Diff of the two buildlogs: -- --- b1/build.log 2022-01-16 20:00:19.292909894 +0000 +++ b2/build.log 2022-01-16 21:09:17.632556365 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 18 13:59:11 -12 2023 -I: pbuilder-time-stamp: 1676771951 +I: Current time: Mon Jan 17 10:00:24 +14 2022 +I: pbuilder-time-stamp: 1642363224 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./htsjdk_2.23.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.duRfP1hM/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 22 01:31:19 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.O9vrbQRF/trustedkeys.kbx': General error +gpgv: Signature made Wed Sep 23 03:31:19 2020 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key @@ -42,135 +42,169 @@ dpkg-source: info: applying 120-fix-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1548974/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1256763/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/1256763/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1256763/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,-fixfilepath parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='94240870b1b04b35aedad53b1858425e' - 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='1548974' - PS1='# ' - PS2='> ' + INVOCATION_ID=abd038c089cb402aa9a1f4296b27bb35 + 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=1256763 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/tmp.SbWHY6Yapd/pbuilderrc_sqIV --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.SbWHY6Yapd/b1 --logfile b1/build.log htsjdk_2.23.0+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://85.184.249.68:3128' + 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/tmp.SbWHY6Yapd/pbuilderrc_p8G1 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.SbWHY6Yapd/b2 --logfile b2/build.log htsjdk_2.23.0+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 9 03:46 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1548974/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jan 17 10:01 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 7 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1256763/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -568,7 +602,7 @@ Get: 326 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk-dev amd64 2.10.9-1 [104 kB] Get: 327 http://deb.debian.org/debian bullseye/main amd64 libngs-java amd64 2.10.9-1 [80.4 kB] Get: 328 http://deb.debian.org/debian bullseye/main amd64 scala-library all 2.11.12-4 [9589 kB] -Fetched 450 MB in 5s (88.4 MB/s) +Fetched 450 MB in 12s (36.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -2084,7 +2118,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/htsjdk-2.23.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../htsjdk_2.23.0+dfsg-2_source.changes +hostname: Name or service not known +I: Running cd /build/htsjdk-2.23.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../htsjdk_2.23.0+dfsg-2_source.changes dpkg-buildpackage: info: source package htsjdk dpkg-buildpackage: info: source version 2.23.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -2129,9 +2164,9 @@ 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=16 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=15 jar javadoc Initialized native services in: /build/htsjdk-2.23.0+dfsg/.gradle/native -Using 16 worker leases. +Using 15 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@58670130 Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@58670130 Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d61eccf @@ -2168,11 +2203,11 @@ Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d61eccf Creating new cache for taskHistory, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3340ce58 Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@5f803481 -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[main,5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.004 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@2e3520ca +Putting task artifact state for task ':compileJava' into context took 0.038 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@16cb6f51 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 @@ -2188,7 +2223,7 @@ 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 1.112 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 17.378 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. @@ -2196,40 +2231,40 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 10.989 secs. -:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[main,5,main]) completed. Took 1 mins 24.483 secs. +:processResources (Thread[main,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/htsjdk-2.23.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.014 secs. -:classes (Thread[Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[main,5,main]) completed. Took 0.083 secs. +:classes (Thread[main,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[main,5,main]) completed. Took 0.001 secs. +:debianMavenPom (Thread[main,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 0.005 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.002 secs. It is not up-to-date because: No history is available. Generating pom file /build/htsjdk-2.23.0+dfsg/build/debian/htsjdk.pom -:debianMavenPom (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.128 secs. -:jar (Thread[Task worker for ':' Thread 2,5,main]) started. +:debianMavenPom (Thread[main,5,main]) completed. Took 1.365 secs. +:jar (Thread[main,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 0.029 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.29 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.392 secs. -:javadoc (Thread[Task worker for ':' Thread 2,5,main]) started. +:jar (Thread[main,5,main]) completed. Took 2.957 secs. +:javadoc (Thread[main,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 0.134 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.828 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc''. Working directory: /build/htsjdk-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc @/build/htsjdk-2.23.0+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc'' @@ -2334,9 +2369,9 @@ /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:303: warning - invalid usage of tag {@link #uniqued(boolean)#getIntervals() /build/htsjdk-2.23.0+dfsg/src/main/java/htsjdk/samtools/util/IntervalList.java:322: warning - invalid usage of tag > 100 warnings -:javadoc (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 11.013 secs. +:javadoc (Thread[main,5,main]) completed. Took 59.193 secs. -BUILD SUCCESSFUL in 27s +BUILD SUCCESSFUL in 3m 22s 4 actionable tasks: 4 executed make[1]: Leaving directory '/build/htsjdk-2.23.0+dfsg' jh_build -O--buildsystem=gradle @@ -2347,9 +2382,9 @@ 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=16 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=15 test Initialized native services in: /build/htsjdk-2.23.0+dfsg/.gradle/native -Using 16 worker leases. +Using 15 worker leases. Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@58670130 Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@58670130 Creating new cache for fileHashes, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d61eccf @@ -2379,11 +2414,11 @@ Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7d61eccf Creating new cache for taskHistory, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@3c2dda7c Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7507d96c -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[main,5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.009 secs. -Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@58825bb2 +Putting task artifact state for task ':compileJava' into context took 0.028 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@45cb5307 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 @@ -2399,33 +2434,33 @@ 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 0.898 secs). +Skipping task ':compileJava' as it is up-to-date (took 4.012 secs). :compileJava UP-TO-DATE -:compileJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.019 secs. -:processResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileJava (Thread[main,5,main]) completed. Took 4.468 secs. +:processResources (Thread[main,5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/build/htsjdk-2.23.0+dfsg/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE -:processResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.003 secs. -:classes (Thread[Task worker for ':' Thread 2,5,main]) started. +:processResources (Thread[main,5,main]) completed. Took 0.054 secs. +:classes (Thread[main,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:findScalaAndJavaTypes (Thread[Task worker for ':' Thread 2,5,main]) started. +:classes (Thread[main,5,main]) completed. Took 0.002 secs. +:findScalaAndJavaTypes (Thread[main,5,main]) started. :findScalaAndJavaTypes executing task ':findScalaAndJavaTypes' ... -Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.012 secs. +Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.01 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-2.23.0+dfsg Command: ./scripts/checkScalaAndJavaFiles.sh Successfully started process 'command './scripts/checkScalaAndJavaFiles.sh'' -:findScalaAndJavaTypes (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.038 secs. -:compileTestJava (Thread[Task worker for ':' Thread 2,5,main]) started. +:findScalaAndJavaTypes (Thread[main,5,main]) completed. Took 0.22 secs. +:compileTestJava (Thread[main,5,main]) started. :compileTestJava executing task ':compileTestJava' ... Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. @@ -2438,7 +2473,7 @@ Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Passing through org.jsr-305:jsr305:jar:0.x -Up-to-date check for task ':compileTestJava' took 2.152 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 11.627 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. @@ -2446,36 +2481,36 @@ Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. -:compileTestJava (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 11.61 secs. -:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) started. +:compileTestJava (Thread[main,5,main]) completed. Took 42.815 secs. +:processTestResources (Thread[main,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 0.503 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 6.071 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 1.196 secs. -:testClasses (Thread[Task worker for ':' Thread 2,5,main]) started. +:processTestResources (Thread[main,5,main]) completed. Took 7.39 secs. +:testClasses (Thread[main,5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.001 secs. -:testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main]) started. +:testClasses (Thread[main,5,main]) completed. Took 0.001 secs. +:testWithDefaultReference (Thread[main,5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... -Putting task artifact state for task ':testWithDefaultReference' into context took 0.0 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.474 secs. It is not up-to-date because: +Putting task artifact state for task ':testWithDefaultReference' into context took 0.002 secs. +Up-to-date check for task ':testWithDefaultReference' took 1.264 secs. It is not up-to-date because: Task.upToDateWhen is false. -Finished generating test XML results (0.001 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.002 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.019 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 0.615 secs. -:test (Thread[Task worker for ':' Thread 2,5,main]) started. +Finished generating test html results (0.103 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[main,5,main]) completed. Took 1.888 secs. +:test (Thread[main,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 0.068 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.233 secs. It is not up-to-date because: Task.upToDateWhen is false. -Starting process 'Gradle Test Executor 1'. Working directory: /build/htsjdk-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath6907843494501589598txt -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-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3115979571208320730txt -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. @@ -2486,13 +2521,13 @@ Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingMultiSampleVCF STANDARD_ERROR - WARNING 2023-02-18 14:01:27 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:12:27 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 2023-02-18 14:01:27 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:12:27 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 2023-02-18 14:01:27 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:12:27 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 @@ -2518,7 +2553,7 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms @@ -2527,13 +2562,13 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+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[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstCompleteContigRead runtime: 1ms + testFirstCompleteContigRead runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstCompleteContigRead runtime: 0ms @@ -2542,28 +2577,28 @@ testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 1ms + testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR testFirstElementOfIterator runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testFirstElementOfIterator runtime: 0ms + testFirstElementOfIterator runtime: 9ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstElementOfIterator[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstElementOfIterator runtime: 0ms @@ -2581,7 +2616,7 @@ testFirstSequence runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequence[4](/build/htsjdk-2.23.0+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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstSequenceExtended runtime: 0ms @@ -2599,31 +2634,31 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 8ms + testLastCompleteContigRead runtime: 25ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 6ms + testLastCompleteContigRead runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 2ms + testLastCompleteContigRead runtime: 7ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 2ms + testLastCompleteContigRead runtime: 7ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 13ms + testLastCompleteContigRead runtime: 17ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 11ms + testLastCompleteContigRead runtime: 14ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testLastCompleteContigRead runtime: 11ms + testLastCompleteContigRead runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 3ms + testLastCompleteContigRead runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testLastCompleteContigRead runtime: 3ms + testLastCompleteContigRead runtime: 12ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastOfChr20[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testFirstOfChr1 runtime: 0ms @@ -2641,31 +2676,31 @@ testFirstOfChr1 runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 1ms + testNextElementOfIterator runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 11ms + testNextElementOfIterator runtime: 14ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 10ms + testNextElementOfIterator runtime: 14ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testNextElementOfIterator runtime: 10ms + testNextElementOfIterator runtime: 14ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testNextElementOfIterator[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testNextElementOfIterator runtime: 2ms + testNextElementOfIterator runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testOpenFile[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testOpenFile runtime: 0ms @@ -2704,7 +2739,7 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadStartingInCenterOfFirstLine runtime: 0ms @@ -2725,7 +2760,7 @@ testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 1ms + testReadStartingInCenterOfMiddleLine runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -2743,46 +2778,46 @@ testReadThroughEndOfContig runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 3ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 4ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReset runtime: 2ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[3](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 2ms + testReset runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 12ms + testReset runtime: 16ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[5](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 11ms + testReset runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[6](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReset runtime: 11ms + testReset runtime: 15ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[7](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 3ms + testReset runtime: 5ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReset[8](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta, /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReset runtime: 3ms + testReset runtime: 5ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2023-02-18 14:02:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:15:13 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@2d57c6bb, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2023-02-18 14:02:18 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@240f06a6, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2022-01-17 10:15:13 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 2023-02-18 14:02:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:15:13 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 2023-02-18 14:02:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:15:13 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 2023-02-18 14:02:18 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 10:15:13 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 @@ -3842,17 +3877,17 @@ NoCoordinateCount= 279 Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.7154515541807258100.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.5255291075197305934.bai - #BAMIndexWriterTest diff /tmp/javaBai.7154515541807258100.bai /tmp/cBai.5255291075197305934.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.1189589672921770419.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.3653902830125767564.bai + #BAMIndexWriterTest diff /tmp/javaBai.1189589672921770419.bai /tmp/cBai.3653902830125767564.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.10965845939466245241.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.1369591468068011715java.bai - #BAMIndexWriterTest diff /tmp/javaBai.1369591468068011715java.bai.txt /tmp/cBai.10965845939466245241.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.3933807344116455777.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.15110707357628192332java.bai + #BAMIndexWriterTest diff /tmp/javaBai.15110707357628192332java.bai.txt /tmp/cBai.3933807344116455777.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT - 0ms to write + 15ms to write Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT 0ms to write @@ -3860,28 +3895,32 @@ 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.17379519537120836245.gz + Creating file /tmp/BCOST.5551435146848201165.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.11738318444828442577.gz + Creating file /tmp/testCustomDeflater.12247555801560666553.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.8992119013972155149.gz + Creating file /tmp/BCOST.6579059708952175836.gz + Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2023-02-18 14:03:59 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2023-02-18 14:03:59 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2022-01-17 10:21:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2022-01-17 10:21:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testContigNotFoundInRef STANDARD_ERROR - WARNING 2023-02-18 14:04:08 ReferenceSource Sequence not found: chrSheila + WARNING 2022-01-17 10:21:54 ReferenceSource Sequence not found: chrSheila Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2023-02-18 14:04:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2023-02-18 14:04:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2022-01-17 10:21:56 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2022-01-17 10:21:56 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testUnsorted STANDARD_ERROR - WARNING 2023-02-18 14:04:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2023-02-18 14:04:08 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2022-01-17 10:21:56 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2022-01-17 10:21:56 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + Gradle is still running, please be patient... + Gradle is still running, please be patient... + Gradle is still running, please be patient... Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference STANDARD_ERROR @@ -4591,68 +4630,66 @@ Resetting tmpdir Resetting tmpdir Resetting tmpdir - -Gradle suite > Gradle test > htsjdk.samtools.util.DiskBackedQueueTest.spillToDiskTest STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.66859798451740323.tmp - -Gradle suite > Gradle test STANDARD_ERROR Resetting tmpdir +Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.4800780698729432036.tmp + Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[0](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[2](src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[3](src/test/resources/htsjdk/samtools/reference/crlf.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[0](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[1](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[2](src/test/resources/htsjdk/samtools/reference/header_with_white_space.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testCreate[3](src/test/resources/htsjdk/samtools/reference/crlf.fasta) STANDARD_ERROR - WARNING 2023-02-18 14:19:51 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2022-01-17 11:03:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.tribble.gff.Gff3CodecTest.basicDecodeTest[2](src/test/resources/htsjdk/tribble/gff/ref_ASM69900v1_top_level.small.gff3, 185) STANDARD_ERROR - WARNING 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:41 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 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:41 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 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 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 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 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 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2023-02-18 14:19:54 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2022-01-17 11:03:42 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 2023-02-18 14:19:55 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2022-01-17 11:03:43 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 2023-02-18 14:19:55 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2022-01-17 11:03:43 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.samtools.util.IOUtilTest.testDeleteSingleWithDeletePaths STANDARD_ERROR Could not delete file tmp - Could not delete file file15247077708186568453.bad + Could not delete file file4852041112487582943.bad Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 50 milliseconds - Queried for the same 100-length mapping 78986606 times in 10 seconds. + Time to construct a tree with 50000 nodes: 146 milliseconds + Queried for the same 100-length mapping 59154818 times in 10 seconds. Gradle suite > Gradle test > htsjdk.samtools.filter.JavascriptSamRecordFilterTest.testJavascriptFilters[0](unsorted.sam, samFilter01.js, 8) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release @@ -4661,96 +4698,96 @@ Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > htsjdk.samtools.liftover.LiftOverTest.loadLiftOverFromInputStream[0](chr3:50911035-50911051 + ., null) STANDARD_ERROR - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2022-01-17 11:04:14 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2022-01-17 11:04:14 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2022-01-17 11:04:14 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) @@ -4910,7 +4947,7 @@ 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 2023-02-18 14:20:09 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2022-01-17 11:04:14 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 @@ -4932,135 +4969,135 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT - b d e - a c + b + a Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2023-02-18 14:20:46 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2022-01-17 11:05:13 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 2023-02-18 14:20:46 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2022-01-17 11:05:13 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 2023-02-18 14:20:46 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2022-01-17 11:05:13 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 2023-02-18 14:20:46 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2022-01-17 11:05:13 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 2023-02-18 14:20:46 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2022-01-17 11:05:13 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2023-02-18 14:20:46 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2023-02-18 14:20:46 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2022-01-17 11:05:13 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2022-01-17 11:05:13 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 2023-02-18 14:20:46 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.9685683931089883983..cram - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.4108070063932840380..cram + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension354714231486945724.cram + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension1726891160848037775.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.16686144060359002072.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.8135483207724259831.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 2023-02-18 14:20:46 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension14040360399950123332.cram - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension10218671686944985885.cram + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension14299918980739358024 + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension11530060087230575151 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension10036931672826817498.png + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension4951585933545961436.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://7dd4edeb-77ab-478c-8d2f-b8737dcebb39/work/testMakeWriterPathsam + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://3cdc1516-3fc2-4f9f-bf4a-6bc222408927/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 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://945f30af-fa47-4e64-8789-c69ca2b01da7/work/testMakeWriterPathbam + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c6bb95a3-a229-4f8c-872b-4f39fdaa850c/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 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://75a9e01c-74a8-4009-a512-b438f72ffa2f/work/testMakeWriterPathcram + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://d9565e49-e781-4940-bdc3-22f27bd0c6b0/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 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://13e989b6-9d64-4d9c-99c7-523ec66e4c17/work/testMakeWriterPathsam + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2e35e0ea-9161-48c8-acf3-1f9458f6e80a/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 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://fbf02c24-2ee0-4a39-b5b7-2d7d8c865b5a/work/testMakeWriterPathbam + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c5879b36-d37a-43d7-b397-292fddc9e2ce/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 2023-02-18 14:20:46 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://bba6fefe-121e-4cc4-8763-2c865f0682d0/work/testMakeWriterPathcram + INFO 2022-01-17 11:05:13 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://4759e62c-5a4e-42ee-8359-ee608d1f2224/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), SAMSequenceRecord(name=chr1,length=0,dict_index=0,assembly=null), false) STANDARD_ERROR - ERROR 2023-02-18 14:20:47 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2022-01-17 11:05:15 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-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai) STANDARD_ERROR - WARNING 2023-02-18 14:20:47 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam - WARNING 2023-02-18 14:20:47 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2022-01-17 11:05:15 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam + WARNING 2022-01-17 11:05:15 SamFiles The index file /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai was found by resolving the canonical path of a symlink: /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/symlink_without_linked_index.bam -> /build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.customReaderFactoryTest STANDARD_ERROR - INFO 2023-02-18 14:20:49 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2023-02-18 14:20:49 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2023-02-18 14:20:49 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2023-02-18 14:20:49 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2022-01-17 11:05:18 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2022-01-17 11:05:18 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2022-01-17 11:05:18 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2022-01-17 11:05:18 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 2023-02-18 14:20:49 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2022-01-17 11:05:18 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 2023-02-18 14:20:49 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... - INFO 2023-02-18 14:20:49 SamReaderFactoryTest Finished queries in 45ms + INFO 2022-01-17 11:05:18 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 2022-01-17 11:05:19 SamReaderFactoryTest Finished queries in 222ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2023-02-18 14:20:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2022-01-17 11:05:19 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 2023-02-18 14:20:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2022-01-17 11:05:19 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 2023-02-18 14:20:49 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2022-01-17 11:05:19 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. Gradle suite > Gradle test > htsjdk.samtools.SamSpecIntTest.testBamIntegers[1](inttest_large_coordinates.bam) STANDARD_ERROR - WARNING 2023-02-18 14:20:50 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2023-02-18 14:20:50 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2022-01-17 11:05:20 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2022-01-17 11:05:20 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 2023-02-18 14:20:50 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2023-02-18 14:20:50 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2022-01-17 11:05:20 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2022-01-17 11:05:20 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -5073,53 +5110,53 @@ Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 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 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 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 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:50 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:23 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 2023-02-18 14:20:51 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2022-01-17 11:05:23 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. Gradle suite > Gradle test > htsjdk.samtools.util.SortingCollectionTest STANDARD_ERROR Resetting tmpdir @@ -5143,95 +5180,94 @@ Resetting tmpdir Resetting tmpdir -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[0](A, 0, 0, 0, 0, 0, [B@5ee44900) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[0](A, 0, 0, 0, 0, 0, [B@486aafc6) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[1](A, 0, 0, 0, 1, 0, [B@7c0caa45) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[1](A, 0, 0, 0, 1, 0, [B@31763f0d) STANDARD_OUT A:TCGN C:AGTN G:ACTN T:ACGN N:ACGT a:TCGN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[2](A, 0, 1, 2, 3, 4, [B@3168550) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[2](A, 0, 1, 2, 3, 4, [B@7b5e5a71) STANDARD_OUT A:NTGC C:AGTN G:ACTN T:ACGN N:ACGT a:NTGC c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[3](A, 0, 4, 3, 2, 1, [B@20aae1df) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[3](A, 0, 4, 3, 2, 1, [B@27b0ecdc) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[4](C, 0, 0, 0, 0, 0, [B@5b548f82) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[4](C, 0, 0, 0, 0, 0, [B@76d4dddc) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[5](C, 0, 0, 0, 1, 0, [B@7c6b966e) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[5](C, 0, 0, 0, 1, 0, [B@411188) STANDARD_OUT A:CGTN C:TAGN G:ACTN T:ACGN N:ACGT a:CGTN c:TAGN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[6](C, 1, 0, 2, 3, 4, [B@12a8ed56) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[6](C, 1, 0, 2, 3, 4, [B@2b6c10a1) STANDARD_OUT A:CGTN C:NTGA G:ACTN T:ACGN N:ACGT a:CGTN c:NTGA g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[7](C, 4, 0, 3, 2, 1, [B@78f47607) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[7](C, 4, 0, 3, 2, 1, [B@3dfaed43) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[8](G, 0, 0, 0, 0, 0, [B@3a34cc65) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[8](G, 0, 0, 0, 0, 0, [B@3d544a23) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[9](G, 0, 0, 0, 1, 0, [B@5b81e2d4) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[9](G, 0, 0, 0, 1, 0, [B@19e6afee) STANDARD_OUT A:CGTN C:AGTN G:TACN T:ACGN N:ACGT a:CGTN c:AGTN g:TACN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[10](G, 1, 2, 0, 3, 4, [B@326886e5) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[10](G, 1, 2, 0, 3, 4, [B@45e3293d) STANDARD_OUT A:CGTN C:AGTN G:NTCA T:ACGN N:ACGT a:CGTN c:AGTN g:NTCA t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[11](G, 4, 3, 0, 2, 1, [B@11860f00) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[11](G, 4, 3, 0, 2, 1, [B@7cfe5c9e) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[12](T, 0, 0, 0, 0, 0, [B@50beeeb9) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[12](T, 0, 0, 0, 0, 0, [B@31481934) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[13](T, 0, 0, 0, 0, 1, [B@1a5e644d) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[13](T, 0, 0, 0, 0, 1, [B@379ac088) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:NACG N:ACGT a:CGTN c:AGTN g:ACTN t:NACG n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[14](T, 1, 2, 3, 0, 4, [B@23624f23) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[14](T, 1, 2, 3, 0, 4, [B@5831a936) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:NGCA N:ACGT a:CGTN c:AGTN g:ACTN t:NGCA n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[15](T, 4, 3, 2, 0, 1, [B@7dd02bb6) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[15](T, 4, 3, 2, 0, 1, [B@730695d5) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[16](N, 0, 0, 0, 0, 0, [B@7f55023d) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[16](N, 0, 0, 0, 0, 0, [B@1aef3b73) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[17](N, 0, 0, 0, 1, 0, [B@1cf30de2) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[17](N, 0, 0, 0, 1, 0, [B@24a396f1) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:TACG a:CGTN c:AGTN g:ACTN t:ACGN n:TACG -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[18](N, 1, 2, 3, 4, 0, [B@68c41411) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[18](N, 1, 2, 3, 4, 0, [B@1f855e69) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:TGCA a:CGTN c:AGTN g:ACTN t:ACGN n:TGCA -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[19](N, 4, 3, 2, 1, 0, [B@34b710cb) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[19](N, 4, 3, 2, 1, 0, [B@32888f79) STANDARD_OUT A:CGTN C:AGTN G:ACTN T:ACGN N:ACGT a:CGTN c:AGTN g:ACTN t:ACGN n:ACGT -Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[93](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2023-02-18 14:20:53 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - Gradle is still running, please be patient... +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[32](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2022-01-17 11:05:30 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. Gradle Test Executor 1 finished executing tests. -Finished generating test XML results (0.282 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/test +Finished generating test XML results (2.523 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (0.317 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/test -:test (Thread[Task worker for ':' Thread 2,5,main]) completed. Took 21 mins 55.364 secs. +Finished generating test html results (2.443 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/test +:test (Thread[main,5,main]) completed. Took 57 mins 30.077 secs. -BUILD SUCCESSFUL in 22m 14s +BUILD SUCCESSFUL in 58m 48s 6 actionable tasks: 5 executed, 1 up-to-date make[1]: Leaving directory '/build/htsjdk-2.23.0+dfsg' create-stamp debian/debhelper-build-stamp @@ -5337,12 +5373,6 @@ Using 1600780451 as canonical time Normalizing debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar using File::StripNondeterminism::handlers::jar Using 1600780451 as canonical time - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriterManager.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.StaticallyTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.SiteWriter.html using File::StripNondeterminism::handlers::javadoc @@ -5379,10 +5409,14 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCFVersion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism: Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Codec.LazyData.html using File::StripNondeterminism::ha Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFormatHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFilterHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFEncoder.html using File::StripNondeterminism::handlers::javadoc @@ -5425,64 +5459,78 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/CommonInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/Allele.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsj Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ByteArraySeekableStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TestUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::h Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.PairOrientation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMLineParser.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamIndexes.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFormatException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFlagField.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondendlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc +terminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.PLAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.GQAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.DPAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.ADAccessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.Accessor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/IntGenotypeFieldAccessors.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SamRecordFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/ReadNameFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/OverclippedReadFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/JavascriptSamRecordFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/IntervalFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqWriterFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/r Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriterImpl.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriterFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFileValidator.ValidationMetrics.html using File::StripNondeterminism::handlers::javadoc @@ -5518,117 +5566,10 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CustomReaderFactory.ICustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CustomReaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CSIIndex.html usi:handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2LazyGenotypesDecoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.Decoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2GenotypeFieldDecoders.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Decoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/bcf2/BCF2Codec.SitesInfoForDecoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SequenceUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamRecordWithOrdinal.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamRecordTrackingBuffer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamRecordIntervalIteratorFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamLocusIterator.RecordAndOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamLocusIterator.LocusInfo.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamLocusIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SamConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RuntimeScriptException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RuntimeIOException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProgressLoggerInterface.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProgressLogger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProcessExecutor.ExitStatusAndOutput.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Md5CalculatingInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Log.LogLevel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Log.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Iso8601Date.html using Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/ValidationStringency.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TextTagCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TextCigarCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/TagValueAndUnsignedArrayFlag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIterator.RecordRangeInfo.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SRAFileReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMValidationError.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMValidationError.Severity.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMValidationError.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordDuplicateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMReadGroupRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamRedk-java-doc/api/htsjdk/variant/variantcontext/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.OutputType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/VariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/SortingVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/Options.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CSIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMFileReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMCRAIIndexer.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMContainerStreamWriter.html using File::StripNondeterminism::handlers::javadoc @@ -5637,14 +5578,7 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CoordinateSortedPairInfoMap.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CigarOperator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CigarElement.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Cigar.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Chunk.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BrowseableBAMIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexContent.BinList.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexContent.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexBuilder.FeatureToBeIndexed.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Cigar.html usi Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinningIndexBuilder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinList.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BinaryTagCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Bin.html using File::StripNondeterminism::handlers::javadoc @@ -5677,10 +5611,142 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAAlignmentIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAAccession.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/ReferenceCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadng File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CRAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/UserPasswordInput.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekablePathStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableMemoryStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableHTTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFTPStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableFileStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/SeekableBufferedStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ReadableSeekableStreamByteChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ISeekableStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/seekablestream/ByteArraySeek Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.SQBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SQTagUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SecondaryAlignmentSkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndexWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SBIIndex.Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTextHeaderCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTestUtil.SanityCheckFailedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTagUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSortOrderChecker.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceDictionaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMSequenceDictionary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordSetBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordQueryNameComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordQueryHashComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordDuplicateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecordComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecord.SAMTagAndValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMReadGroupRecord.PlatformValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMReadGroupRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReaderFactory.Option.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.ReaderImplementation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.PrimitiveSamReaderToSamReaderAdapter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMProgramRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.SetMateInfoIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.PairOrientation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamPairUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequence.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/IndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaReferenceWriterBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/FastaReferenceWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/VersionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/StringHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/MetricsFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/MetricBase.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/metrics/Header.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/LiftOver.PartialLiftover.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/liftover/LiftOver.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/WholeGenomeReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Tuple.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TrimmingUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TestUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TerminatorlessBlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/TempStreamFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StopWatch.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SortingLongCollection.html using 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/EdgingRecordAndOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/EdgeReadIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/DiskBackedQueue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/DelegatingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/DateParser.InvalidDateException.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CollectionUtil.MultiMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.Factory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CollectionUtil.DefaultingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CollectionUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CodeUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedStreamConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BinaryCodec.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AsyncBufferedIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AsyncBlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc @@ -5699,7 +5765,136 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/nio/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/nio/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/nio/DeleteOnExitPathHook.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/package-tree.html using File::StripNondete Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/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-doc/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-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/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-doc/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-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/RAWExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/RANSExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/LZMAExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/CramVersions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/CRAMVersion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/Utils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/PeekableIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/OverlapDetector.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Murmur3.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/MergingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Md5CalculatingOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTreeMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.ValuesIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.OverlapIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/lief/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc +ng File::StripNondeterminism::handlers::javadoc + Normalizing 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File::StripNondeterminism::handlers::javadoc +-java-doc/api/htsjdk/samtools/SAMLineParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamInputResource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamIndexes.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMHeaderRecordComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFormatException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFlagField.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFlag.html using File::StripNondeterminism::handlers::javadoc +bhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc +ableStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.SAMLocusAndReference.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/SamLocusAndReferenceIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFileWalker.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFileFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/reference/ReferenceSequenceFile.html using File::StripNondeterminism::handlers::javadoc +rminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPStream.html using File::StripNondeterminism::handlers::javadoc @@ -5708,56 +5903,26 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/WholeReadClippedFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/TagFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SolexaNoiseFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SecondaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/SamRecordFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/ReadNameFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/OverclippedReadFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/NotPrimaryAlignmentFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/MappingQualityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/JavascriptSamRecordFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/IntervalKeepPairFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/IntervalFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/InsertSizeFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FilteringSamIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/FailsVendorReadQualityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/DuplicateReadFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AlignedFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AggregateFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/filter/AbstractJavascriptFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libht Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqReader.LineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqConstants.FastqExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/FastqConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/BasicFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/AsyncFastqWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/PrintReadsExample.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/example/ExampleSamUsage.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAMException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/CRAIEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/BAIEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceContextType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/ReferenceContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/GaveUpException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/EnaRefService.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/CRAMReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/LTF8.html using File::StripNondeterminism::handlers::javadoc +c + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RuntimeEOFException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ResourceLimitedMapFunctor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ResourceLimitedMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/RelativeIso8601Date.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityEncodingDetector.FileContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/QualityEncodingDetector.html using File::StripNondeterminism::handlers::javadoc +ibhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/ITF8.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/InputStreamUtils.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/DefaultBitOutputStream.html using File::StripNondeterminism::handlers::javadoc @@ -5775,13 +5940,11 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/ContentDigests.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/Encodingandlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StringUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StringLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/StopWatch.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SortingLongCollection.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SortingCollection.Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/SortingCollection.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/CRAMEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/CRAMCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/ByteArrayLenEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/DataSeriesWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/writer/CramRecordWriter.html using File::StripNondeterminism::handlers::javadoc @@ -5805,202 +5968,7 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/DataSeriesReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/CramRecordReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/SubexponentialIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/GammaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CoreCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/CanonicalHuffmanByteEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/BetaIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/BetaIntegerCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/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-doc/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-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParamsCalculator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/coaderAdapter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.PrimitiveSamReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.Indexing.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamReader.AssertingIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.ValuesIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.RevIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.OverlapIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.Node.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.FwdIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalListWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalListReferenceSequenceMask.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalList.IntervalMergerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalList.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalCoordinateComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Interval.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/HttpUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Histogram.Bin.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Histogram.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.IndexEntry.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.GZIIndexer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/GZIIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FormatUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FileExtensions.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FileAppendStreamLRUCache.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FastqQualityFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/FastLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CloserUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CloseableIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CigarUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BufferedLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockGunzipper.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalUtil.IntervalCombiner.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IntervalTreeMap.html using File::StripNondeterminism::handlers::javadoc -sjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/fastq/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/RANS.ORDER.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/RANS.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/common/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/SliceFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CramSpanContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CRAMReferenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CramIO.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CramContainerIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CramContainerHeaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/ContainerFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/build/CompressionHeaderFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SubstitutionMatrix.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/SliceBlocks.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/Slice.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/ReadTag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/EncodingID.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::Ssamtools/util/BlockCompressedOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.FileTermination.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.DecompressedBlock.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/BlockCompressedFilePointerUtil.html using File::StripNondeterminism::handlers::javadoc -re/huffmanUtils/HuffmanParams.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanBitCode.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/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-doc/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-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombRiceIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombLongEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/experimental/GolombIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/package-tree.html using File::StripNondeterminism::handlers::javadoc -tripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/BinaryFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/s Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.Iterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixIteratorLineReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/SynchronousLineReader.html using File::StripNondeterminism::handlers::javadoc @@ -6008,7 +5976,46 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/Positional.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/LongLineBufferedReader.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/LineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tri Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/help-doc.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::ja Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/help-doc.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/overview-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/index.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/allclasses.html using File::StripNondeterminism::handlers::javadoc @@ -6058,7 +6065,86 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIDHeaderLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderVersion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::ja Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineTranslator.html using File::StripNondeterminism::handlers::ja Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/EncodingDescriptor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/DataSeriesType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/DataSeries.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CramHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CRAMCompressionRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/ContainerHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/Container.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressorCache.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/CompressionHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/AlignmentSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/AlignmentContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/BlockContentType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/BlockCompressionMethod.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/structure/block/Block.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/TimeRandomAccessFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/apps/TimeChannel.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleIndexedFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.UnableToReadIndexFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.UnableToCreateCorrectIndexType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.TabixReaderFailure.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.MalformedFeatureFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InvalidHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InvalidDecodeLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.InternalCodecException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.FeatureFileDoesntExist.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.CorruptedIndexFile.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TribbleException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/Tribble.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/TabixFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/SimpleFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/NameAwareCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/MutableFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureCodecHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/FeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/CloseableTribbleIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/BinaryFeatureCodec.html using File:vadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.HEADER_FIELDS.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeader.html using File::StripNondeterminism::handlers::javadoc +amtools/cram/encoding/external/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalLongEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalIntegerEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ExternalByteArrayCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/external/ByteArrayStopEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/core/package-summary.html using File::StripNondeterminism::handlers::javadoc +vadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalTreeIndex.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalTree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalIndexCreator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/Interval.html using File::StripNondeterminism::handlers::javadoc @@ -6096,74 +6182,24 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/annotation/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/annotation/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/annotation/Strand.html using File::StripNondeterminism::handlers::javadoc -vadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFHeaderLineCount.html using File::StripNondeterminism::handlers::javadoc -bble/readers/LineIteratorImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/LineIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/AsciiLineReaderIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/AsciiLineReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/URLHelperFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/URLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TPair64.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TIntv.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.TIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/TabixUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/RemoteURLHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/ParsingUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/MathUtils.RunningStat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/MathUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/LittleEndianOutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/LittleEndianInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/HTTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/FTPHelper.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/IntervalList/IntervalListCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/TribbleIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/MutableIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.IndexBalanceApproach.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexFactory.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/IndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/Index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/DynamicIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/Block.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.IndexType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.BlockStats.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/AbstractIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/TabixFormat.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/StreamBasedTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/tabix/AllRefsTabixIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndexCreator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/linear/LinearIndex.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/index/interval/IntervalTreeIndex.ChrIndex.html using File::StripNondeterminism::handlers::javadoc +:StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AsciiFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureReader.ComponentMethods.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/AbstractFeatureCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.TPair64.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/TabixReader.TIndex.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-2.23.0+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-2.23.0+dfsg' + cd '/build/htsjdk-2.23.0+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 @@ -6194,8 +6230,8 @@ dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/libhtsjdk-java .. dpkg-deb --root-owner-group --build debian/libhtsjdk-java-doc .. -dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_2.23.0+dfsg-2_all.deb'. dpkg-deb: building package 'libhtsjdk-java-doc' in '../libhtsjdk-java-doc_2.23.0+dfsg-2_all.deb'. +dpkg-deb: building package 'libhtsjdk-java' in '../libhtsjdk-java_2.23.0+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../htsjdk_2.23.0+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6203,12 +6239,14 @@ 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/1256763/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1256763/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/1548974 and its subdirectories -I: Current time: Sat Feb 18 14:23:23 -12 2023 -I: pbuilder-time-stamp: 1676773403 +I: removing directory /srv/workspace/pbuilder/1256763 and its subdirectories +I: Current time: Mon Jan 17 11:09:16 +14 2022 +I: pbuilder-time-stamp: 1642367356