959 +I: Current time: Sat Sep 26 10:29:08 +14 2026 +I: pbuilder-time-stamp: 1790368148 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/70849/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/208588/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 25 20:29 /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/208588/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/208588/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='5852287ae5e34e9495ebdf9d547f8473' - 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='70849' - PS1='# ' - PS2='> ' + INVOCATION_ID=83dfa055d8e94ddaa6f514f659303676 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=208588 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.oFuNmtwG/pbuilderrc_8XP4 --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.oFuNmtwG/b1 --logfile b1/build.log htsjdk_4.1.3+dfsg-2.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFuNmtwG/pbuilderrc_I83u --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.oFuNmtwG/b2 --logfile b2/build.log htsjdk_4.1.3+dfsg-2.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/70849/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/208588/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -96,7 +128,7 @@ Depends: default-jdk, javahelper, gradle-debian-helper, maven-repo-helper, debhelper-compat (= 13), libjson-java, libcommons-jexl2-java, libcommons-logging-java, libjaxb-api-java, libjaxb-java, librhino-java, libsnappy-java, libcommons-compress-java, libngs-java, default-jdk-doc, junit4, libcommons-lang3-java, libjimfs-java, scala-library dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 20003 files and directories currently installed.) +(Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -559,10 +591,10 @@ Get: 402 http://deb.debian.org/debian forky/main arm64 libngs-jni arm64 3.2.1+dfsg-5 [27.8 kB] Get: 403 http://deb.debian.org/debian forky/main arm64 libngs-java arm64 3.2.1+dfsg-5 [114 kB] Get: 404 http://deb.debian.org/debian forky/main arm64 scala-library all 2.11.12-6 [9586 kB] -Fetched 341 MB in 1s (230 MB/s) +Fetched 341 MB in 5s (69.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20003 files and directories currently installed.) +(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 ... 19969 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_257.7-1_arm64.deb ... Unpacking libsystemd-shared:arm64 (257.7-1) ... Selecting previously unselected package libapparmor1:arm64. @@ -570,7 +602,7 @@ Unpacking libapparmor1:arm64 (4.1.0-1) ... Setting up libsystemd-shared:arm64 (257.7-1) ... Selecting previously unselected package systemd. -(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 ... 20016 files and directories currently installed.) +(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 ... 19982 files and directories currently installed.) Preparing to unpack .../systemd_257.7-1_arm64.deb ... Unpacking systemd (257.7-1) ... Setting up libapparmor1:arm64 (4.1.0-1) ... @@ -584,7 +616,7 @@ Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. -(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 ... 20954 files and directories currently installed.) +(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 ... 20920 files and directories currently installed.) Preparing to unpack .../00-systemd-sysv_257.7-1_arm64.deb ... Unpacking systemd-sysv (257.7-1) ... Selecting previously unselected package libdbus-1-3:arm64. @@ -624,7 +656,7 @@ Setting up libexpat1:arm64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.6-1) ... Selecting previously unselected package python3-minimal. -(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 ... 21404 files and directories currently installed.) +(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 ... 21370 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.5-1_arm64.deb ... Unpacking python3-minimal (3.13.5-1) ... Selecting previously unselected package media-types. @@ -660,7 +692,7 @@ Unpacking libpython3-stdlib:arm64 (3.13.5-1) ... Setting up python3-minimal (3.13.5-1) ... Selecting previously unselected package python3. -(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 ... 22419 files and directories currently installed.) +(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 ... 22385 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.5-1_arm64.deb ... Unpacking python3 (3.13.5-1) ... Selecting previously unselected package libproc2-0:arm64. @@ -1886,8 +1918,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Aug 23 13:33:23 UTC 2025. -Universal Time is now: Sat Aug 23 13:33:23 UTC 2025. +Local time is now: Fri Sep 25 20:30:41 UTC 2026. +Universal Time is now: Fri Sep 25 20:30:41 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2433,7 +2465,11 @@ 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/208588/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/208588/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 @@ -2449,7 +2485,7 @@ dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" Duplicate specification "u=s" for option "u" rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper @@ -2500,18 +2536,18 @@ To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.964 secs. -The client will now receive all logging from the daemon (pid: 88386). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-88386.out.log +An attempt to start the daemon took 1.953 secs. +The client will now receive all logging from the daemon (pid: 255566). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-255566.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@40e77406 -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@40e77406 -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@2289ed04 +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@2908a7cc +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@2908a7cc +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@4ffb2d87 Starting Build Compiling initialization script '/build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -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@1926353a +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@6ca5f276 Compiling initialization script '/build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/htsjdk-4.1.3+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2531,16 +2567,16 @@ 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@243dab87 +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@6b672383 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@2289ed04 -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@892ec61 -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1bfe2bb -:compileJava (Thread[#57,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@4ffb2d87 +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@5590e665 +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7f04bb3a +:compileJava (Thread[#55,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.007 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a413688 +Putting task artifact state for task ':compileJava' into context took 0.008 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@2a03811c 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 @@ -2575,7 +2611,7 @@ 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 1.83 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 3.762 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. @@ -2593,34 +2629,34 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileJava (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 9.612 secs. -:processResources (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 28.142 secs. +:processResources (Thread[#65,Task worker for ':' Thread 11,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.002 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[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.025 secs. -:classes (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[#65,Task worker for ':' Thread 11,5,main]) completed. Took 0.047 secs. +:classes (Thread[#36,Daemon worker,5,main]) started. :classes Skipping task ':classes' as it has no actions. -:classes (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[#36,Daemon worker,5,main]) completed. Took 0.0 secs. +:debianMavenPom (Thread[#55,Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.005 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[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.068 secs. -:jar (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[#55,Task worker for ':',5,main]) completed. Took 0.118 secs. +:jar (Thread[#64,Task worker for ':' Thread 10,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.024 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.05 secs. It is not up-to-date because: No history is available. -:jar (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 0.313 secs. -:javadoc (Thread[#57,Task worker for ':' Thread 2,5,main]) started. +:jar (Thread[#64,Task worker for ':' Thread 10,5,main]) completed. Took 0.723 secs. +:javadoc (Thread[#64,Task worker for ':' Thread 10,5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. -Up-to-date check for task ':javadoc' took 0.273 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 1.002 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc''. Working directory: /build/reproducible-path/htsjdk-4.1.3+dfsg Command: /usr/lib/jvm/java-21-openjdk-arm64/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-arm64/bin/javadoc'' @@ -2939,9 +2975,9 @@ * Features content type (see {@link htsjdk.beta.plugin.features} for related formats) ^ 100 warnings -:javadoc (Thread[#57,Task worker for ':' Thread 2,5,main]) completed. Took 10.897 secs. +:javadoc (Thread[#64,Task worker for ':' Thread 10,5,main]) completed. Took 31.316 secs. -BUILD SUCCESSFUL in 26s +BUILD SUCCESSFUL in 1m 12s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' jh_build -O--buildsystem=gradle @@ -2960,17 +2996,17 @@ 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-arm64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 0.818 secs. -The client will now receive all logging from the daemon (pid: 110576). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-110576.out.log +An attempt to start the daemon took 2.141 secs. +The client will now receive all logging from the daemon (pid: 285602). The daemon log file: /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/daemon/4.4.1/daemon-285602.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 12 worker leases. -Creating new cache for fileHashes, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@689ac8b2 -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@689ac8b2 -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@20daa3bd +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@29808ae4 +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@29808ae4 +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@36d85b6c 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@738c61fe +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@5a4c37e1 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'] @@ -2985,15 +3021,15 @@ 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@166c353b +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@4cd81cba 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@20daa3bd -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@45667561 -Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1373d29e -:compileJava (Thread[#57,Task worker for ':' Thread 3,5,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@36d85b6c +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@39ae05a1 +Creating new cache for outputFiles, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4774effe +:compileJava (Thread[#55,Task worker for ':',5,main]) started. :compileJava -Putting task artifact state for task ':compileJava' into context took 0.005 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/htsjdk-4.1.3+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@bd309c2 +Putting task artifact state for task ':compileJava' into context took 0.018 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@4b7e9f5e 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 @@ -3028,21 +3064,21 @@ 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 1.055 secs). +Skipping task ':compileJava' as it is up-to-date (took 2.605 secs). :compileJava UP-TO-DATE -:compileJava (Thread[#57,Task worker for ':' Thread 3,5,main]) completed. Took 1.089 secs. -:processResources (Thread[#57,Task worker for ':' Thread 3,5,main]) started. +:compileJava (Thread[#55,Task worker for ':',5,main]) completed. Took 2.695 secs. +:processResources (Thread[#55,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 0.008 secs). +Skipping task ':processResources' as it is up-to-date (took 0.012 secs). :processResources UP-TO-DATE -:processResources (Thread[#57,Task worker for ':' Thread 3,5,main]) completed. Took 0.024 secs. -:classes (Thread[#55,Task worker for ':',5,main]) started. +:processResources (Thread[#55,Task worker for ':',5,main]) completed. Took 0.019 secs. +:classes (Thread[#60,Task worker for ':' Thread 6,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[#55,Task worker for ':',5,main]) completed. Took 0.001 secs. -:compileTestJava (Thread[#55,Task worker for ':',5,main]) started. +:classes (Thread[#60,Task worker for ':' Thread 6,5,main]) completed. Took 0.0 secs. +:compileTestJava (Thread[#60,Task worker for ':' Thread 6,5,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. @@ -3595,7 +3631,7 @@ Passing through org.jsr-305:jsr305:jar:0.x Passing through com.google.errorprone:error_prone_annotations:jar:debian Passing through com.google.errorprone:error_prone_parent:jar:debian -Up-to-date check for task ':compileTestJava' took 1.329 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 3.93 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. @@ -3730,28 +3766,28 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 42 warnings -:compileTestJava (Thread[#55,Task worker for ':',5,main]) completed. Took 9.098 secs. -:processTestResources (Thread[#55,Task worker for ':',5,main]) started. +:compileTestJava (Thread[#60,Task worker for ':' Thread 6,5,main]) completed. Took 21.289 secs. +:processTestResources (Thread[#58,Task worker for ':' Thread 4,5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.479 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.857 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[#55,Task worker for ':',5,main]) completed. Took 1.189 secs. -:testClasses (Thread[#55,Task worker for ':',5,main]) started. +:processTestResources (Thread[#58,Task worker for ':' Thread 4,5,main]) completed. Took 2.344 secs. +:testClasses (Thread[#58,Task worker for ':' Thread 4,5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[#55,Task worker for ':',5,main]) completed. Took 0.0 secs. -:testWithDefaultReference (Thread[#56,Task worker for ':' Thread 2,5,main]) started. +:testClasses (Thread[#58,Task worker for ':' Thread 4,5,main]) completed. Took 0.0 secs. +:testWithDefaultReference (Thread[#58,Task worker for ':' Thread 4,5,main]) started. :testWithDefaultReference -Putting task artifact state for task ':testWithDefaultReference' into context took 0.005 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.207 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 0.488 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath6287401035967224834txt -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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.reference_fasta=src/test/resources/htsjdk/samtools/cram/ce.fa @/tmp/gradle-worker-classpath11778128680761840335txt -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 2025-08-23 01:34:31 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 2026-09-26 10:33:12 Defaults Found file for property samjdk.reference_fasta: /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/cram/ce.fa Finished 200 tests Finished 400 tests Finished 600 tests @@ -3763,128 +3799,128 @@ Finished 1800 tests Finished 2000 tests Finished 2200 tests -Finished 2400 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[311](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:35:33 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[329](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[330](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[331](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[332](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[333](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[334](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[335](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[336](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[337](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[338](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[339](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[431](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[432](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[433](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[434](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[435](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[436](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[437](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[438](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[439](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[440](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[441](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:35:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[128](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[129](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[130](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[131](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[132](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[133](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:32 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[134](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[135](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[136](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[137](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[138](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[191](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[192](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[193](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[194](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[195](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[196](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[197](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[198](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[199](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[200](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[201](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:33:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[211](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:33:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. +Finished 2400 tests Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2025-08-23 01:35:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:35:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2025-08-23 01:35:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:35:45 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 2025-08-23 01:35:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:35:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 3000 tests Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR @@ -3960,7 +3996,7 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[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 - testFirstCompleteContigRead runtime: 1ms + 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: 0ms @@ -3972,7 +4008,7 @@ 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: 1ms + testFirstCompleteContigRead runtime: 0ms 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: 0ms @@ -3981,7 +4017,7 @@ 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: 0ms + 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: 0ms @@ -3996,13 +4032,13 @@ 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: 0ms + testFirstElementOfIterator runtime: 1ms 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 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 + testFirstElementOfIterator runtime: 0ms 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 @@ -4041,31 +4077,31 @@ 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: 11ms + testLastCompleteContigRead runtime: 8ms 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: 7ms 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: 3ms + testLastCompleteContigRead runtime: 10ms 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: 3ms + testLastCompleteContigRead runtime: 1ms 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: 13ms + testLastCompleteContigRead runtime: 11ms 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: 16ms 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: 28ms 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: 3ms + testLastCompleteContigRead runtime: 9ms 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: 2ms + testLastCompleteContigRead runtime: 8ms 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 @@ -4080,34 +4116,34 @@ 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: 5ms 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: 4ms + 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: 3ms + testNextElementOfIterator runtime: 1ms 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: 2ms + testNextElementOfIterator runtime: 13ms 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: 0ms + 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: 7ms + testNextElementOfIterator runtime: 23ms 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: 7ms + testNextElementOfIterator runtime: 11ms 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: 6ms + testNextElementOfIterator runtime: 19ms 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 @@ -4143,7 +4179,7 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 1ms + testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms @@ -4152,7 +4188,7 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms @@ -4191,41 +4227,41 @@ 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 + testReset runtime: 2ms 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 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: 7ms + testReset runtime: 15ms 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: 7ms + testReset runtime: 21ms 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: 7ms + testReset runtime: 15ms 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: 3ms + testReset runtime: 5ms 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 Finished 13000 tests Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2025-08-23 01:36:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:37:05 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@1ed5527c, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2025-08-23 01:36:30 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@72423076, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-09-26 10:37:05 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 2025-08-23 01:36:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:37:05 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2025-08-23 01:36:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:37:05 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 2025-08-23 01:36:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:37:05 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 @@ -5286,14 +5322,14 @@ Finished 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.18298702157456129495.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.14797887176805067742.bai - #BAMIndexWriterTest diff /tmp/javaBai.18298702157456129495.bai /tmp/cBai.14797887176805067742.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.1603365713391817746.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.8075975178321284769.bai + #BAMIndexWriterTest diff /tmp/javaBai.1603365713391817746.bai /tmp/cBai.8075975178321284769.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.3181778928291176490.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.18272643075625189786java.bai - #BAMIndexWriterTest diff /tmp/javaBai.18272643075625189786java.bai.txt /tmp/cBai.3181778928291176490.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.9246393819012012423.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.10454350363641652707java.bai + #BAMIndexWriterTest diff /tmp/javaBai.10454350363641652707java.bai.txt /tmp/cBai.9246393819012012423.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 0ms to write @@ -5304,13 +5340,13 @@ 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.13456536513662052783.gz + Creating file /tmp/BCOST.719110810364482642.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.17598166169853181365.gz + Creating file /tmp/testCustomDeflater.16486444451372578111.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.5327849574666138857.gz + Creating file /tmp/BCOST.3856491862155132932.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.beta.io.bundle.BundleJSONTest.testAcceptSingleBundleJSONAsCollection[0]({ @@ -5330,10 +5366,10 @@ 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 2025-08-23 01:37:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:37:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:37:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:37:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:38:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:38:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:38:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:38:41 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 @@ -5342,18 +5378,18 @@ 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 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:12 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 @@ -5364,415 +5400,415 @@ 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 2025-08-23 01:38:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2025-08-23 01:38:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2025-08-23 01:38:47 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-08-23 01:38:47 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2025-08-23 01:38:47 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-08-23 01:38:47 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-09-26 10:40:21 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-09-26 10:40:21 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-09-26 10:40:21 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-09-26 10:40:21 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 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 13600 tests 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 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:38:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2025-08-23 01:38:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:38:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:40:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:40:25 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2025-08-23 01:38:51 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-08-23 01:38:51 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2025-08-23 01:38:51 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-08-23 01:38:51 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-09-26 10:40:25 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-09-26 10:40:25 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-09-26 10:40:25 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-09-26 10:40:25 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 2025-08-23 01:38:51 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:38:51 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2025-08-23 01:38:51 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:38:51 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-09-26 10:40:25 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:40:25 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-09-26 10:40:25 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:40:25 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 - INFO 2025-08-23 01:43:03 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 2025-08-23 01:43:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:43:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-09-26 10:44:17 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 2026-09-26 10:44:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:44:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2025-08-23 01:43:03 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:43:03 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2025-08-23 01:43:03 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:43:03 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... + WARNING 2026-09-26 10:44:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:44:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-09-26 10:44:17 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:44:17 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@7e45392e, [Ljava.lang.String;@57c47107) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4380c0a4, [Ljava.lang.String;@1bacb584) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@207fe362, [Ljava.lang.String;@7f1e4977) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1bac74b9, [Ljava.lang.String;@1ff264ea) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@69e863ff, [Ljava.lang.String;@18a3b5b9) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 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;@52fa3263, [Ljava.lang.String;@5446a993) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6729b344, [Ljava.lang.String;@673e4807) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@44776b39, [Ljava.lang.String;@56a7e68f) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@e6c0284, [Ljava.lang.String;@2da3b26e) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@78034657, [Ljava.lang.String;@822e707) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@26bb4add, [Ljava.lang.String;@4a6dbc56) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@4bd9fe20, [Ljava.lang.String;@63ab036f) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@757ff921, [Ljava.lang.String;@1bdf27eb) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@38fde186, [Ljava.lang.String;@28d2abbe) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29337cf6, [Ljava.lang.String;@54bd2f9) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@7146b78a, [Ljava.lang.String;@3ae543b4) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1439023a, [Ljava.lang.String;@2a32a68a) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@75613a7, [Ljava.lang.String;@20cc4862) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78a45df2, [Ljava.lang.String;@2b4c8a67) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@5809b469, [Ljava.lang.String;@4137ea0d) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2e7a59de, [Ljava.lang.String;@526bd784) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:29 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;@3c823e10) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 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;@7f550f0b) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@6dfacbfa) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@30709ad0) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@22fa1271) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@26cd6) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@37fc5806) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@581df23e) STANDARD_ERROR - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:29 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@7e4a2f07, [Ljava.lang.String;@290cc83a) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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;@7c8874d5, [Ljava.lang.String;@1bb972fd) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@d19ecee, [Ljava.lang.String;@fac593f) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@4f3488ab, [Ljava.lang.String;@d590e39) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4049c6ae, [Ljava.lang.String;@5195d485) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@759c8714, [Ljava.lang.String;@4bc6dc14) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2a8aa6f6, [Ljava.lang.String;@10738bc2) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@19ca5d58, [Ljava.lang.String;@55c9f91b) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@209363d5, [Ljava.lang.String;@68815412) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@61d553ad, [Ljava.lang.String;@748fe1f0) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@29eea4d3, [Ljava.lang.String;@5955d246) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@18c30772, [Ljava.lang.String;@367af9e0) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@71b74566, [Ljava.lang.String;@32341bce) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@21a06ec, [Ljava.lang.String;@6929a5a0) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3bcf0645, [Ljava.lang.String;@47a3ccf) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@7953ebff, [Ljava.lang.String;@29239b45) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1ad944df, [Ljava.lang.String;@3622a03a) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:19 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;@1f93b37) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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;@4ceaff94) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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;@57b5060) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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;@46ec9e3c) STANDARD_ERROR + WARNING 2026-09-26 10:52:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:19 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;@26ccebd0) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@27d395e9) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@508cb3b6) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@358de1cf) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@37f3c441, [Ljava.lang.String;@147bc021) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@2a15749b, [Ljava.lang.String;@23247123) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@fab11a9, [Ljava.lang.String;@296c5a6b) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@280fcf1d, [Ljava.lang.String;@6ac69436) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c4bd224, [Ljava.lang.String;@172868ab) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@4b896957, [Ljava.lang.String;@32491f23) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@10b73692, [Ljava.lang.String;@26bb3701) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@730510f0, [Ljava.lang.String;@24e78473) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6841ef3e, [Ljava.lang.String;@76bb5a61) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@2a27cf92, [Ljava.lang.String;@7ec1b92d) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1935bf24, [Ljava.lang.String;@5e6f4c90) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@9963cc2, [Ljava.lang.String;@74c38a44) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30c31636, [Ljava.lang.String;@468c17c4) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@64a3ebfe, [Ljava.lang.String;@6c4bd098) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@18a2b490, [Ljava.lang.String;@3d4a24cc) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@780655a0, [Ljava.lang.String;@2dbee20c) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1176692b, [Ljava.lang.String;@82ad9b8) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:30 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;@26b29870) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@2cf32971) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@6abc20e) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@7be5fec5) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@2e81dae9) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@6f776198) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@2b34fbad) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@4bbed557) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@3920a3c2) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@1b0a4e11) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 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;@3ab8af8) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@54e45ea7) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@7a9a2ee5) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@3c6712ea) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedFalse[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@150b2604) STANDARD_ERROR - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySequenceContainedTrue[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@658101a0) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@2b57d28) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@6bee2cae) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@3ac206c8) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@2cb8a882) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@4c2f526f) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@36b146bb) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@46b582f8, [Ljava.lang.String;@40ffd224) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@4ec62872, [Ljava.lang.String;@688bb5d7) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5e4bec1, [Ljava.lang.String;@77b92aa0) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@11da7b41, [Ljava.lang.String;@63a30d2d) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c11f933, [Ljava.lang.String;@1755d2d) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@2416268, [Ljava.lang.String;@78d9441a) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7358c403, [Ljava.lang.String;@38c57856) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@3b791ee3, [Ljava.lang.String;@ab52e6d) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@54d064a8, [Ljava.lang.String;@ee4a4c7) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@6071b64c, [Ljava.lang.String;@7c05d7a1) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7cf086a1, [Ljava.lang.String;@2ee46a63) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@28ae3348, [Ljava.lang.String;@21bcc650) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6609ed74, [Ljava.lang.String;@9bb4322) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@8b2f692, [Ljava.lang.String;@4edffa5e) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41646f48, [Ljava.lang.String;@5739cffb) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@f176ff0, [Ljava.lang.String;@14feeed8) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@37a8423, [Ljava.lang.String;@3b0bb9a9) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:20 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;@60dbe4a8) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@3268addf) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@5126dfa7) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@2fe7b1fe) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@5f1264ff) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@55269a85) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@6e9b42c5) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@17fc4308) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@63be801e) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@7824eb7d) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@6f38f140) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@461b1f17) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@61f54c32) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@38cecb4a) STANDARD_ERROR + WARNING 2026-09-26 10:52:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:20 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;@e789d0) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@684a4a70) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@28b4c688) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@3b8f47ab) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@66d9d962) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@37f1afc4) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@7465a32e) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@1b5867f6) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests -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;@13b55335) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@29f204db) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@651b301a) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@1fc8b36c) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@1e7a215) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@54c7a4f2) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@1949125e) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@79c1096e) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.15080168145239693374.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5230eba) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:31 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;@38235322, 5) STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:31 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;@449d6eb) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@6e22cda) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@405ce4c6) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@c24baee) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@7531813c) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@6f517567) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@2983af4a) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 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;@6dd70b0e) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.11212771703380453705.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3fff10e5) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:21 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;@44b1777d, 5) STANDARD_ERROR + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2025-08-23 01:48:32 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-09-26 10:52:22 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 2025-08-23 01:48:32 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 2026-09-26 10:52:22 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 2025-08-23 01:48:32 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 2026-09-26 10:52:22 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 2025-08-23 01:48:32 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 2026-09-26 10:52:22 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 @@ -6431,12 +6467,12 @@ Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2025-08-23 01:48:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:23 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:23 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2025-08-23 01:48:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:23 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:23 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -6490,10 +6526,8 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.3131551145604460585.tmp Resetting tmpdir - -Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.15978064866899345474.tmp Finished 14800 tests Finished 15000 tests Finished 15200 tests @@ -6502,492 +6536,493 @@ Finished 15800 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-08-23 01:48:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:52:39 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 2025-08-23 01:48:49 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:52:39 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + Gradle is still running, please be patient... Finished 16000 tests Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 01:48:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 01:48:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 01:48:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-08-23 01:48:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 01:48:50 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 01:48:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 01:48:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 10:52:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2025-08-23 01:48:51 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-09-26 10:52:40 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 2025-08-23 01:48:51 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-09-26 10:52:40 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@9cc9673, [Ljava.lang.String;@78e8e39b) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44d4e135, [Ljava.lang.String;@7e7c7d39) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 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;@7623dcee, [Ljava.lang.String;@23386ad4) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2cac69a9, [Ljava.lang.String;@3c2a9e97) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@7ce959e5) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@650ae774) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@7f304d7d) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@3bc22c8e) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@3a758e19) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@5e76577d) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@20a912a7) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@615d37ec) STANDARD_ERROR - WARNING 2025-08-23 01:48:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:51 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;@2100de79, [Ljava.lang.String;@3f14e13a) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@78c4df9, [Ljava.lang.String;@79224644) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e3912ea, [Ljava.lang.String;@1729bcb8) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@582a8243, [Ljava.lang.String;@7e127a34) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@219674a3, [Ljava.lang.String;@21dbe788) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@77eda09c, [Ljava.lang.String;@489b0fe1) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d94e2f, [Ljava.lang.String;@65babab6) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@74a812e, [Ljava.lang.String;@723c05b6) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4348239c, [Ljava.lang.String;@2eb14349) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27263409, [Ljava.lang.String;@554001a8) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fd4fdb9, [Ljava.lang.String;@120e69ba) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4fc8270c, [Ljava.lang.String;@38db6802) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f338ff3, [Ljava.lang.String;@23e4b588) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17fa25db, [Ljava.lang.String;@5a9a1319) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70062ccd, [Ljava.lang.String;@6aafe1a3) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@573ad076, [Ljava.lang.String;@45d2f004) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@403f1e5, [Ljava.lang.String;@79872950) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@51cf1f61) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@efde9e6) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@7100fafa) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@1faf8f8) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@6de48dc) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@56e8c049) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@420ed9be) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@34305580) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@31a9c32e, [Ljava.lang.String;@47beaef6) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 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;@2ea3e614, [Ljava.lang.String;@5f9fc67b) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@757b069d, [Ljava.lang.String;@67a7a1f9) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@f3fd3b9, [Ljava.lang.String;@54c3bf2b) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1214ba68, [Ljava.lang.String;@17bc0947) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@557da1df, [Ljava.lang.String;@49f5f849) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b304ad5, [Ljava.lang.String;@6f437f5b) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@326c4694, [Ljava.lang.String;@75d04099) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@456cb99d, [Ljava.lang.String;@7fade475) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@34ed8b6a, [Ljava.lang.String;@1610fb2d) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@61e8e1a5, [Ljava.lang.String;@32419cc6) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@7cf0aba9, [Ljava.lang.String;@368ba068) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7594ecc2, [Ljava.lang.String;@411d841e) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@733e96bb, [Ljava.lang.String;@765b41ad) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d65584f, [Ljava.lang.String;@619392c7) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 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;@6ca57dc7, [Ljava.lang.String;@5b4395e3) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@720248f3, [Ljava.lang.String;@62e7ed58) STANDARD_ERROR + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:52 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6fb62aa1) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@60eabb50) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@5a2d7823) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@6cd687d8) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@4f0a8bf7) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@ef96b24, [Ljava.lang.String;@5e9b7a1) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@350fe56a, [Ljava.lang.String;@7fc7c9d8) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@431dfcc1, [Ljava.lang.String;@421ff8e8) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d9fe082, [Ljava.lang.String;@2cd6ef14) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5a458b29, [Ljava.lang.String;@57801d5f) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@615b228, [Ljava.lang.String;@5b155d31) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c5584a5, [Ljava.lang.String;@11cae001) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7065900b, [Ljava.lang.String;@130730f9) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d723fd9, [Ljava.lang.String;@34787d6c) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72ea934c, [Ljava.lang.String;@8759f60) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@16fd8131, [Ljava.lang.String;@5550b7ec) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 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;@6dfc9049, [Ljava.lang.String;@484e9106) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6769196d, [Ljava.lang.String;@19ad429f) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@36f5aff1, [Ljava.lang.String;@3f43a9) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@509ca3d2, [Ljava.lang.String;@1d178a39) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ae838cc, [Ljava.lang.String;@24f4a965) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17df1db6, [Ljava.lang.String;@536c020d) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@543af74d) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@37419958) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@2fa2289f) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@48ae7f58) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@52866e59) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@18d08761) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@44b3a846) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.5182817552158285482.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@5194f5f9) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 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;@44a3f97b) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@14dfb242) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@df18842) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@336bff39) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@52f65fb0) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@dad9665) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@20dc2cd2) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@3498f694) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@ea93d18) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:42 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;@416ceb73) STANDARD_ERROR + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 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;@61576130) STANDARD_ERROR + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 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;@2607bac4) STANDARD_ERROR + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 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;@1a0b2a1b) STANDARD_ERROR + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 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;@1d9843ea) STANDARD_ERROR + WARNING 2026-09-26 10:52:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:42 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;@16898ccd, [Ljava.lang.String;@7d9b8bdb) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@394e510, [Ljava.lang.String;@3acf9451) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d5fa948, [Ljava.lang.String;@46bf7c11) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@5514647d, [Ljava.lang.String;@66e002f) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7b8b9b03, [Ljava.lang.String;@2f0d6d01) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@7a8967cc, [Ljava.lang.String;@63c2806f) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a605734, [Ljava.lang.String;@1a3efed4) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@2bc86e74, [Ljava.lang.String;@5cc5ad7f) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b577637, [Ljava.lang.String;@386fcbc5) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@55060f61, [Ljava.lang.String;@1a9ca588) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@732b5a9a, [Ljava.lang.String;@12e15cfe) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@275f6dd3, [Ljava.lang.String;@ea66a36) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1a68a42f, [Ljava.lang.String;@4267c321) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@68fdb866, [Ljava.lang.String;@145acd50) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@76066503, [Ljava.lang.String;@12396d0b) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@1a9929a4, [Ljava.lang.String;@53649479) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7aec1240, [Ljava.lang.String;@45387de9) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@1e2f8d7e) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@55236c2f) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@4459c788) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@2f525e95) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@229a104b) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@71ee6596) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@6e91890b) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.10740415324994001851.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@89ac8da) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 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;@3fa6e5bb) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@5a88898f) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@171256d2) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@361aabcc) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@4b20ca4c) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@b9cc13d) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@63a3f680) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@212241a3) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@4598aa35) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 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;@75764ec7, 5) STANDARD_ERROR - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:48:53 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 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;@66062180, 5) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:52:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 16400 tests -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6985c4b0, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6d4b12f2], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 01:48:54 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6ac83292, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@75660f51], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 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 2025-08-23 01:48:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2026-09-26 10:52:43 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@11412401, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71ce6d2d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767694b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@797ca1b7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@471426ff], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 01:48:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@35925bcb, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71a50f45, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c493c11, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@489d43a0, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@63401756], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 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@11412401, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71ce6d2d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767694b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@797ca1b7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@471426ff], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 01:48:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@35925bcb, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71a50f45, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c493c11, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@489d43a0, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@63401756], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 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@11412401, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71ce6d2d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@767694b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@797ca1b7, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@471426ff], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 01:48:54 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Finished 16600 tests -some stuffFinished 16800 tests +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@35925bcb, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@71a50f45, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@6c493c11, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@489d43a0, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@63401756], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 10:52:43 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) +some stuffFinished 16600 tests +Finished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file4761034672551425199.bad + Could not delete file file16298741275781555626.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 34 milliseconds - Queried for the same 100-length mapping 207169418 times in 10 seconds. + Time to construct a tree with 50000 nodes: 20 milliseconds + Queried for the same 100-length mapping 206651868 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[280](chr3:14174511-14175398 + ., null) STANDARD_ERROR - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 10:52:57 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 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-09-26 10:52:57 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) @@ -7149,7 +7184,7 @@ Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-08-23 01:49:07 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 10:52:57 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Finished 18600 tests @@ -7173,102 +7208,102 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - d b - a + d e c + a Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2025-08-23 01:49:44 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-09-26 10:53:28 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 2025-08-23 01:49:44 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-09-26 10:53:28 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2025-08-23 01:49:44 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-09-26 10:53:28 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 2025-08-23 01:49:44 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-09-26 10:53:28 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 2025-08-23 01:49:44 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-09-26 10:53:28 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2025-08-23 01:49:44 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2025-08-23 01:49:44 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-09-26 10:53:28 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-09-26 10:53:28 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.4883601228013950079..cram - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2025-08-23 01:49:44 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 2026-09-26 10:53:28 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.8950240149461231452..cram + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-09-26 10:53:28 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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension17316847740161977760.cram + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension6937191875339900382.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.8496020767211079144.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.30003891829025258.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 2025-08-23 01:49:44 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension11387116532039193392.cram - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false - INFO 2025-08-23 01:49:44 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 2026-09-26 10:53:28 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension12842485505240327549.cram + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): src/test/resources/htsjdk/samtools/cram/ce.fa + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-09-26 10:53:28 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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension8009580785112270701 + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension6236847950154485892 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension17277486762358875232.png + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension11015834631799324877.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://65119d9d-e063-4c57-b70f-eb155aaa69a9/work/testMakeWriterPathsam + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://43114697-2381-4375-b975-1f0b7bb623c9/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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://cecf67f6-ac8e-4321-bf60-83ae47f6041c/work/testMakeWriterPathbam + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d62dee1f-60f1-4a5d-bc83-ec8265f6da14/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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://673a0cab-58bb-4939-b1a2-12beadff91cc/work/testMakeWriterPathcram + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://792911be-bf95-4334-8b0e-e8c03fe2d92d/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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ca205e8b-b1be-40fb-b101-3f129c1b2802/work/testMakeWriterPathsam + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://db43c5b9-f180-459f-989c-3e3390d5717f/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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://664531bf-2f3d-46c8-8ea5-c46c838e8f8f/work/testMakeWriterPathbam + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8bd118da-44aa-4660-8010-61755b0ff4b8/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 2025-08-23 01:49:44 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://b16e9d20-2ccf-4ea1-a46b-bf0c12c111c2/work/testMakeWriterPathcram + INFO 2026-09-26 10:53:28 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ebe2ab45-d07f-4b0f-b34d-cafbb2cb5891/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Finished 19200 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2025-08-23 01:49:56 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-09-26 10:53:40 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Finished 19400 tests Gradle suite > Gradle test > htsjdk.samtools.sra.SRAAccessionTest STANDARD_ERROR @@ -7307,103 +7342,103 @@ Gradle suite > Gradle test > htsjdk.samtools.sra.SRAReferenceTest.testReferenceMt[0](SRR353866, [AAAB01001871.1:1-50 = TGACGCGCATGAATGGATTAACGAGATTCCCTCTGTCCCTATCTACTATC, AAAB01001871.1:901-950 = ACCAAGCGTACGATTGTTCACCCTTTCAAGGGAACGTGAGCTGGGTTTAG, AAAB01008987.1:1-50 = TTTTGGACGATGTTTTTGGTGAACAGAAAACGAGCTCAATCATCCAGAGC, AAAB01008859.1:1-50 = CAAAACGATGCCACAGATCAGAAGTTAATTAACGCACATTCTCCACCCAC]) SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2025-08-23 01:49:56 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 2025-08-23 01:49:56 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 2026-09-26 10:53:41 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 2026-09-26 10:53:41 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 2025-08-23 01:49:57 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2025-08-23 01:49:57 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2025-08-23 01:49:57 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2025-08-23 01:49:57 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-09-26 10:53:42 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-09-26 10:53:42 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-09-26 10:53:42 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-09-26 10:53:42 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 2025-08-23 01:49:57 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-09-26 10:53:42 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 2025-08-23 01:49:57 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 2025-08-23 01:49:58 SamReaderFactoryTest Finished queries in 66ms + INFO 2026-09-26 10:53:42 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 2026-09-26 10:53:42 SamReaderFactoryTest Finished queries in 51ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2025-08-23 01:49:58 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-09-26 10:53:42 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 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 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 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:49:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + INFO 2026-09-26 10:53:42 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 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:53:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2025-08-23 01:49:58 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-08-23 01:49:58 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-09-26 10:53:42 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-09-26 10:53:42 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 2025-08-23 01:49:58 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-08-23 01:49:58 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-09-26 10:53:42 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-09-26 10:53:42 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -7418,54 +7453,54 @@ Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 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 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 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 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:49:58 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:53:43 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 2025-08-23 01:49:58 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2025-08-23 01:49:58 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-09-26 10:53:43 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-09-26 10:53:43 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 @@ -7570,30 +7605,30 @@ 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 (0.245 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.228 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.251 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 15 mins 32.569 secs. -:testWithOptimisticVCF4_4 (Thread[#56,Task worker for ':' Thread 2,5,main]) started. +Finished generating test html results (0.332 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[#58,Task worker for ':' Thread 4,5,main]) completed. Took 20 mins 37.958 secs. +:testWithOptimisticVCF4_4 (Thread[#58,Task worker for ':' Thread 4,5,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 0.042 secs. It is not up-to-date because: +Up-to-date check for task ':testWithOptimisticVCF4_4' took 0.044 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath9651087182075283082txt -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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false -Dsamjdk.optimistic_vcf_4_4=true @/tmp/gradle-worker-classpath15844901441901410918txt -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. Results: SUCCESS (0 tests, 0 successes, 0 failures, 0 skipped) Finished generating test XML results (0.0 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/testWithOptimisticVCF4_4 Generating HTML test report... -Finished generating test html results (0.001 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/testWithOptimisticVCF4_4 -:testWithOptimisticVCF4_4 (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 1.441 secs. -:test (Thread[#56,Task worker for ':' Thread 2,5,main]) started. +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[#58,Task worker for ':' Thread 4,5,main]) completed. Took 1.552 secs. +:test (Thread[#58,Task worker for ':' Thread 4,5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.051 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.069 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath18025458392805690358txt -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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath17728525011803504984txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 3' Successfully started process 'Gradle Test Executor 3' Gradle Test Executor 3 started executing tests. Finished 200 tests @@ -7607,128 +7642,128 @@ Finished 1800 tests Finished 2000 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[46](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[47](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[48](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[49](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[50](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[51](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[52](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[53](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[54](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[55](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[56](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[74](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[75](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[76](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[77](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[78](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[79](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[80](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[81](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[82](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[83](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[84](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2200 tests -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[94](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[95](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[96](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[97](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[98](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[99](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[100](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[101](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[102](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[103](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[104](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:50:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[106](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 01:50:12 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[232](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[233](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[234](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[235](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[236](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[237](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[238](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[239](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[240](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[241](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[242](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:54:00 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 2400 tests + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[337](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 10:54:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Finished 2600 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2025-08-23 01:51:43 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 2800 tests Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2025-08-23 01:51:43 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2025-08-23 01:51:43 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:07 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 3000 tests Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR @@ -7813,40 +7848,40 @@ 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 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: 0ms + testFirstCompleteContigRead runtime: 1ms 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: 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: 0ms + 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: 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: 1ms + 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 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 + testFirstElementOfIterator runtime: 1ms 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: 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 + testFirstElementOfIterator runtime: 0ms 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 @@ -7885,31 +7920,31 @@ testFirstSequenceExtended runtime: 0ms 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: 5ms + testLastCompleteContigRead runtime: 4ms 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: 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: 2ms + testLastCompleteContigRead runtime: 1ms 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: 11ms + testLastCompleteContigRead runtime: 10ms 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: 7ms 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: 4ms + 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: 5ms + testLastCompleteContigRead runtime: 3ms 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 @@ -7939,19 +7974,19 @@ 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: 6ms + testNextElementOfIterator runtime: 7ms 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: 6ms + testNextElementOfIterator runtime: 7ms 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: 6ms + testNextElementOfIterator runtime: 7ms 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 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 @@ -7984,7 +8019,7 @@ testReadPastEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[0](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[1](/build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms @@ -8029,16 +8064,16 @@ testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[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 - testReset runtime: 0ms + testReset runtime: 1ms 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: 0ms + 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: 0ms + testReset runtime: 2ms 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: 0ms + testReset runtime: 1ms 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: 7ms @@ -8047,29 +8082,29 @@ testReset runtime: 7ms 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: 6ms + testReset runtime: 17ms 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: 3ms + testReset runtime: 2ms Finished 13000 tests Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2025-08-23 01:52:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@d9b0ed1, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2025-08-23 01:52:29 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@73476091, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2026-09-26 10:55:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2025-08-23 01:52:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2025-08-23 01:52:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2025-08-23 01:52:29 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 10:55:52 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 @@ -9130,31 +9165,31 @@ Finished 13200 tests Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.781833457899758542.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.7590453030185637537.bai - #BAMIndexWriterTest diff /tmp/javaBai.781833457899758542.bai /tmp/cBai.7590453030185637537.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.17079177328032533803.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.10723645105514658870.bai + #BAMIndexWriterTest diff /tmp/javaBai.17079177328032533803.bai /tmp/cBai.10723645105514658870.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.14578370810108843520.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.8440355695586807627java.bai - #BAMIndexWriterTest diff /tmp/javaBai.8440355695586807627java.bai.txt /tmp/cBai.14578370810108843520.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.5890010433783101715.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.6140486033435425288java.bai + #BAMIndexWriterTest diff /tmp/javaBai.6140486033435425288java.bai.txt /tmp/cBai.5890010433783101715.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 0ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT - 1ms to write + 0ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater SKIPPED Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testBasic STANDARD_OUT - Creating file /tmp/BCOST.16439127168442888408.gz + Creating file /tmp/BCOST.17061504477238812839.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.4948532609522536704.gz + Creating file /tmp/testCustomDeflater.8560404054404910410.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.10084182734547776825.gz + Creating file /tmp/BCOST.7210038425307363049.gz Finished 13400 tests Gradle suite > Gradle test > htsjdk.beta.io.bundle.BundleJSONTest.testAcceptSingleBundleJSONAsCollection[0]({ @@ -9174,31 +9209,30 @@ 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 2025-08-23 01:53:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:53:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:53:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:53:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:56:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:56:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:56:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:56:41 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 Gradle suite > Gradle test > htsjdk.samtools.CRAMAllEncodingStrategiesTest.testRoundTripDefaultEncodingStrategy[2](src/test/resources/htsjdk/samtools/cram/NA12878.unmapped.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.1-100.fasta, false, false) SKIPPED - Gradle is still running, please be patient... 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 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:57:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:57:59 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 @@ -9209,405 +9243,405 @@ 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 2025-08-23 01:54:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2025-08-23 01:54:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2025-08-23 01:54:43 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-08-23 01:54:43 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2025-08-23 01:54:43 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2025-08-23 01:54:43 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-09-26 10:58:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-09-26 10:58:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2026-09-26 10:58:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2026-09-26 10:58:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[4](src/test/resources/htsjdk/samtools/cram/test.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 13600 tests 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 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 01:54:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2025-08-23 01:54:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:54:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 10:58:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 10:58:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2025-08-23 01:54:47 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-08-23 01:54:47 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2025-08-23 01:54:47 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2025-08-23 01:54:47 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-09-26 10:58:13 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-09-26 10:58:13 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2026-09-26 10:58:13 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2026-09-26 10:58:13 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 2025-08-23 01:54:47 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:54:47 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2025-08-23 01:54:47 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:54:47 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-09-26 10:58:13 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:58:13 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2026-09-26 10:58:13 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 10:58:13 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCRAMReader1_ReferenceRequired STANDARD_ERROR - WARNING 2025-08-23 01:58:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 01:58:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:01:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:01:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2025-08-23 01:58:32 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:58:32 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2025-08-23 01:58:32 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2025-08-23 01:58:32 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-09-26 11:01:59 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 11:01:59 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2026-09-26 11:01:59 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2026-09-26 11:01:59 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + Gradle is still running, please be patient... Finished 13800 tests Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@7bbd54d9, [Ljava.lang.String;@42584d31) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2bf6a0c9, [Ljava.lang.String;@161b37f9) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@4ca2a986, [Ljava.lang.String;@74381f0e) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30268ec4, [Ljava.lang.String;@59748c1c) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 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 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@79e899db, [Ljava.lang.String;@6583c6d2) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 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;@605e86f8, [Ljava.lang.String;@421cdff4) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7c3941d4, [Ljava.lang.String;@3591b567) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@71a8afb7, [Ljava.lang.String;@5e1af966) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ee3d3a7, [Ljava.lang.String;@13c3ea96) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@6076f87, [Ljava.lang.String;@5d8deeab) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6bbc30dc, [Ljava.lang.String;@62e42643) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@55333382, [Ljava.lang.String;@35ad51fb) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@741d0168, [Ljava.lang.String;@507ed376) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@6af9de68, [Ljava.lang.String;@71e244d7) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1f91a27f, [Ljava.lang.String;@7c341d8a) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@3fac9c38, [Ljava.lang.String;@2168be1f) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@361b99c3, [Ljava.lang.String;@186df56b) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@7970043a, [Ljava.lang.String;@78684d1f) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@170f0878, [Ljava.lang.String;@4931c75a) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@2b26a294, [Ljava.lang.String;@2e485795) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@eaf483b, [Ljava.lang.String;@45721cfd) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:16 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;@3b827bfe) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 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;@21c38ea5) STANDARD_ERROR - WARNING 2025-08-23 02:04:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:16 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;@5da14014) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@40c35060) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@24016240) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@550b2f58) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - Gradle is still running, please be patient... - -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;@516cd64e) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@54f32219) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@6cd88ce4, [Ljava.lang.String;@16e41126) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:26 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;@38e23448, [Ljava.lang.String;@47dafbca) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5b3f4847, [Ljava.lang.String;@42fe28de) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@3ddefeaa, [Ljava.lang.String;@7e17de39) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@9558c1c, [Ljava.lang.String;@af8da54) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@3dc6acf0, [Ljava.lang.String;@67385594) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@133f23ae, [Ljava.lang.String;@47e01435) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@3c7c51d4, [Ljava.lang.String;@7d6aff68) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@34cc5158, [Ljava.lang.String;@211ede14) STANDARD_ERROR + WARNING 2026-09-26 11:06:26 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:26 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;@8c6b896, [Ljava.lang.String;@4677e7a9) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@14f892b2, [Ljava.lang.String;@5eb58d8b) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@13dbbc6a, [Ljava.lang.String;@6d3f4231) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7651f184, [Ljava.lang.String;@1153c0ac) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@549025d2, [Ljava.lang.String;@78ef3d7e) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@51b3eb66, [Ljava.lang.String;@5b5802aa) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@484dc2b6, [Ljava.lang.String;@2f64fe57) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@753dff7a, [Ljava.lang.String;@13b59991) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@17308be0) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@a537dea) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@4f18ec03) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@7560536f) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@24e50011) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@751e1f6d) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@7bffe447) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@14870bd6) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 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;@17c4589e, [Ljava.lang.String;@4780c056) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:17 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;@7741d344, [Ljava.lang.String;@3cda4ac9) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@59587019, [Ljava.lang.String;@f18478e) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 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;@3a700380, [Ljava.lang.String;@20d51935) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79ca9812, [Ljava.lang.String;@70c6111) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 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;@76c6518e, [Ljava.lang.String;@686e2790) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@435b49ca, [Ljava.lang.String;@6363d207) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 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;@15d620ce, [Ljava.lang.String;@71b5ac9a) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f6a0b59, [Ljava.lang.String;@3edb1ae3) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 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;@c9f0e9a, [Ljava.lang.String;@320a397) STANDARD_ERROR - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@10858e87, [Ljava.lang.String;@7bafcac9) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 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;@491b66ca, [Ljava.lang.String;@1a851c1d) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@692e60ad, [Ljava.lang.String;@3af54690) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 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;@7b24453b, [Ljava.lang.String;@25eeed51) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2616eb14, [Ljava.lang.String;@5ebac7) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 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;@6264cba2, [Ljava.lang.String;@2b91538) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7792a4bf, [Ljava.lang.String;@15d60760) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:18 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;@7a496372) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@4c0d3048) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@316ac49) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@771c58a5) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@52169fc6) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@73a703ba) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@49c9e482) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@6aea6983) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@5d86f455) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@45f5c295) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@1b5567d6) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@618d997a) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@391775c4) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@2255e17a) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@7735348) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@2319d60) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@50835664) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@42269c99) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@3bf4b972) STANDARD_ERROR - WARNING 2025-08-23 02:04:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:18 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;@74afed50) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@5a4707d5) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@652f96bc) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@c40725b, [Ljava.lang.String;@5ede6996) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@6ad5d28a, [Ljava.lang.String;@5c29c92b) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43e25a29, [Ljava.lang.String;@2784bb4e) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@2c18ea69, [Ljava.lang.String;@5d1055c) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@66cf2759, [Ljava.lang.String;@227860d0) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@1e9524c2, [Ljava.lang.String;@707cb9af) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@49125ed9, [Ljava.lang.String;@5fe761ab) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@356e9712, [Ljava.lang.String;@38364309) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@27102f59, [Ljava.lang.String;@28025dfb) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@103cffae, [Ljava.lang.String;@67601a5d) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43eb8c6f, [Ljava.lang.String;@20d12ccb) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@207b23ff, [Ljava.lang.String;@20bc0bd2) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@48871a17, [Ljava.lang.String;@27e43c62) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@1a0e3957, [Ljava.lang.String;@25c9d62c) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5ed5b3c, [Ljava.lang.String;@62355065) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@189da6b4, [Ljava.lang.String;@3d2ff442) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@690fdea5, [Ljava.lang.String;@565fc5e2) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:27 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;@4519e1d6) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@4b575292) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@1678dfbc) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@47f13092) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@5ed0d27) STANDARD_ERROR + WARNING 2026-09-26 11:06:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:27 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;@149ca194) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@41f95a31) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@3f8d2c9e) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@83625fe) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@35f82838) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@677f0449) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@76b71dbf) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@742dec66) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@5e2c361b) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@3ce35b98) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@1251e0da) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@122a7978) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@5be9ffde) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@3f693d22) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@5776864e) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@53a8c61f) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@2f9a0190) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 14000 tests -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;@45b7c60d) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@26a9bc32) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@30eda6a0) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@4050f573) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@1cc2e8ce) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@728bca8f) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@234baae3) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@789daed4) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.1164492707237332401.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4717b7c6) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:19 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;@7153b2ce, 5) STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:19 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;@446c51d6) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@9c9102e) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@10887d31) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@aef316c) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@488b6f9f) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@6b86bf95) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@1dd13236) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 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;@35e28438) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.5820722924440204702.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@756aaeb2) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:28 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;@76071787, 5) STANDARD_ERROR + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:28 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2025-08-23 02:04:20 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2026-09-26 11:06:29 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 @@ -10268,12 +10302,12 @@ Finished 14400 tests Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2025-08-23 02:04:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2025-08-23 02:04:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:21 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.util.CoordSpanInputSteamTest.test_3_ranges_byte_single_read STANDARD_ERROR Adding chunk: 0 - 100 @@ -10327,7 +10361,7 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.8779634902998282189.tmp + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.6397868905640705290.tmp Resetting tmpdir Finished 14800 tests Finished 15000 tests @@ -10337,492 +10371,492 @@ Finished 15800 tests Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-08-23 02:04:38 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 11:06:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2025-08-23 02:04:38 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2026-09-26 11:06:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Finished 16000 tests Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicShallowDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.codecFilterOutFieldsTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZipped[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.testGZippedShallow[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3.gz) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3WriterTest.testRoundTrip[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3) STANDARD_ERROR - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2025-08-23 02:04:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2026-09-26 11:06:48 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 Gradle suite > Gradle test > htsjdk.samtools.cram.encoding.core.GolombLongEncodingTest.testToString STANDARD_ERROR - WARNING 2025-08-23 02:04:40 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-09-26 11:06:48 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 2025-08-23 02:04:40 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2026-09-26 11:06:48 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Finished 16200 tests Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@6673f30c, [Ljava.lang.String;@7abd59a3) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5d4f45ad, [Ljava.lang.String;@24dfb3bc) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@3587c149, [Ljava.lang.String;@3469f2d) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69aeeffc, [Ljava.lang.String;@1932c24d) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, 2) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryAlignmentStart[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, 24) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@3682f38a) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@51a1df04) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@abfd7d) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@15e8418c) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@4741db6d) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@4f6963a) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@2a39a782) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@691161f3) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@644aead0, [Ljava.lang.String;@27d1aea8) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:41 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;@168698fd, [Ljava.lang.String;@54c5ba0c) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38ad77ec, [Ljava.lang.String;@28ed278c) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@5fe59c56, [Ljava.lang.String;@750bfceb) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4e16ea72, [Ljava.lang.String;@7d063ff) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@315d4ead, [Ljava.lang.String;@5e335d64) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@163f8999, [Ljava.lang.String;@449ca169) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@de966c5, [Ljava.lang.String;@67aac724) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a06e49f, [Ljava.lang.String;@30151c52) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@76428914, [Ljava.lang.String;@227bab78) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1fab6072, [Ljava.lang.String;@3ed78397) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@4c42e020, [Ljava.lang.String;@7f539149) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a46754c, [Ljava.lang.String;@bd5bda1) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@17ef4503, [Ljava.lang.String;@713e46e7) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3ec90cdf, [Ljava.lang.String;@2508a30) STANDARD_ERROR - WARNING 2025-08-23 02:04:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:41 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;@48491312, [Ljava.lang.String;@5570d2f8) STANDARD_ERROR - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@61c6c1b9, [Ljava.lang.String;@5bd1dd7b) STANDARD_ERROR - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2c8da21f) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@3b8d931b) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@4882ea62) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@2ac88eca) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@44fc6c61) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@2b5d3093) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@3e87785f) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@681d722a) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@7c6d11ca, [Ljava.lang.String;@4773750b) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 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;@4d21ce6b, [Ljava.lang.String;@3dd4cd48) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@79f3b0b6, [Ljava.lang.String;@d04bf07) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@79981380, [Ljava.lang.String;@38f50d6b) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2eb8fca6, [Ljava.lang.String;@4026c367) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@7362d3ad, [Ljava.lang.String;@3f5308bc) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@303b9d94, [Ljava.lang.String;@4eb1806d) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@273579e1, [Ljava.lang.String;@67b67495) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@10c38bf, [Ljava.lang.String;@27fc6e2d) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@251a32d4, [Ljava.lang.String;@3eaca2ee) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@760fe1a1, [Ljava.lang.String;@7fb47f9a) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@3bdcb6ff, [Ljava.lang.String;@3df3a9e) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@69f841e2, [Ljava.lang.String;@6ca7aa1a) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@5d0af4ea, [Ljava.lang.String;@f43e616) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@50e9a26e, [Ljava.lang.String;@f878a22) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 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;@99daedd, [Ljava.lang.String;@538560a1) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@160eefbd, [Ljava.lang.String;@3a6c733c) STANDARD_ERROR + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMate[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 20, 100013, f) STANDARD_ERROR - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryMateEnsureInternalIteratorsClosed[4](src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTestGATKGen.cram, src/test/resources/htsjdk/samtools/cram/mitoAlignmentStartTest.fa, Mito, 631, IL29_4505:7:30:11521:4492#2) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@50fde819) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@2f5e4692) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@663ff31f) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@3d24d258) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@13b7ab27) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@2c09fa7a, [Ljava.lang.String;@36da168d) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@5d2e3a62, [Ljava.lang.String;@5a2c036f) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6833008b, [Ljava.lang.String;@4940b9d3) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@a6fb715, [Ljava.lang.String;@2bfead1e) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b65351e, [Ljava.lang.String;@7c40b8f1) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@4897f7b8, [Ljava.lang.String;@17961960) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@174c7c1a, [Ljava.lang.String;@2199e48c) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@60e79668, [Ljava.lang.String;@2af7ed3d) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6be48bab, [Ljava.lang.String;@22529462) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@5673430, [Ljava.lang.String;@4cbc0444) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1f9a51ed, [Ljava.lang.String;@50fb8690) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@233200de, [Ljava.lang.String;@4227bbc3) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@53a0390e, [Ljava.lang.String;@24edbb9) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@2e84baa5, [Ljava.lang.String;@4cecbc28) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@28479db9, [Ljava.lang.String;@4dd2da3) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@2c002034, [Ljava.lang.String;@5c28325c) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68baa31b, [Ljava.lang.String;@843f3df) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:43 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;@13a35ade) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@42cd423) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@e15b073) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@4dc7eb1e) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@3e473ef5) STANDARD_ERROR - WARNING 2025-08-23 02:04:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:43 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;@4f4ed54c) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@590d9e15) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.13927060914935208537.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@15d9cf09) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:44 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;@74c24090) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@5161137d) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@9d36e39) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@de1f33c) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@51893662) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@693d1ddc) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@f08130c) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@652e4177) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@578c6ab4) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@42cdbcaf) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@540d6525) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@1cdb6ea2) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@5af3f3a2) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@42e314b) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@bbcc142, [Ljava.lang.String;@402de2b0) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@18132e25, [Ljava.lang.String;@1438132) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2a13c1d4, [Ljava.lang.String;@73a473ef) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@2ff0a886, [Ljava.lang.String;@64e44db4) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f2e4e84, [Ljava.lang.String;@47dbf0f6) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@1cb4f757, [Ljava.lang.String;@67722216) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@501c5388, [Ljava.lang.String;@73f79669) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@6bcd97c6, [Ljava.lang.String;@528090aa) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@446729de, [Ljava.lang.String;@34e32503) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@6c942ad, [Ljava.lang.String;@11606e2f) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3e2916a5, [Ljava.lang.String;@60cce434) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@44006611, [Ljava.lang.String;@ff09976) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@606feca7, [Ljava.lang.String;@2a76c265) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@799f4059, [Ljava.lang.String;@46515b47) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1de2488e, [Ljava.lang.String;@6cc43e05) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@47bf80af, [Ljava.lang.String;@7a13e671) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6ddad349, [Ljava.lang.String;@542b1055) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:50 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;@752c99f9) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@2ac58707) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@6054f1ab) STANDARD_ERROR + WARNING 2026-09-26 11:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:50 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;@418e2810) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@7be403b7) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@522ed928) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@59a29147) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.4772312838682947954.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@3a8ee780) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 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;@34e315b) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@6f6a74fc) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@7398b376) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@6365d46d) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@350e0d79) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@39776b5a) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@490e0f49) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@a9bbe1c) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@21240ce5) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueries[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 12, 7) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 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;@307a4afb, 5) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:04:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 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;@15b6e669, 5) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:06:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Finished 16400 tests -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@441e94ae, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@4e53f7e1], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) +Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@9a62b06, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7ad2202c], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 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 2025-08-23 02:04:44 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2026-09-26 11:06:51 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@443ada99, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2c98596d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@17b5651c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2e61b09b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@12b2b172], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 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@7fe71b3c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@cb00e0a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@347b932d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@105840f6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5ae2a76e], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 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@443ada99, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2c98596d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@17b5651c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2e61b09b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@12b2b172], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 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@7fe71b3c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@cb00e0a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@347b932d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@105840f6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5ae2a76e], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 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@443ada99, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2c98596d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@17b5651c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2e61b09b, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@12b2b172], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2025-08-23 02:04:44 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@7fe71b3c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@cb00e0a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@347b932d, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@105840f6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@5ae2a76e], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2026-09-26 11:06:51 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) Finished 16600 tests some stuffFinished 16800 tests Finished 17000 tests Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file15686307102010022689.bad + Could not delete file file13064088552924562360.bad Finished 17200 tests Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 31 milliseconds - Queried for the same 100-length mapping 205723650 times in 10 seconds. + Time to construct a tree with 50000 nodes: 21 milliseconds + Queried for the same 100-length mapping 207109351 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17400 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) Finished 17600 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 17800 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testBasic[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2026-09-26 11:07:04 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 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2026-09-26 11:07:04 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) @@ -10984,7 +11018,7 @@ Finished 18200 tests Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2025-08-23 02:04:58 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2026-09-26 11:07:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) Finished 18400 tests Finished 18600 tests @@ -11010,196 +11044,196 @@ Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT d e - c b a + c Finished 18800 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2025-08-23 02:05:29 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2026-09-26 11:07:36 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 2025-08-23 02:05:29 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2026-09-26 11:07:36 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 2025-08-23 02:05:29 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2026-09-26 11:07:36 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Finished 19000 tests Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2025-08-23 02:05:29 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2026-09-26 11:07:36 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 2025-08-23 02:05:29 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2026-09-26 11:07:36 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2025-08-23 02:05:29 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2025-08-23 02:05:29 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-09-26 11:07:36 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2026-09-26 11:07:36 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeCRAMWriterWithNoReference STANDARD_ERROR - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.9954847335702474655..cram - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.11361625033204450361..cram + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension877734259301517330.cram + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension12612248448775997679.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.14606594670300981628.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.15195292175559953985.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 2025-08-23 02:05:29 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension14739381655343904684.cram - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension2009785675262533208.cram + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension17399637291986647264 + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension7871980772549245846 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension7055719705774770791.png + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension8837735656038600016.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://71dc4ae7-fdff-4172-8f97-fee682c3bf4c/work/testMakeWriterPathsam + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://eb438c8a-856b-4309-bbad-ef6e064c6639/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 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://5ad35a8e-6108-47b7-82ee-873b297ba3ef/work/testMakeWriterPathbam + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://930575ea-a333-43ea-9789-a46dd188e2d9/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 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c99eca3e-130e-4fe0-b189-c86633868226/work/testMakeWriterPathcram + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4ab60796-f898-4238-80cf-041d8a90aa40/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 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f0c5f48e-2e54-44b0-bd04-09f5a578c8c9/work/testMakeWriterPathsam + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c27e1104-e504-41d4-982e-d19869f1764f/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 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://3d97d52f-3627-4cfc-8525-b562fbeb6574/work/testMakeWriterPathbam + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://23ee2141-3add-42c1-9a83-b53a6c9c494f/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 2025-08-23 02:05:29 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://5528549f-23f1-4c08-9571-81ccb17ea82b/work/testMakeWriterPathcram + INFO 2026-09-26 11:07:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2d7dac29-7845-4afc-9aa9-9779c8d6237c/work/testMakeWriterPathcram Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /work/testMakeWriterPathcram, Error parsing SAM header. @RG line missing SM tag. Line: @RG ID:1 Finished 19200 tests Gradle suite > Gradle test > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7](SAMSequenceRecord(name=chr1,length=101,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null,alternate_names=[]), false) STANDARD_ERROR - ERROR 2025-08-23 02:05:41 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2026-09-26 11:07:48 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Finished 19400 tests Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/reproducible-path/htsjdk-4.1.3+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2025-08-23 02:05:41 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 2025-08-23 02:05:41 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 2026-09-26 11:07:48 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 2026-09-26 11:07:48 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 2025-08-23 02:05:42 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2025-08-23 02:05:42 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2025-08-23 02:05:42 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2025-08-23 02:05:42 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2026-09-26 11:07:49 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2026-09-26 11:07:49 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2026-09-26 11:07:49 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2026-09-26 11:07:49 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 2025-08-23 02:05:42 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2026-09-26 11:07:49 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 2025-08-23 02:05:42 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 2025-08-23 02:05:42 SamReaderFactoryTest Finished queries in 42ms + INFO 2026-09-26 11:07:49 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2026-09-26 11:07:49 SamReaderFactoryTest Finished queries in 47ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2025-08-23 02:05:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 11:07:49 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 2025-08-23 02:05:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 11:07:49 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 2025-08-23 02:05:42 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2026-09-26 11:07:49 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Finished 19600 tests Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2025-08-23 02:05:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2026-09-26 11:07:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2025-08-23 02:05:43 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-08-23 02:05:43 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-09-26 11:07:50 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2025-08-23 02:05:43 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2026-09-26 11:07:50 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2026-09-26 11:07:50 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -11214,54 +11248,54 @@ Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2025-08-23 02:05:43 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2026-09-26 11:07:50 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 2025-08-23 02:05:44 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2025-08-23 02:05:44 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2026-09-26 11:07:50 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2026-09-26 11:07:50 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 @@ -11366,12 +11400,12 @@ 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 (0.118 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/test +Finished generating test XML results (0.124 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.131 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/test -:test (Thread[#56,Task worker for ':' Thread 2,5,main]) completed. Took 15 mins 44.709 secs. +Finished generating test html results (0.181 secs) into: /build/reproducible-path/htsjdk-4.1.3+dfsg/build/reports/tests/test +:test (Thread[#58,Task worker for ':' Thread 4,5,main]) completed. Took 14 mins 5.214 secs. -BUILD SUCCESSFUL in 31m 35s +BUILD SUCCESSFUL in 35m 22s 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 @@ -11386,7 +11420,7 @@ 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" 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/ @@ -11421,14 +11455,14 @@ make[1]: Leaving directory '/build/reproducible-path/htsjdk-4.1.3+dfsg' jh_classpath -O--buildsystem=gradle jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-compress.jar /usr/share/java/commons-jexl2.jar /usr/share/java/json-lib.jar /usr/share/java/ngs-java.jar /usr/share/java/rhino.jar /usr/share/java/snappy-java.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar -Duplicate specification "version|V" for option "V" -Duplicate specification "version|V" for option "V" +Duplicate specification "V:s" for option "V" +Duplicate specification "V:s" for option "V" Updating symlinked /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) Reading manifest from /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar Updating manifest in /build/reproducible-path/htsjdk-4.1.3+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-4.1.3.jar jh_manifest -O--buildsystem=gradle -Duplicate specification "version|V" for option "V" Duplicate specification "V:s" for option "V" +Duplicate specification "version|V" for option "V" find debian/libhtsjdk-java -name '*.jar' Found usr/share/java/htsjdk-4.1.3.jar Found symlink usr/share/java/htsjdk.jar @@ -11485,6 +11519,185 @@ 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/beta/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-su Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/help-doc.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/search.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index-all.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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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/BetaAPI.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/package-summary.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/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.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/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 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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/HtsContentType.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/variants/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/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/VariantsDecoderOptions.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/VariantsCodec.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/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using Fi 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/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/sharle::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/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc @@ -11533,56 +11746,176 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using 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/MutableFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism:: Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc + 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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-d 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/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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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/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/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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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/BCF2Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.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/BCF2Decoder.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/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htse/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.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/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc +mmary.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/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc @@ -11631,56 +11964,54 @@ 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/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/ap 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/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/AbstractBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/shar File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/ap Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.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/cram/CRAIEntry.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/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/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/ref/package-tree.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/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.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/CRAMLazyReferenceSource.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/digest/ContentDigests.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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.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/CramContainerHeaderIterator.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/CompressionHeaderFactory.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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/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/ExternalCompressor.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/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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compr File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc @@ -11716,124 +12047,127 @@ 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/SamReader.Type.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/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/CRAMDecoderV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMCodecV3_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/package-summary.html using File::StripNondeterminism::handlers::javadoc - 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/CRAMDecoderV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV2_1/CRAMCodecV2_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/BAMEncoderOptions.html using File::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/BAMDecoderOptions.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/BAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/bam/bamV1_0/BAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/IOPath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/io/HtsPath.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/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/example/PrintVariantsExample.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/VCFHeaderReader.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/GeneralUtils.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/bcf2/package-tree.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/BCFVersion.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/BCF2Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.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/BCF2Decoder.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/BCF2Codec.LazyData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htshandlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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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-d 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/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/core/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.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/core/experimental/GolombIntegerEncoding.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/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.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/Insertion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.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/Bases.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/structure/package-tree.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/SubstitutionMatrix.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/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/c 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/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc @@ -12009,292 +12339,41 @@ Normalizing 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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/InternalAPI.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/beta/exception/package-tree.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/HtsjdkUnsupportedOperationException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkPluginException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkIOException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/exception/HtsjdkException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/VariantsFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/variants/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/VariantsDecoderOptions.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/VariantsCodec.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/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using Fi Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/IOPathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SignatureStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/SeekableStreamResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/OutputStreamResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/IOPathResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/InputStreamResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResourceBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleJSON.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/BundleBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/bundle/Bundle.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/VariantsCodecUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFDecoderV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_3/VCFCodecV4_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFEncoderV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFDecoderV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_2/VCFCodecV4_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-su Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/CRAMException.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/cram/CRAIEntry.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/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/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/ref/package-tree.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/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/ref/EnaRefService.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/CRAMLazyReferenceSource.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/digest/ContentDigests.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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/build/CramIO.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/CramContainerHeaderIterator.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/CompressionHeaderFactory.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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/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/ExternalCompressor.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/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/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compr 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/core/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-dohandlers::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/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc ession/rans/RANS.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/package-summary.html using File::StripNondeterminism::handlers::javadoc @@ -12332,77 +12411,6 @@ 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/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc -le::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/ReadsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsBundle.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryRule.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQueryInterval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsQuery.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsIntervalUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/interval/HtsInterval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/VariantsResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/ReadsResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsDefaultRegistry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HtsCodecRegistry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/registry/HaploidReferenceResolver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HapRefDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/hapref/HaploidReferenceCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/io/package-tree.html using File::StripNondeterminism::handlers::javadoc -mmary.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/VCFDecoderV3_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/VCFCodecV3_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc ram/structure/EncodingID.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/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc @@ -12443,6 +12451,32 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc +c/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractAsyncWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc + 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/HtsgetResponse.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/HtsgetRequest.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetPOSTRequest.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetMalformedResponseException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/htsget/HtsgetErrorResponse.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/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/ftp/FTPUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ftp/FTPClient.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/nio/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/zip/package-tree.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/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 sr/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/VCFIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc @@ -12488,16 +12522,16 @@ cd debian/libhtsjdk-java-doc chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian - chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.3+dfsg' + chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/reproducible-path/htsjdk-4.1.3+dfsg' dh_fixperms -O--buildsystem=gradle find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/libhtsjdk-java/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 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 @@ -12515,13 +12549,13 @@ echo misc:Depends= >> debian/libhtsjdk-java-doc.substvars echo misc:Pre-Depends= >> debian/libhtsjdk-java-doc.substvars dpkg-gencontrol -plibhtsjdk-java-doc -ldebian/changelog -Tdebian/libhtsjdk-java-doc.substvars -cdebian/control -Pdebian/libhtsjdk-java-doc - chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control + chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control dh_md5sums -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java/DEBIAN install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN - cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + install -m0755 -d debian/libhtsjdk-java/DEBIAN cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle @@ -12536,12 +12570,14 @@ 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/208588/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/208588/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/70849 and its subdirectories -I: Current time: Sat Aug 23 02:06:05 -12 2025 -I: pbuilder-time-stamp: 1755957965 +I: removing directory /srv/workspace/pbuilder/208588 and its subdirectories +I: Current time: Sat Sep 26 11:08:10 +14 2026 +I: pbuilder-time-stamp: 1790370490