Diff of the two buildlogs: -- --- b1/build.log 2023-05-20 04:12:35.874555147 +0000 +++ b2/build.log 2023-05-20 04:45:35.179944401 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 19 14:34:13 -12 2023 -I: pbuilder-time-stamp: 1684550053 +I: Current time: Sat Jun 22 00:35:46 +14 2024 +I: pbuilder-time-stamp: 1718966146 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./htsjdk_3.0.4+dfsg.orig.tar.xz] I: copying [./htsjdk_3.0.4+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Jan 23 15:26:04 2023 -12 +gpgv: Signature made Tue Jan 24 17:26:04 2023 +14 gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htsjdk_3.0.4+dfsg-2.dsc: no acceptable signature found @@ -41,135 +41,167 @@ dpkg-source: info: applying 150-use-rhino-as-JS-engine.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2998534/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1251667/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 22 00:36 /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/1251667/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1251667/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d887c7e1181345ea8d98e3cc88e673a2' - 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='2998534' - PS1='# ' - PS2='> ' + INVOCATION_ID=bff77bc590de4238b6800215f9f7d86d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1251667 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.mW0GNFHU/pbuilderrc_TDwC --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mW0GNFHU/b1 --logfile b1/build.log htsjdk_3.0.4+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.mW0GNFHU/pbuilderrc_h2Gt --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mW0GNFHU/b2 --logfile b2/build.log --extrapackages usrmerge htsjdk_3.0.4+dfsg-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2998534/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 22 00:36 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1251667/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -606,7 +638,7 @@ Get: 363 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-5 [23.4 kB] Get: 364 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-5 [110 kB] Get: 365 http://deb.debian.org/debian bookworm/main amd64 scala-library all 2.11.12-5 [9588 kB] -Fetched 492 MB in 19s (26.1 MB/s) +Fetched 492 MB in 7s (73.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -2274,8 +2306,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/htsjdk-3.0.4+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_3.0.4+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/1251667/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1251667/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/htsjdk-3.0.4+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_3.0.4+dfsg-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 3.0.4+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2317,7 +2360,7 @@ dh_auto_build -- jar javadoc mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=15 jar javadoc + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=16 jar javadoc openjdk version "17.0.6" 2023-01-17 OpenJDK Runtime Environment (build 17.0.6+10-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing) @@ -2325,18 +2368,18 @@ 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/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 4.448 secs. -The client will now receive all logging from the daemon (pid: 3055417). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-3055417.out.log +An attempt to start the daemon took 1.107 secs. +The client will now receive all logging from the daemon (pid: 1269368). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-1269368.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 15 worker leases. -Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e92ab36 -Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e92ab36 -Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cff778e +Using 16 worker leases. +Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d344c49 +Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d344c49 +Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d13ef15 Starting Build Compiling initialization script '/build/htsjdk-3.0.4+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@84e2422 +Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@54e8a00b Compiling initialization script '/build/htsjdk-3.0.4+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2356,17 +2399,17 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : -Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@39881598 +Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@6ea847bd 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/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cff778e -Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@b87eaef -Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@59db739d +Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d13ef15 +Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@43a80a3e +Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1bfe8a14 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.015 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@d53b9b +Putting task artifact state for task ':compileJava' into context took 0.005 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@396f2349 Loading the Maven rules... Replacing org.apache.commons:commons-jexl:jar:2.1.1 -> org.apache.commons:commons-jexl:jar:debian Passing through org.apache.commons:commons-parent:jar:debian @@ -2384,7 +2427,7 @@ javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies. Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian -Up-to-date check for task ':compileJava' took 4.852 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 1.467 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. @@ -2402,39 +2445,39 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 warnings -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 56.405 secs. -:processResources (Thread[Task worker for ':' Thread 13,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 12.426 secs. +:processResources (Thread[Task worker for ':',5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. -Up-to-date check for task ':processResources' took 0.016 secs. It is not up-to-date because: +Up-to-date check for task ':processResources' took 0.011 secs. It is not up-to-date because: No history is available. -:processResources (Thread[Task worker for ':' Thread 13,5,main]) completed. Took 0.131 secs. -:classes (Thread[Task worker for ':' Thread 13,5,main]) started. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.042 secs. +:classes (Thread[Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 13,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 13,5,main]) started. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.006 secs. +:debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom executing task ':debianMavenPom' ... Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. -Up-to-date check for task ':debianMavenPom' took 0.008 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.001 secs. It is not up-to-date because: No history is available. Generating pom file /build/htsjdk-3.0.4+dfsg/build/debian/htsjdk.pom -:debianMavenPom (Thread[Task worker for ':' Thread 13,5,main]) completed. Took 0.34 secs. -:jar (Thread[Task worker for ':' Thread 13,5,main]) started. +:debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.108 secs. +:jar (Thread[Task worker for ':',5,main]) started. :jar executing task ':jar' ... Putting task artifact state for task ':jar' into context took 0.0 secs. -Up-to-date check for task ':jar' took 0.144 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.046 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 13,5,main]) completed. Took 1.425 secs. -:javadoc (Thread[Task worker for ':' Thread 13,5,main]) started. +:jar (Thread[Task worker for ':',5,main]) completed. Took 0.437 secs. +:javadoc (Thread[Task worker for ':',5,main]) started. :javadoc executing task ':javadoc' ... Putting task artifact state for task ':javadoc' into context took 0.0 secs. -Up-to-date check for task ':javadoc' took 0.693 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.187 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc''. Working directory: /build/htsjdk-3.0.4+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc @/build/htsjdk-3.0.4+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc'' @@ -2753,9 +2796,9 @@ * @return 1-based inclusive leftmost position of the clipped sequence, or 0 if there is no position. ^ 100 warnings -:javadoc (Thread[Task worker for ':' Thread 13,5,main]) completed. Took 45.738 secs. +:javadoc (Thread[Task worker for ':',5,main]) completed. Took 16.285 secs. -BUILD SUCCESSFUL in 2m 7s +BUILD SUCCESSFUL in 35s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/htsjdk-3.0.4+dfsg' jh_build -O--buildsystem=gradle @@ -2766,7 +2809,7 @@ dh_auto_build -- test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ - gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=15 test + gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 --parallel --max-workers=16 test openjdk version "17.0.6" 2023-01-17 OpenJDK Runtime Environment (build 17.0.6+10-Debian-1) OpenJDK 64-Bit Server VM (build 17.0.6+10-Debian-1, mixed mode, sharing) @@ -2774,17 +2817,17 @@ 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/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' -An attempt to start the daemon took 2.558 secs. -The client will now receive all logging from the daemon (pid: 3077872). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-3077872.out.log +An attempt to start the daemon took 1.45 secs. +The client will now receive all logging from the daemon (pid: 1270684). The daemon log file: /build/htsjdk-3.0.4+dfsg/.gradle/daemon/4.4.1/daemon-1270684.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 15 worker leases. -Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7fab68df -Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7fab68df -Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a0e73f0 +Using 16 worker leases. +Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e92ab36 +Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7e92ab36 +Creating new cache for fileHashes, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cff778e Starting Build -Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@cef7c8 +Creating new cache for metadata-1.1/results, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@3984aea0 Settings evaluated using settings file '/build/htsjdk-3.0.4+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-3.0.4+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] @@ -2799,16 +2842,16 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : -Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@73d8ab8e +Creating new cache for annotation-processors, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@1d8abbe1 Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':findScalaAndJavaTypes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':testWithDefaultReference', task ':test'] -Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@3a0e73f0 -Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@59fdabd9 -Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@4ea3521e +Creating new cache for resourceHashesCache, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6cff778e +Creating new cache for taskHistory, path /build/htsjdk-3.0.4+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@20b07ce +Creating new cache for outputFiles, path /build/htsjdk-3.0.4+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@1f48eeed :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.026 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@4efacb13 +Putting task artifact state for task ':compileJava' into context took 0.008 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-3.0.4+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@40db5bbe Loading the Maven rules... Replacing org.apache.commons:commons-jexl:jar:2.1.1 -> org.apache.commons:commons-jexl:jar:debian Passing through org.apache.commons:commons-parent:jar:debian @@ -2826,31 +2869,31 @@ javax.activation:javax.activation-api:debian is relocated to com.sun.activation:javax.activation:debian. Please update your dependencies. Passing through com.sun.activation:javax.activation:jar:debian Passing through com.sun.activation:all:jar:debian -Skipping task ':compileJava' as it is up-to-date (took 16.69 secs). +Skipping task ':compileJava' as it is up-to-date (took 0.952 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':',5,main]) completed. Took 16.901 secs. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 1.025 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. -Skipping task ':processResources' as it is up-to-date (took 0.025 secs). +Skipping task ':processResources' as it is up-to-date (took 0.01 secs). :processResources UP-TO-DATE -:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.047 secs. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.014 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.002 secs. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) started. :findScalaAndJavaTypes executing task ':findScalaAndJavaTypes' ... -Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.007 secs. +Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.001 secs. Up-to-date check for task ':findScalaAndJavaTypes' took 0.0 secs. It is not up-to-date because: Task has not declared any outputs. Starting process 'command './scripts/checkScalaAndJavaFiles.sh''. Working directory: /build/htsjdk-3.0.4+dfsg Command: ./scripts/checkScalaAndJavaFiles.sh Successfully started process 'command './scripts/checkScalaAndJavaFiles.sh'' -:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) completed. Took 0.098 secs. +:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) completed. Took 0.031 secs. :compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava executing task ':compileTestJava' ... @@ -2867,7 +2910,7 @@ 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 9.215 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 2.509 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. @@ -3086,14 +3129,14 @@ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 70 warnings -:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 40.573 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 14.598 secs. :processTestResources (Thread[Task worker for ':',5,main]) started. :processTestResources executing task ':processTestResources' ... Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.726 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 0.473 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 2.253 secs. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 1.121 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses executing task ':testClasses' ... @@ -3102,141 +3145,141 @@ :testWithDefaultReference (Thread[Task worker for ':',5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... -Putting task artifact state for task ':testWithDefaultReference' into context took 0.001 secs. -Up-to-date check for task ':testWithDefaultReference' took 1.278 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 0.454 secs. It is not up-to-date because: Task.upToDateWhen is false. -Finished generating test XML results (0.002 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.001 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.028 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[Task worker for ':',5,main]) completed. Took 1.531 secs. +Finished generating test html results (0.017 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[Task worker for ':',5,main]) completed. Took 0.598 secs. :test (Thread[Task worker for ':',5,main]) started. :test executing task ':test' ... Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.153 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.066 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 1'. Working directory: /build/htsjdk-3.0.4+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath11422367763993771806txt -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/htsjdk-3.0.4+dfsg Command: /usr/lib/jvm/java-17-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath1403050485383831123txt -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 suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[69](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[70](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[71](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[72](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[73](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[74](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[75](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[76](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[77](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[78](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[79](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:43:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[151](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[152](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[153](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[154](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[155](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[156](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[157](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[158](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[159](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[160](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[161](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:48:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[366](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 14:49:48 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[24](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.otherMultipleIntervals(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[25](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.iteratorStateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[26](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[27](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.singleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[28](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[29](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalOverlapping(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[30](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.serialQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[31](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.alignmentStartQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[32](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.multipleIntervalContained(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[33](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.mateQueries(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[34](public java.lang.Object[][] htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.unmappedMultiSliceTest(), class htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:40:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[91](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedMultiSliceTest(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[92](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.mateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[93](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.serialQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[94](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[95](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.alignmentStartQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[96](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.unmappedQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[97](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.multipleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[98](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalContained(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[99](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.iteratorStateQueries(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[100](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.otherMultipleIntervals(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[101](public java.lang.Object[][] htsjdk.samtools.CRAMIndexQueryTest.singleIntervalOverlapping(), class htsjdk.samtools.CRAMIndexQueryTest) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:42:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[169](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 00:42:19 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2023-05-19 14:49:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:42:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2023-05-19 14:49:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:42:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2023-05-19 14:49:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:42:47 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops @@ -3257,7 +3300,6 @@ at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:833) - Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms @@ -3269,31 +3311,31 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+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/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+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/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+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/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 9ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+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[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms @@ -3308,13 +3350,13 @@ testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+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[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+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.testFirstSequence[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstSequence runtime: 0ms + testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequence runtime: 0ms @@ -3326,10 +3368,10 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequence runtime: 0ms + testFirstSequence runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstSequenceExtended runtime: 1ms + testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms @@ -3344,31 +3386,31 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 43ms + testLastCompleteContigRead runtime: 8ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 23ms + testLastCompleteContigRead runtime: 6ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 11ms + testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 3ms + testLastCompleteContigRead runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 60ms + testLastCompleteContigRead runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 49ms + testLastCompleteContigRead runtime: 13ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 42ms + testLastCompleteContigRead runtime: 11ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 30ms + testLastCompleteContigRead runtime: 10ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 13ms + testLastCompleteContigRead runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms @@ -3380,37 +3422,37 @@ testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testFirstOfChr1 runtime: 1ms + testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstOfChr1 runtime: 9ms + testFirstOfChr1 runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 19ms + testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 10ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 11ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 38ms + testNextElementOfIterator runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 43ms + testNextElementOfIterator runtime: 13ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 39ms + testNextElementOfIterator runtime: 13ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 12ms + testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 20ms + testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms @@ -3452,10 +3494,10 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 1ms + testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms @@ -3470,10 +3512,10 @@ testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 9ms + testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadThroughEndOfContig runtime: 8ms + testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -3491,43 +3533,43 @@ testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 42ms + testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 15ms + testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 4ms + testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 55ms + testReset runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 48ms + testReset runtime: 13ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 48ms + testReset runtime: 14ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 22ms + testReset runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 5ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2023-05-19 14:54:21 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:44:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream -Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testFromStream[2](java.io.ByteArrayInputStream@3f24915b, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2023-05-19 14:54:21 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@340132a1, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2024-06-22 00:44:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.testReadLines STANDARD_ERROR - WARNING 2023-05-19 14:54:21 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:44:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLength STANDARD_ERROR - WARNING 2023-05-19 14:54:21 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:44:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.readers.AsciiLineReaderTest.voidTestLineEndingLengthAtEof STANDARD_ERROR - WARNING 2023-05-19 14:54:21 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 00:44:15 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.BAMFileIndexTest.testQueryUnmapped STANDARD_OUT Found start of unmapped reads. Num mapped reads: 9721 @@ -4587,14 +4629,14 @@ NoCoordinateCount= 279 Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.10395306712166357142.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.296222603190153503.bai - #BAMIndexWriterTest diff /tmp/javaBai.10395306712166357142.bai /tmp/cBai.296222603190153503.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.16482340824713782403.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.7438646415571483126.bai + #BAMIndexWriterTest diff /tmp/javaBai.16482340824713782403.bai /tmp/cBai.7438646415571483126.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.2938500042359818300.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.6029523476813693641java.bai - #BAMIndexWriterTest diff /tmp/javaBai.6029523476813693641java.bai.txt /tmp/cBai.2938500042359818300.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.16708916913684050275.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.8787349129604351586java.bai + #BAMIndexWriterTest diff /tmp/javaBai.8787349129604351586java.bai.txt /tmp/cBai.16708916913684050275.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 1ms to write @@ -4605,416 +4647,412 @@ 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.14821234267417158181.gz + Creating file /tmp/BCOST.16348329084576296731.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.15878563406412472885.gz + Creating file /tmp/testCustomDeflater.10005056336352778066.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.1322830462771702708.gz + Creating file /tmp/BCOST.11332756063171249871.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromContainer STANDARD_ERROR - WARNING 2023-05-19 14:59:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:59:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMCRAIIndexerTest.testCRAIIndexerFromStream STANDARD_ERROR - WARNING 2023-05-19 14:59:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:59:16 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:09 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2023-05-19 14:59:16 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2023-05-19 14:59:16 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2023-05-19 14:59:16 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 - WARNING 2023-05-19 14:59:16 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2024-06-22 00:46:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2024-06-22 00:46:09 Slice Slice mapped outside of reference bases length 10: slice reference context=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2024-06-22 00:46:09 CRAMReferenceRegion The bases of length 10 returned by the reference source do not satisfy the requested fragment length 12 + WARNING 2024-06-22 00:46:09 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 2023-05-19 14:59:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:59:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testCRAMThroughBAMRoundTrip[5](src/test/resources/htsjdk/samtools/cram/test2.cram, src/test/resources/htsjdk/samtools/cram/auxf.fa) STANDARD_ERROR - WARNING 2023-05-19 14:59:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:59:30 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.testObsoleteDataSeriesNotWritten STANDARD_ERROR - WARNING 2023-05-19 14:59:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 14:59:31 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:20 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2023-05-19 14:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 14:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:46:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:46:24 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2023-05-19 14:59:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2023-05-19 14:59:42 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2023-05-19 14:59:42 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 - WARNING 2023-05-19 14:59:42 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2024-06-22 00:46:25 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2024-06-22 00:46:25 Slice Slice mapped outside of reference bases length 1: slice reference context=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2024-06-22 00:46:25 CRAMReferenceRegion The bases of length 1 returned by the reference source do not satisfy the requested fragment length 3 + WARNING 2024-06-22 00:46:25 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 2023-05-19 14:59:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2023-05-19 14:59:42 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2023-05-19 14:59:42 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2023-05-19 14:59:42 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 is still running, please be patient... + WARNING 2024-06-22 00:46:25 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2024-06-22 00:46:25 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2024-06-22 00:46:25 CRAMReferenceRegion The bases of length 36 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2024-06-22 00:46:25 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 - WARNING 2023-05-19 15:25:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:25:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 00:54:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 00:54:27 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.CRAMFileReaderTest.testCramIteratorWithoutCallingHasNextFirst STANDARD_ERROR - WARNING 2023-05-19 15:25:37 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2023-05-19 15:25:37 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. - WARNING 2023-05-19 15:25:37 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 - WARNING 2023-05-19 15:25:37 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... - Gradle is still running, please be patient... + WARNING 2024-06-22 00:54:27 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2024-06-22 00:54:27 Slice Slice mapped outside of reference bases length 200000000: slice reference context=SINGLE_REFERENCE: 0, start=2, span=36, counter=0. + WARNING 2024-06-22 00:54:27 CRAMReferenceRegion The bases of length 35 returned by the reference source do not satisfy the requested fragment length 37 + WARNING 2024-06-22 00:54:27 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... Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest STANDARD_ERROR - WARNING 2023-05-19 15:59:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:33 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 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;@61d791f1, [Ljava.lang.String;@98237f3) STANDARD_ERROR - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1620c2de, [Ljava.lang.String;@5d7c51d4) STANDARD_ERROR - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:34 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;@3e06e4a1, [Ljava.lang.String;@5879b932) STANDARD_ERROR + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@233cd854, [Ljava.lang.String;@73b22d29) STANDARD_ERROR + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 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 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:34 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:11 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 2023-05-19 15:59:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:11 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:11 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;@638431a5, [Ljava.lang.String;@5a253f1f) STANDARD_ERROR - WARNING 2023-05-19 15:59:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:36 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@43d4221f, [Ljava.lang.String;@74ca1d5c) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7be85212, [Ljava.lang.String;@6f5492e) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@5291d7fb, [Ljava.lang.String;@cf9b447) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68313dc4, [Ljava.lang.String;@6e91d84e) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@70774697, [Ljava.lang.String;@5ceb6d4b) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@74ef455, [Ljava.lang.String;@25bf9168) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@7ffde00e, [Ljava.lang.String;@67e577d5) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d0fc142, [Ljava.lang.String;@d492075) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@1f82723e, [Ljava.lang.String;@1ed71e00) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6d2ae897, [Ljava.lang.String;@5586838e) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@19195938, [Ljava.lang.String;@62904e27) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3feabb13, [Ljava.lang.String;@32e7c7cd) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 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;@67a86bd0, [Ljava.lang.String;@64d9e4ff) STANDARD_ERROR - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:37 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5b7eec60, [Ljava.lang.String;@49048f76) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@30f81329, [Ljava.lang.String;@56657b9c) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2c7b7e44, [Ljava.lang.String;@18d7aeea) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@2c2f6a79) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@3e2ad1ea) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@2c41cc9a) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSequence[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@5e28709b) STANDARD_ERROR - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:38 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedSingleInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@20be315) STANDARD_ERROR - WARNING 2023-05-19 15:59:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:39 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;@2c7ef194) STANDARD_ERROR - WARNING 2023-05-19 15:59:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:39 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;@6a0fb7d1) STANDARD_ERROR - WARNING 2023-05-19 15:59:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:39 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;@300b228e) STANDARD_ERROR - WARNING 2023-05-19 15:59:39 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:39 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;@38d24325, [Ljava.lang.String;@2150f07) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@cf7ba88, [Ljava.lang.String;@564b2dbb) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3c968084, [Ljava.lang.String;@34024779) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@337a3aee, [Ljava.lang.String;@7a292520) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@708c45f4, [Ljava.lang.String;@6a2ed02c) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@30542df9, [Ljava.lang.String;@170598e2) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7eb57dfc, [Ljava.lang.String;@d206302) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@426c9a3d, [Ljava.lang.String;@719a88a8) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@587e03be, [Ljava.lang.String;@288d583) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@68731800, [Ljava.lang.String;@272646fd) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5575936a, [Ljava.lang.String;@34f51e0b) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@61fb985f, [Ljava.lang.String;@192916ed) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2f2229d3, [Ljava.lang.String;@6f7b6672) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@368deb7, [Ljava.lang.String;@233569af) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@52e496f1, [Ljava.lang.String;@34587a31) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@1941332f, [Ljava.lang.String;@29a4aba8) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7d326986, [Ljava.lang.String;@56b3972b) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 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;@34f90f8f) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@8781b7a) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@25390084) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@2f50dfd4) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@62efd4d0) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@1b6568ee) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@5b3b0420) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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;@39fb19b5) STANDARD_ERROR + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:40 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:12 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 2023-05-19 15:59:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:41 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:41 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;@7a5dfad4, [Ljava.lang.String;@1ebd80f5) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:42 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;@3ccb6175, [Ljava.lang.String;@23563268) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7cc384, [Ljava.lang.String;@20a96636) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 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;@3e101537, [Ljava.lang.String;@6db7b359) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1b13722d, [Ljava.lang.String;@5f578ccf) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 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;@4ee7338c, [Ljava.lang.String;@371d41b5) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1b25960c, [Ljava.lang.String;@6f3f189d) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 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;@295bc6aa, [Ljava.lang.String;@e4dfb51) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1bf3ca70, [Ljava.lang.String;@5cd461a5) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 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;@3628b34, [Ljava.lang.String;@54bbafd0) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@18f7db60, [Ljava.lang.String;@77fde25a) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 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;@52895c1c, [Ljava.lang.String;@4f9ac105) STANDARD_ERROR - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:42 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7dcef645, [Ljava.lang.String;@6faf5f3e) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:43 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;@31197d8a, [Ljava.lang.String;@5c005874) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@34425ba8, [Ljava.lang.String;@445da943) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:43 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;@21733ed6, [Ljava.lang.String;@75257212) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5c2d5672, [Ljava.lang.String;@32e481ef) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:43 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;@6f776755) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:43 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;@91a2308) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:43 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;@6a1f624f) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:43 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;@1a8e8279) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:43 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;@540e0a99) STANDARD_ERROR - WARNING 2023-05-19 15:59:43 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:43 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;@29395804) STANDARD_ERROR - WARNING 2023-05-19 15:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:44 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;@4f2a8df1) STANDARD_ERROR - WARNING 2023-05-19 15:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:44 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;@705354d1) STANDARD_ERROR - WARNING 2023-05-19 15:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:44 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;@1da59455) STANDARD_ERROR - WARNING 2023-05-19 15:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:44 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;@3dd100de) STANDARD_ERROR - WARNING 2023-05-19 15:59:44 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:44 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;@5519b3e) STANDARD_ERROR - WARNING 2023-05-19 15:59:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:45 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;@6a254e55) STANDARD_ERROR - WARNING 2023-05-19 15:59:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:45 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;@54ccf12) STANDARD_ERROR - WARNING 2023-05-19 15:59:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:45 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;@22761137) STANDARD_ERROR - WARNING 2023-05-19 15:59:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:45 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;@5e8029ae) STANDARD_ERROR - WARNING 2023-05-19 15:59:45 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:45 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;@aecd611) STANDARD_ERROR - WARNING 2023-05-19 15:59:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:46 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;@73bddbb7) STANDARD_ERROR - WARNING 2023-05-19 15:59:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:46 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;@18b2f733) STANDARD_ERROR - WARNING 2023-05-19 15:59:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:46 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;@40be57ce) STANDARD_ERROR - WARNING 2023-05-19 15:59:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:46 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;@3dbef14c) STANDARD_ERROR - WARNING 2023-05-19 15:59:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:47 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;@42e6d2e0) STANDARD_ERROR - WARNING 2023-05-19 15:59:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:47 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;@6e2661c2) STANDARD_ERROR - WARNING 2023-05-19 15:59:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:47 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;@2a0bc244) STANDARD_ERROR - WARNING 2023-05-19 15:59:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:47 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;@6305e106) STANDARD_ERROR - WARNING 2023-05-19 15:59:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:47 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;@1ab7b948) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@50c84dc4) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@668b4035) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQuerySingleIntervalContainedTrue[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6419c1f2) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@1b952a5a) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@408a33f5) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.2329802056401229111.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@58e2f82d) STANDARD_ERROR - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6f4433c4, 5) STANDARD_ERROR - WARNING 2023-05-19 15:59:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 15:59:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@420e7994, [Ljava.lang.String;@5b716dfa) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@218a159e, [Ljava.lang.String;@2f5b1b89) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@32b2950e, [Ljava.lang.String;@441d00f) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@7f09924b, [Ljava.lang.String;@62c2ba26) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3d8e5f65, [Ljava.lang.String;@3eb7b50a) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@2b3646d5, [Ljava.lang.String;@2a650ad9) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@175c9029, [Ljava.lang.String;@190c2273) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@392ae3ca, [Ljava.lang.String;@510f35b2) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@c305e46, [Ljava.lang.String;@395b0693) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@601d7c3d, [Ljava.lang.String;@7f54193e) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62017363, [Ljava.lang.String;@504b0953) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@7bcb51c8, [Ljava.lang.String;@6ae6fd89) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@f5ac201, [Ljava.lang.String;@66c43113) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@3b98cabb, [Ljava.lang.String;@126fe8d3) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6f24a62a, [Ljava.lang.String;@20494a90) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@30942b35, [Ljava.lang.String;@3487616e) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryOverlappingMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2cba383e, [Ljava.lang.String;@3959c4a2) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:13 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;@41d821f5) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@7bb7a4c9) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@30072cb) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@1f211527) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@41e87316) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@224a431a) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@4b2098c0) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@68caad26) STANDARD_ERROR + WARNING 2024-06-22 01:06:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:13 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;@366b9e03) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@2b2c841e) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@5b3f531e) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@7da8db0e) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@64931c5c) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@43d3d1) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@5d36b19d) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@314f66c6) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@37dc6f25) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@1303d685) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@5fdd967f) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@1c13cbfd) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@388cab62) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@6d1e5406) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@5d8743c7) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@7670cfeb) STANDARD_ERROR + WARNING 2024-06-22 01:06:14 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:14 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;@c8f07a7) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 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;@19cffa01) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 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;@2cb60057) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 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;@3c9ffd86) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 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;@3088db9f) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 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;@502e16cc) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.samtools.CRAMIndexQueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.9658987445924983278.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4a938df1) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:15 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;@6350c650, 5) STANDARD_ERROR + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.CRAMMergerTest.test STANDARD_ERROR - WARNING 2023-05-19 15:59:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 15:59:51 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:15 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.cram.ref.CRAMReferenceRegionTest.testGetReferenceBasesByRegionExceedsContigLength STANDARD_ERROR - WARNING 2023-05-19 16:00:49 CRAMReferenceRegion The bases of length 5000 returned by the reference source do not satisfy the requested fragment length 15000 + WARNING 2024-06-22 01:06:16 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 @@ -5673,12 +5711,12 @@ Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 352, Read name 20GAVAAXX100126:8:6:11319:64357, Mate Alignment start (9999780) must be <= reference sequence length (200) on reference 21 Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testAllCRAMEncodingsRoundTripThroughStream STANDARD_ERROR - WARNING 2023-05-19 16:01:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:01:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN Gradle suite > Gradle test > htsjdk.samtools.cram.structure.CompressionHeaderEncodingMapTest.testIgnoreObsoleteDataseriesOnRead STANDARD_ERROR - WARNING 2023-05-19 16:01:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:01:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:18 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:18 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 @@ -5733,487 +5771,486 @@ Resetting tmpdir Resetting tmpdir -Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.1670773001968667441.tmp - Gradle is still running, please be patient... +Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests STANDARD_ERROR + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.11343981962824716958.tmp 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 2023-05-19 16:02:44 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 01:06:42 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 2023-05-19 16:02:45 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2024-06-22 01:06:42 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.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2023-05-19 16:02:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:44 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 2023-05-19 16:02:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:44 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 2023-05-19 16:02:51 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:44 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 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 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 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 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 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-05-19 16:02:52 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2024-06-22 01:06:45 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 2023-05-19 16:02:53 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2024-06-22 01:06:45 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 2023-05-19 16:02:53 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2024-06-22 01:06:45 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest STANDARD_ERROR - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@4ca350fe, [Ljava.lang.String;@3d8afce2) STANDARD_ERROR - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@45f3656, [Ljava.lang.String;@3b7835e) STANDARD_ERROR - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 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;@4e495feb, [Ljava.lang.String;@18ee40c4) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testOtherMultipleIntervals[2](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@12a20fa0, [Ljava.lang.String;@ce76b54) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:56 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@68c0e4fe) STANDARD_ERROR - WARNING 2023-05-19 16:02:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:57 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;@163691e) STANDARD_ERROR - WARNING 2023-05-19 16:02:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:57 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;@3a944f11) STANDARD_ERROR - WARNING 2023-05-19 16:02:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:57 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;@48ddc9fd) STANDARD_ERROR - WARNING 2023-05-19 16:02:57 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:57 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;@24a3e59) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:58 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;@2dbb30dd) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:58 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;@65f13b57) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:58 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;@fe56730) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:58 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;@1c6ec936, [Ljava.lang.String;@652da599) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:58 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;@3960bcc2, [Ljava.lang.String;@97caff2) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1d38f523, [Ljava.lang.String;@3b7dbd78) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 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;@61c3c1d8, [Ljava.lang.String;@19c786b0) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7fd51a98, [Ljava.lang.String;@1e470125) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 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;@31774c97, [Ljava.lang.String;@20e3056c) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@68a550c3, [Ljava.lang.String;@75fee0f6) STANDARD_ERROR - WARNING 2023-05-19 16:02:58 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:58 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;@50a48934, [Ljava.lang.String;@6590701e) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@255e3b2d, [Ljava.lang.String;@26a6950e) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@17421caa, [Ljava.lang.String;@719f0c52) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4678d1d7, [Ljava.lang.String;@42e0fa8e) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 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;@50b07953, [Ljava.lang.String;@7a14601e) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6c64f3aa, [Ljava.lang.String;@626449ab) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 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;@31b5beb2, [Ljava.lang.String;@17eb46b9) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@38b4d3e2, [Ljava.lang.String;@4261e95c) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 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;@6bd0c090, [Ljava.lang.String;@75437e48) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@aab2778, [Ljava.lang.String;@42580b60) STANDARD_ERROR - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 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;@43d070bb) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@6fcef216) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@30c98ae3) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@6434a897) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@788a4bef) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@1dd7197f) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@427bf295) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@7a4fb77a) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@7ff7b861, [Ljava.lang.String;@59d1c311) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:46 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;@56e3a16a, [Ljava.lang.String;@3674d69f) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@55ffc9f7, [Ljava.lang.String;@7d284383) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@2f76a8a5, [Ljava.lang.String;@7d0555a5) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1691c012, [Ljava.lang.String;@4fd2564b) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@21f90f91, [Ljava.lang.String;@184629c6) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4db8ef0d, [Ljava.lang.String;@7569a29) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@51cacd66, [Ljava.lang.String;@723d9bb4) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5697627e, [Ljava.lang.String;@3c3b3467) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@2c4f894d, [Ljava.lang.String;@7409be05) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72713650, [Ljava.lang.String;@5b93a144) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@6e325f62, [Ljava.lang.String;@3393d37d) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@16e49089, [Ljava.lang.String;@65df047c) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 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;@23ae4257, [Ljava.lang.String;@43a0c233) STANDARD_ERROR + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:46 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@6b65c256, [Ljava.lang.String;@6c3cffbe) STANDARD_ERROR + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44b21f8f, [Ljava.lang.String;@547ccf8a) STANDARD_ERROR + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryContainedMultipleIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b50fdb7, [Ljava.lang.String;@4adab43c) STANDARD_ERROR + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 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 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:02:59 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 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 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:01 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 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 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:02 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:47 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:47 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 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:03 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:03 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;@2eaa4089) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@2b9c98c3) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 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;@6d06ef86) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 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;@b6eaaad) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 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;@26f0e42f) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 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;@1b2b8ac, [Ljava.lang.String;@a3c8507) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:04 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;@2e112f92, [Ljava.lang.String;@62259334) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1902cf28, [Ljava.lang.String;@22f3091) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 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;@76f06ec, [Ljava.lang.String;@2d97299b) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5fc6e7e1, [Ljava.lang.String;@3c6d75a9) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 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;@21c9dac4, [Ljava.lang.String;@3f601c22) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3a49c046, [Ljava.lang.String;@64477587) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 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;@276ce659, [Ljava.lang.String;@5a1afba) STANDARD_ERROR - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:04 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7faa5170, [Ljava.lang.String;@68fffb50) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@31413c51, [Ljava.lang.String;@395a0df9) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@62780a33, [Ljava.lang.String;@5e3395df) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@a040182, [Ljava.lang.String;@77875564) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@d7e250b, [Ljava.lang.String;@11d7309b) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5a4f6ff1, [Ljava.lang.String;@3b38d0fb) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@44793fac, [Ljava.lang.String;@37eb9272) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@42a39805, [Ljava.lang.String;@1499cebc) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4b059d57, [Ljava.lang.String;@4cd7c80b) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@49c98698) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@1ba3c3e8) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@51e7f50e) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2f71f78b) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@b01fb1f) STANDARD_ERROR - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:05 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@12b7bebc) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@4f170895) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.2625068325882101441.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@ebc52fd) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@73f07636) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@5f84187d) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@3553391d) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@14e2142d) STANDARD_ERROR - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:06 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@41ab7d85) STANDARD_ERROR - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 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;@78be7119) STANDARD_ERROR - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 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;@29c66fe7) STANDARD_ERROR - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 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;@9096459) STANDARD_ERROR - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 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;@397ce596) STANDARD_ERROR - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@4207434c) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@631bccb4) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@636dfb85) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2e9edd95) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsInterval[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@3e30eb37) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Lhtsjdk.samtools.QueryInterval;@5df0cf35, [Ljava.lang.String;@684599a0) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@3ce9ed34, [Ljava.lang.String;@27215c3d) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[4](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@7bf6455e, [Ljava.lang.String;@118d37ae) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[5](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@854730c, [Ljava.lang.String;@41084176) STANDARD_ERROR + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:48 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[6](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@797f3d21, [Ljava.lang.String;@4bd40f89) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[7](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@757896bc, [Ljava.lang.String;@59731eba) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[8](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@72078ec5, [Ljava.lang.String;@a9ce427) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[9](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4d3a69c5, [Ljava.lang.String;@755ff7eb) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[10](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@1b96e8e8, [Ljava.lang.String;@6d291d0f) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[11](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@194e2952, [Ljava.lang.String;@5954387b) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[12](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@d230208, [Ljava.lang.String;@49af543e) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[13](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@41b75363, [Ljava.lang.String;@126b97fe) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[14](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@4a99e3f7, [Ljava.lang.String;@6339700d) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[15](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@241bd0c0, [Ljava.lang.String;@187a2f42) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[16](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@5081f100, [Ljava.lang.String;@6f830340) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[17](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@70cc0197, [Ljava.lang.String;@65f26efe) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingHtsIntervals[18](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Lhtsjdk.samtools.QueryInterval;@2882c30f, [Ljava.lang.String;@25ea90ae) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@6eb5de4e) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@25769c5e) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@43817bc4) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@2ac465b7) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryOverlappingIntervalComponents[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@33167c2c) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, [Ljava.lang.String;@ecb48f) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[3](src/test/resources/htsjdk/samtools/cram/cramQueryTest.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@50a6582b) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryUnmapped[4](/tmp/cramQueryReadsWithLocalCRAI.10037768648679231948.cram, src/test/resources/htsjdk/samtools/cram/../hg19mini.fasta, [Ljava.lang.String;@48e3ce8a) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100013-100070, [Ljava.lang.String;@39ad7599) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100100, [Ljava.lang.String;@2c0968d) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100010-0, [Ljava.lang.String;@115775ab) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@2739a9c9) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@1be360aa) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[5](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100011, [Ljava.lang.String;@20a2c4) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[8](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-100010, [Ljava.lang.String;@386a3f3e) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[11](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100015-0, [Ljava.lang.String;@5e95793f) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + +Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testQueryWithRule[14](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:1-0, [Ljava.lang.String;@6a834d6b) STANDARD_ERROR + WARNING 2024-06-22 01:06:49 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:49 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 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:07 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - -Gradle suite > Gradle test > htsjdk.beta.codecs.reads.cram.HtsCRAMCodec30And21QueryTest.testSerialQueriesOnRemoteFile[2](src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram, src/test/resources/htsjdk/samtools/cram/human_g1k_v37.20.21.10M-10M200k.fasta, 0:100009-100009, [Ljava.lang.String;@3c61fcfe, 5) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:03:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:03:08 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:50 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;@47e32eef, 5) STANDARD_ERROR + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:06:50 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForDecodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@20bf89fe, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@10693058], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 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@43a1013c, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@20d4e1f2], ALIGNED_READS/1 resource(s), No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2024-06-22 01:06:50 HtsCodecResolver The specified format string (BOGUS_FORMAT) does not correspond to any registered codec for content type (ALIGNED_READS) Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[1]([], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) + WARNING 2024-06-22 01:06:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[2]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@13b8c83a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c3e0e7f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@50c6fb28, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1bf8bcd2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3ec19559], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 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@171507e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@733d6af6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@52154d54, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7c4cc141, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d513a65], ALIGNED_READS/1 resource(s), 1.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2024-06-22 01:06:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[4]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@13b8c83a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c3e0e7f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@50c6fb28, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1bf8bcd2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3ec19559], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 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@171507e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@733d6af6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@52154d54, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7c4cc141, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d513a65], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2024-06-22 01:06:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) -Gradle suite > Gradle test > htsjdk.beta.plugin.registry.HtsCodecResolverTest.testResolveCodecForEncodingFails[5]([htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@13b8c83a, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@c3e0e7f, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@50c6fb28, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@1bf8bcd2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@3ec19559], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR - WARNING 2023-05-19 16:03:08 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@171507e2, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@733d6af6, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@52154d54, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@7c4cc141, htsjdk.beta.plugin.registry.testcodec.HtsTestCodec@2d513a65], ALIGNED_READS/1 resource(s), 3.0.0, No registered codec accepts the provided resource) STANDARD_ERROR + WARNING 2024-06-22 01:06:50 HtsCodecResolver The specified format string (FILE_FORMAT_1) does not correspond to any registered codec for content type (ALIGNED_READS) some stuff Gradle suite > Gradle test > htsjdk.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file191922386945753376.bad + Could not delete file file14090437402809013221.bad Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 121 milliseconds - Queried for the same 100-length mapping 24027671 times in 10 seconds. + Time to construct a tree with 50000 nodes: 43 milliseconds + Queried for the same 100-length mapping 86662611 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2024-06-22 01:07:04 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[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2024-06-22 01:07:04 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.loadLiftOverFromInputStream[281](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2024-06-22 01:07:04 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[279](chr2:111013693-111013832 + ., null) STANDARD_ERROR - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2024-06-22 01:07:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2024-06-22 01:07:04 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 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2024-06-22 01:07:04 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) @@ -6373,7 +6410,7 @@ chrX:48774611-48775058 + null intersection null (len 448)=>null using chain 8 Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.testLiftoverCounter[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2023-05-19 16:03:41 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2024-06-22 01:07:04 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.MergingSamRecordIteratorTest.testVanillaCoordinateMultiIterator STANDARD_OUT read_28833_29006_6945 0 chr21 28833 255 36M * 0 0 AAGCTGGAGATTACCATACTTAGGCTCATGTAGCCA ?.QC5:&34LA#;K;A'5L*!.;.LJ?)FO?'?D2< RG:Z:1 @@ -6403,185 +6440,185 @@ Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2023-05-19 16:05:36 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2024-06-22 01:07:55 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 2023-05-19 16:05:36 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2024-06-22 01:07:55 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 2023-05-19 16:05:36 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2024-06-22 01:07:55 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 2023-05-19 16:05:36 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2024-06-22 01:07:55 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 2023-05-19 16:05:36 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2024-06-22 01:07:55 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2023-05-19 16:05:36 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2023-05-19 16:05:36 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2024-06-22 01:07:55 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2024-06-22 01:07:55 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 2023-05-19 16:05:36 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.1542644429678474526..cram - INFO 2023-05-19 16:05:36 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2023-05-19 16:05:36 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2023-05-19 16:05:36 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.17725478182183221480..cram + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2023-05-19 16:05:36 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension7969185908711332841.cram + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension11717323383644222884.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.4514673148971690805.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.15757820538528334300.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 2023-05-19 16:05:39 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension1094875108647361415.cram - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension6825041804916360376.cram + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension13428320405524145547 + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension12372330680856284554 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension8810881084739010930.png + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension14945218939858457834.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f8a9309f-aa0b-47e4-9e39-f3fdc809a8fc/work/testMakeWriterPathsam + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://fc336250-f8f8-4b86-be29-bec1b7fe2905/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 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://96ddd20d-181e-4f5d-904b-1062e5d007b4/work/testMakeWriterPathbam + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://a40fe2ca-388e-4b0c-b868-666d8d77d07a/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 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://57c6918c-567b-42fd-961d-fac243541bb1/work/testMakeWriterPathcram + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://8974ae09-d8e1-42ee-976d-534c69e4053e/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 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://9c4ffa7d-d184-473d-a9ce-fe464623d3b4/work/testMakeWriterPathsam + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d8626a60-8658-4165-a555-1ea642315b3b/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 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://78e536a8-d256-4c32-9bc2-28923ef5a071/work/testMakeWriterPathbam + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://83793fba-5705-44f5-9ccd-563c1d3966dc/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 2023-05-19 16:05:39 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://88d95df2-4414-4ef0-9122-a2bfa1f9249f/work/testMakeWriterPathcram + INFO 2024-06-22 01:07:55 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://99a13d81-37e3-467f-b471-7d3c782b3823/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.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 2023-05-19 16:06:10 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2024-06-22 01:08:10 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. Gradle suite > Gradle test > htsjdk.samtools.SamFilesTest.testIndexSymlinking[2](src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam, /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2023-05-19 16:06:11 SamFiles The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2023-05-19 16:06:11 SamFiles The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2024-06-22 01:08:10 SamFiles The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2024-06-22 01:08:10 SamFiles The index file /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-3.0.4+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2023-05-19 16:06:15 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2023-05-19 16:06:15 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2023-05-19 16:06:15 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2023-05-19 16:06:15 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2024-06-22 01:08:12 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2024-06-22 01:08:12 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2024-06-22 01:08:12 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2024-06-22 01:08:12 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2023-05-19 16:06:15 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2024-06-22 01:08:12 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2023-05-19 16:06:17 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 2023-05-19 16:06:17 SamReaderFactoryTest Finished queries in 210ms + INFO 2024-06-22 01:08:12 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2024-06-22 01:08:12 SamReaderFactoryTest Finished queries in 81ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURL STANDARD_ERROR - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLNoIndexFile STANDARD_ERROR - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testCRAMReaderFromURLStream STANDARD_ERROR - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:17 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:12 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2023-05-19 16:06:17 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2024-06-22 01:08:12 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 2023-05-19 16:06:17 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2024-06-22 01:08:12 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 2023-05-19 16:06:17 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2024-06-22 01:08:12 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 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[1](cram_with_bai_index.cram, hg19mini.fasta, 3:700-0, k) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.CRAMIndexTest[2](cram_with_crai_index.cram, hg19mini.fasta, 2:350-0, i) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testIterateCRAMWithIndex[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[0](cram_with_bai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamReaderTest.testReferenceRequiredForCRAM[1](cram_with_crai_index.cram, hg19mini.fasta) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN - WARNING 2023-05-19 16:06:19 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TN + WARNING 2024-06-22 01:08:13 CompressionHeaderEncodingMap Ignoring obsolete CRAM dataseries: TC Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2023-05-19 16:06:19 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2024-06-22 01:08:13 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2024-06-22 01:08:13 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testSamIntegers[1](inttest_large_coordinates.sam) STANDARD_ERROR - WARNING 2023-05-19 16:06:19 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2023-05-19 16:06:19 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2024-06-22 01:08:13 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2024-06-22 01:08:13 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -6594,54 +6631,54 @@ Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests.sliceStateTest[6]([htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772, htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111, htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0, htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f, htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee, htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d, htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c, htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb, htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a, htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09], true, UNMAPPED_UNPLACED, 0, 0) STANDARD_ERROR - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 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 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2023-05-19 16:06:26 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2024-06-22 01:08:13 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 2023-05-19 16:06:27 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 - WARNING 2023-05-19 16:06:27 Slice Slice mapped outside of reference bases length 20: slice reference context=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2024-06-22 01:08:13 CRAMReferenceRegion The bases of length 19 returned by the reference source do not satisfy the requested fragment length 20 + WARNING 2024-06-22 01:08:13 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 @@ -6664,17 +6701,17 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir +Gradle Test Executor 1 finished executing tests. WARNING: A terminally deprecated method in java.lang.System has been called WARNING: System::setSecurityManager has been called by org.gradle.api.internal.tasks.testing.worker.TestWorker (file:/usr/share/gradle/lib/plugins/gradle-testing-base-4.4.1.jar) WARNING: Please consider reporting this to the maintainers of org.gradle.api.internal.tasks.testing.worker.TestWorker WARNING: System::setSecurityManager will be removed in a future release -Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (12.84 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/test +Finished generating test XML results (0.529 secs) into: /build/htsjdk-3.0.4+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (9.003 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/test -:test (Thread[Task worker for ':',5,main]) completed. Took 1 hrs 25 mins 20.737 secs. +Finished generating test html results (0.417 secs) into: /build/htsjdk-3.0.4+dfsg/build/reports/tests/test +:test (Thread[Task worker for ':',5,main]) completed. Took 28 mins 27.958 secs. -BUILD SUCCESSFUL in 1h 26m 46s +BUILD SUCCESSFUL in 28m 52s 7 actionable tasks: 5 executed, 2 up-to-date make[1]: Leaving directory '/build/htsjdk-3.0.4+dfsg' create-stamp debian/debhelper-build-stamp @@ -6782,6 +6819,100 @@ Using 1674530174 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-3.0.4.jar using File::StripNondeterminism::handlers::jar Using 1674530174 as canonical time + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/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/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/lib Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/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/VCFInfoHe 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 @@ -6825,124 +6956,7 @@ 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/l Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/v Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTADecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/hapref/fasta/FASTACodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/ReadsCodecUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/SAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMEncoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMDecoderV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/sam/samV1_0/SAMCodecV1_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/HtsgetBAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMDecoderV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/htsget/htsgetBAMV1_2/HtsgetBAMCodecV1_2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/reads/cram/cramV3_0/CRAMEncoderV3_0.html using File::StripNondeterminism::handlers::javadoc - 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/ibhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFEncoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFDecoderV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_1/VCFCodecV4_1.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFEncoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFDecoderV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv4_0/VCFCodecV4_0.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFEncoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFDecoderV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_3/VCFCodecV3_3.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/vcf/vcfv3_2/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/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 -cf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/codecs/variants/v Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc @@ -6991,7 +7005,215 @@ 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/libhtsjhtsjdk-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 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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/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/SimpleAllele.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Genotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/CommonInfo.html Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::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 + 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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handl Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordDupl Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + 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-ddk-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 @@ -7005,119 +7227,22 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/example/IndicesAreEqual.html using File: Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/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 - 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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/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::hand Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSetIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/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/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CSIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Chunk.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.htm Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc +cf/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/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc @@ -7150,18 +7275,159 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.html using Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/StopWatch.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SortingCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SolexaQualityConverter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SnappyLoader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.SequenceListsDifferException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordWithOrdinal.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SAMRecordPrefetchingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.LocusInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamLocusIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/SamConstants.html using File::StripNondeterminism::handlers::javadoc + NormalizingaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc + using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc + 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/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/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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/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 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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/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/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Chunk.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc + 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 Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PeekableIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc @@ -7198,211 +7464,19 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::jav Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.MultiMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CodeUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/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::Strip 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 - 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc -Nondeterminism::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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordDuplicateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/sicateComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc @@ -7430,14 +7504,42 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFlagField.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriterFactory.html using File::StripNo 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/SAMFileWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/QueryInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/IndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/HtsgetBAMFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSetIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/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/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CustomReaderFactory.ICoc/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 @@ -7453,6 +7555,18 @@ 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 +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/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 @@ -7477,115 +7591,7 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/clers::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/cram/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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc -adoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.InvalidDateException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/al 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 -ram/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-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc @@ -7605,136 +7611,10 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc -ndeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/QueryInterval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/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/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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/constant-values.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/x.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/resources/glass.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/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 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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoderOptions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/HtsDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/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/reads/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsQuery.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/ReadsFormats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/beta/plugin/reads/pi/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc -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/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/ers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc @@ -7749,53 +7629,210 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/SBIIndexWriter.html using 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 + debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeScriptException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeIOException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ProcessExecutor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/PositionalOutputStream.html using File::StripNondeterminism::handlers::javadoc + 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 +amtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgingRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.InvalidDateException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.MultiMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/core/experimental/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/cram/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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/DataSeriustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CRAMBAIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc +doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/encoding/external/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 + 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/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CodeUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/util/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 +es.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java cd debian/libhtsjdk-java-doc chmod a-x usr/share/doc/libhtsjdk-java/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java/changelog.Debian + cd '/build/htsjdk-3.0.4+dfsg' chmod a-x usr/share/doc/libhtsjdk-java-doc/changelog.Debian gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/htsjdk-3.0.4+dfsg' - cd '/build/htsjdk-3.0.4+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-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 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 - 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/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--buildsystem=gradle dh_installdeb -O--buildsystem=gradle install -m0755 -d debian/libhtsjdk-java/DEBIAN @@ -7812,15 +7849,15 @@ chmod 0644 -- debian/libhtsjdk-java/DEBIAN/control chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/control dh_md5sums -O--buildsystem=gradle - install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN install -m0755 -d debian/libhtsjdk-java/DEBIAN + install -m0755 -d debian/libhtsjdk-java-doc/DEBIAN cd debian/libhtsjdk-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhtsjdk-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java/DEBIAN/md5sums chmod 0644 -- debian/libhtsjdk-java-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle - dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. + dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_3.0.4+dfsg-2_all.deb'. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_3.0.4+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../htsjdk_3.0.4+dfsg-2_amd64.buildinfo @@ -7830,12 +7867,14 @@ 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/1251667/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1251667/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/2998534 and its subdirectories -I: Current time: Fri May 19 16:12:34 -12 2023 -I: pbuilder-time-stamp: 1684555954 +I: removing directory /srv/workspace/pbuilder/1251667 and its subdirectories +I: Current time: Sat Jun 22 01:08:40 +14 2024 +I: pbuilder-time-stamp: 1718968120