Diff of the two buildlogs: -- --- b1/build.log 2021-07-25 17:29:23.841352837 +0000 +++ b2/build.log 2021-07-25 18:13:58.773232298 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 27 11:08:24 -12 2022 -I: pbuilder-time-stamp: 1661641704 +I: Current time: Mon Jul 26 07:29:29 +14 2021 +I: pbuilder-time-stamp: 1627234169 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.tMqKqEuh/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 22 01:31:19 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.3OiOE3qz/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/9676/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25642/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +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/25642/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25642/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='9676' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=25642 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.MIoc04BtYq/pbuilderrc_em4j --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MIoc04BtYq/b1 --logfile b1/build.log htsjdk_2.23.0+dfsg-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.MIoc04BtYq/pbuilderrc_S5wA --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.MIoc04BtYq/b2 --logfile b2/build.log --extrapackages usrmerge htsjdk_2.23.0+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Feb 7 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Feb 7 2021 more - -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount - -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 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 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 26 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Feb 7 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Feb 7 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/9676/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Feb 8 04:38 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more + -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 26 07:29 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 24 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/25642/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -566,7 +600,7 @@ Get: 324 http://deb.debian.org/debian bullseye/main arm64 libngs-sdk-dev arm64 2.10.9-1 [91.9 kB] Get: 325 http://deb.debian.org/debian bullseye/main arm64 libngs-java arm64 2.10.9-1 [80.4 kB] Get: 326 http://deb.debian.org/debian bullseye/main arm64 scala-library all 2.11.12-4 [9589 kB] -Fetched 428 MB in 36s (11.9 MB/s) +Fetched 428 MB in 28s (15.4 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 ... 19646 files and directories currently installed.) @@ -2073,8 +2107,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1430 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 41603 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. 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: Temporary failure in name resolution +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 @@ -2115,16 +2186,16 @@ install -d /build/htsjdk-2.23.0\+dfsg/debian/.debhelper/generated/_source/home jh_linkjars -O--buildsystem=gradle debian/rules override_dh_auto_build -make[1]: Entering directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt binnengegaan 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=8 jar javadoc Initialized native services in: /build/htsjdk-2.23.0+dfsg/.gradle/native Using 8 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@4cc61eb1 -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@4cc61eb1 -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@66eb985d +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@2d8f2f3a +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@2d8f2f3a +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@6a9287b1 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access using Lookup on org.gradle.internal.reflect.JavaMethod (file:/usr/share/gradle/lib/gradle-base-services-4.4.1.jar) to class java.lang.ClassLoader WARNING: Please consider reporting this to the maintainers of org.gradle.internal.reflect.JavaMethod @@ -2132,7 +2203,7 @@ WARNING: All illegal access operations will be denied in a future release Starting Build Compiling initialization script '/build/htsjdk-2.23.0+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. -Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@2b4d4327 +Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@16da1abc Compiling initialization script '/build/htsjdk-2.23.0+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle' using BuildScriptTransformer. @@ -2152,17 +2223,17 @@ Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : -Creating new cache for annotation-processors, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@2697c156 +Creating new cache for annotation-processors, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@533d7c61 Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] -Creating new cache for resourceHashesCache, path /build/htsjdk-2.23.0+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@66eb985d -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@3d405fe5 -Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@20163008 -:compileJava (Thread[Task worker for ':',5,main]) started. +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@6a9287b1 +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@52c6e959 +Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@60ef30b1 +:compileJava (Thread[main,5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.013 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@1b34a54 +Putting task artifact state for task ':compileJava' into context took 0.014 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@58a7ca42 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 @@ -2178,7 +2249,7 @@ 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 2.754 secs. It is not up-to-date because: +Up-to-date check for task ':compileJava' took 4.449 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. @@ -2186,40 +2257,40 @@ 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 ':',5,main]) completed. Took 33.809 secs. -:processResources (Thread[Task worker for ':',5,main]) started. +:compileJava (Thread[main,5,main]) completed. Took 47.917 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 ':',5,main]) completed. Took 0.021 secs. -:classes (Thread[Task worker for ':',5,main]) started. +:processResources (Thread[main,5,main]) completed. Took 0.016 secs. +:classes (Thread[main,5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. -:classes (Thread[Task worker for ':',5,main]) completed. Took 0.002 secs. -:debianMavenPom (Thread[Task worker for ':',5,main]) started. +:classes (Thread[main,5,main]) completed. Took 0.003 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 0.009 secs. It is not up-to-date because: +Up-to-date check for task ':debianMavenPom' took 0.003 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 ':',5,main]) completed. Took 0.51 secs. -:jar (Thread[Task worker for ':',5,main]) started. +:debianMavenPom (Thread[main,5,main]) completed. Took 0.364 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 0.131 secs. It is not up-to-date because: +Up-to-date check for task ':jar' took 0.082 secs. It is not up-to-date because: No history is available. -:jar (Thread[Task worker for ':',5,main]) completed. Took 1.271 secs. -:javadoc (Thread[Task worker for ':',5,main]) started. +:jar (Thread[main,5,main]) completed. Took 1.467 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 0.401 secs. It is not up-to-date because: +Up-to-date check for task ':javadoc' took 0.409 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-arm64/bin/javadoc''. Working directory: /build/htsjdk-2.23.0+dfsg Command: /usr/lib/jvm/java-11-openjdk-arm64/bin/javadoc @/build/htsjdk-2.23.0+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-arm64/bin/javadoc'' @@ -2324,15 +2395,15 @@ /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 ':',5,main]) completed. Took 45.759 secs. +:javadoc (Thread[main,5,main]) completed. Took 46.039 secs. -BUILD SUCCESSFUL in 1m 33s +BUILD SUCCESSFUL in 1m 54s 4 actionable tasks: 4 executed -make[1]: Leaving directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt verlaten jh_build -O--buildsystem=gradle rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log debian/rules override_dh_auto_test -make[1]: Entering directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt binnengegaan # testng bug 895886: testng: jcommander classes not found dh_auto_build -- test mkdir -p .gradle/init.d @@ -2349,7 +2420,7 @@ WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Starting Build -Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@41b13f3d +Creating new cache for metadata-1.1/results, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@62b93086 Settings evaluated using settings file '/build/htsjdk-2.23.0+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/htsjdk-2.23.0+dfsg/build.gradle'. Included projects: [root project 'htsjdk'] @@ -2369,11 +2440,11 @@ 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@66eb985d 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@4ebed2b3 Creating new cache for outputFiles, path /build/htsjdk-2.23.0+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@e5864c2 -:compileJava (Thread[main,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) started. :compileJava executing task ':compileJava' ... -Putting task artifact state for task ':compileJava' into context took 0.012 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@3b77940f +Putting task artifact state for task ':compileJava' into context took 0.026 secs. +Creating new cache for metadata-2.36/module-metadata, path /build/htsjdk-2.23.0+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@18dec74f 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 @@ -2389,33 +2460,33 @@ 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 1.653 secs). +Skipping task ':compileJava' as it is up-to-date (took 2.713 secs). :compileJava UP-TO-DATE -:compileJava (Thread[main,5,main]) completed. Took 1.797 secs. -:processResources (Thread[main,5,main]) started. +:compileJava (Thread[Task worker for ':',5,main]) completed. Took 3.003 secs. +:processResources (Thread[Task worker for ':',5,main]) started. :processResources executing task ':processResources' ... Putting task artifact state for task ':processResources' into context took 0.0 secs. 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[main,5,main]) completed. Took 0.006 secs. -:classes (Thread[main,5,main]) started. +:processResources (Thread[Task worker for ':',5,main]) completed. Took 0.011 secs. +:classes (Thread[Task worker for ':',5,main]) started. :classes executing task ':classes' ... Skipping task ':classes' as it has no actions. :classes UP-TO-DATE -:classes (Thread[main,5,main]) completed. Took 0.003 secs. -:findScalaAndJavaTypes (Thread[main,5,main]) started. +:classes (Thread[Task worker for ':',5,main]) completed. Took 0.009 secs. +:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) started. :findScalaAndJavaTypes executing task ':findScalaAndJavaTypes' ... -Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.003 secs. +Putting task artifact state for task ':findScalaAndJavaTypes' into context took 0.005 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[main,5,main]) completed. Took 0.044 secs. -:compileTestJava (Thread[main,5,main]) started. +:findScalaAndJavaTypes (Thread[Task worker for ':',5,main]) completed. Took 0.071 secs. +:compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava executing task ':compileTestJava' ... Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. @@ -2428,7 +2499,7 @@ 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 4.788 secs. It is not up-to-date because: +Up-to-date check for task ':compileTestJava' took 11.348 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. @@ -2436,36 +2507,36 @@ 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[main,5,main]) completed. Took 30.307 secs. -:processTestResources (Thread[main,5,main]) started. +:compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 1 mins 11.297 secs. +:processTestResources (Thread[Task worker for ':',5,main]) started. :processTestResources executing task ':processTestResources' ... Putting task artifact state for task ':processTestResources' into context took 0.0 secs. -Up-to-date check for task ':processTestResources' took 0.772 secs. It is not up-to-date because: +Up-to-date check for task ':processTestResources' took 1.545 secs. It is not up-to-date because: No history is available. -:processTestResources (Thread[main,5,main]) completed. Took 1.945 secs. -:testClasses (Thread[main,5,main]) started. +:processTestResources (Thread[Task worker for ':',5,main]) completed. Took 3.163 secs. +:testClasses (Thread[Task worker for ':',5,main]) started. :testClasses executing task ':testClasses' ... Skipping task ':testClasses' as it has no actions. -:testClasses (Thread[main,5,main]) completed. Took 0.002 secs. -:testWithDefaultReference (Thread[main,5,main]) started. +:testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.007 secs. +:testWithDefaultReference (Thread[Task worker for ':',5,main]) started. :testWithDefaultReference executing task ':testWithDefaultReference' ... Putting task artifact state for task ':testWithDefaultReference' into context took 0.002 secs. -Up-to-date check for task ':testWithDefaultReference' took 0.915 secs. It is not up-to-date because: +Up-to-date check for task ':testWithDefaultReference' took 1.914 secs. It is not up-to-date because: Task.upToDateWhen is false. -Finished generating test XML results (0.005 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/testWithDefaultReference +Finished generating test XML results (0.011 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/testWithDefaultReference Generating HTML test report... -Finished generating test html results (0.051 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/testWithDefaultReference -:testWithDefaultReference (Thread[main,5,main]) completed. Took 1.303 secs. -:test (Thread[main,5,main]) started. +Finished generating test html results (0.148 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/testWithDefaultReference +:testWithDefaultReference (Thread[Task worker for ':',5,main]) completed. Took 2.85 secs. +:test (Thread[Task worker for ':',5,main]) started. :test executing task ':test' ... Putting task artifact state for task ':test' into context took 0.0 secs. -Up-to-date check for task ':test' took 0.172 secs. It is not up-to-date because: +Up-to-date check for task ':test' took 0.317 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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath3000859616779688074txt -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-arm64/bin/java -Djava.awt.headless=true -Dorg.gradle.native=false @/tmp/gradle-worker-classpath15471851984581206645txt -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. @@ -2476,13 +2547,13 @@ 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 2022-08-27 11:13:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:36:42 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSingleSampleVCF STANDARD_ERROR - WARNING 2022-08-27 11:13:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:36:42 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.vcf.VCFHeaderUnitTest.testVCFHeaderSampleRenamingSitesOnlyVCF STANDARD_ERROR - WARNING 2022-08-27 11:13:36 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:36:42 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream Gradle suite > Gradle test > htsjdk.variant.variantcontext.writer.VariantContextWriterBuilderUnitTest.demonstrateTestWriteToPipeDoesNotHang_1 STANDARD_ERROR java.lang.RuntimeException: oops @@ -2517,7 +2588,7 @@ 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: 1ms @@ -2526,10 +2597,10 @@ testFirstCompleteContigRead runtime: 1ms 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: 1ms + testFirstCompleteContigRead runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstCompleteContigRead[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 - testFirstCompleteContigRead runtime: 0ms + testFirstCompleteContigRead runtime: 5ms 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: 0ms @@ -2538,16 +2609,16 @@ testFirstElementOfIterator runtime: 0ms 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 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: 1ms + testFirstElementOfIterator runtime: 5ms 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: 1ms + testFirstElementOfIterator runtime: 0ms 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 @@ -2571,7 +2642,7 @@ 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 @@ -2586,13 +2657,13 @@ testFirstSequenceExtended runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testFirstSequenceExtended[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testFirstSequenceExtended runtime: 0ms + testFirstSequenceExtended runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testLastCompleteContigRead[0](/build/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: 22ms + testLastCompleteContigRead runtime: 27ms 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: 12ms + testLastCompleteContigRead runtime: 16ms 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: 3ms @@ -2601,19 +2672,19 @@ testLastCompleteContigRead runtime: 3ms 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: 16ms + 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: 16ms + testLastCompleteContigRead runtime: 17ms 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: 23ms + testLastCompleteContigRead runtime: 16ms 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: 6ms + testLastCompleteContigRead runtime: 7ms 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: 5ms + testLastCompleteContigRead runtime: 6ms 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 @@ -2631,10 +2702,10 @@ 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: 22ms + 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: 15ms + testNextElementOfIterator runtime: 4ms 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: 3ms @@ -2643,19 +2714,19 @@ testNextElementOfIterator runtime: 3ms 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: 15ms + testNextElementOfIterator runtime: 17ms 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: 14ms + testNextElementOfIterator runtime: 17ms 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: 14ms + testNextElementOfIterator runtime: 16ms 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: 4ms + testNextElementOfIterator runtime: 6ms 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: 4ms + testNextElementOfIterator runtime: 6ms 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 @@ -2673,7 +2744,7 @@ testOpenFile runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - testReadPastEndOfContig runtime: 0ms + testReadPastEndOfContig runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadPastEndOfContig[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadPastEndOfContig runtime: 0ms @@ -2700,13 +2771,13 @@ testReadStartingInCenterOfFirstLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfFirstLine[4](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta.gz) STANDARD_ERROR - testReadStartingInCenterOfFirstLine runtime: 0ms + testReadStartingInCenterOfFirstLine runtime: 1ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[0](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR - testReadStartingInCenterOfMiddleLine runtime: 1ms + testReadStartingInCenterOfMiddleLine runtime: 0ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadStartingInCenterOfMiddleLine[2](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR testReadStartingInCenterOfMiddleLine runtime: 0ms @@ -2715,10 +2786,10 @@ 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: 0ms 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 + testReadThroughEndOfContig runtime: 11ms Gradle suite > Gradle test > htsjdk.samtools.reference.AbstractIndexedFastaSequenceFileTest.testReadThroughEndOfContig[1](/build/htsjdk-2.23.0+dfsg/src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta) STANDARD_ERROR testReadThroughEndOfContig runtime: 0ms @@ -2733,46 +2804,46 @@ 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: 3ms + testReset runtime: 6ms 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: 3ms + 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: 3ms + 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 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: 16ms + testReset runtime: 19ms 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: 17ms + testReset runtime: 25ms 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: 16ms + testReset runtime: 25ms 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: 6ms + testReset runtime: 9ms 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: 6ms Gradle suite > Gradle test > htsjdk.tribble.AsciiFeatureCodecTest.testMakeIndexableSourceFromUnknownStream STANDARD_ERROR - WARNING 2022-08-27 11:15:34 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:39:04 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@9cb4295, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR - WARNING 2022-08-27 11:15:34 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@1823f58, class htsjdk.tribble.readers.AsciiLineReader) STANDARD_ERROR + WARNING 2021-07-26 07:39:04 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 2022-08-27 11:15:34 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:39:04 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 2022-08-27 11:15:34 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:39:04 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 2022-08-27 11:15:34 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 07:39:04 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 @@ -3832,14 +3903,14 @@ NoCoordinateCount= 279 Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteBinary STANDARD_OUT - #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.6545457970689248412.bai - #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.10214969813598142039.bai - #BAMIndexWriterTest diff /tmp/javaBai.6545457970689248412.bai /tmp/cBai.10214969813598142039.bai + #BAMIndexWriterTest Wrote binary java BAM Index file /tmp/javaBai.8426170295727608449.bai + #BAMIndexWriterTest Wrote sorted C binary BAM Index file /tmp/cBai.6788374546993142890.bai + #BAMIndexWriterTest diff /tmp/javaBai.8426170295727608449.bai /tmp/cBai.6788374546993142890.bai Gradle suite > Gradle test > htsjdk.samtools.BAMIndexWriterTest.testWriteText STANDARD_OUT - #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.9916486215430743919.bai.txt - #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.17286807427898877642java.bai - #BAMIndexWriterTest diff /tmp/javaBai.17286807427898877642java.bai.txt /tmp/cBai.9916486215430743919.bai.txt + #BAMIndexWriterTest Wrote textual C BAM Index file /tmp/cBai.9507175994914039022.bai.txt + #BAMIndexWriterTest Wrote binary Java BAM Index file /tmp/javaBai.7534684118696364030java.bai + #BAMIndexWriterTest diff /tmp/javaBai.7534684118696364030java.bai.txt /tmp/cBai.9507175994914039022.bai.txt Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.readPastEndOfFile STANDARD_OUT 1ms to write @@ -3850,28 +3921,28 @@ 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.11036192139936991057.gz + Creating file /tmp/BCOST.17771829109318197015.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testCustomDeflater STANDARD_OUT - Creating file /tmp/testCustomDeflater.11042018725678549893.gz + Creating file /tmp/testCustomDeflater.10508888156047404109.gz Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedOutputStreamTest.testOverflow STANDARD_OUT - Creating file /tmp/BCOST.4150872373476218129.gz + Creating file /tmp/BCOST.14661792614328263620.gz Gradle suite > Gradle test > htsjdk.samtools.CRAMComplianceTest.fullVerificationTest[0](c1#bounds) STANDARD_ERROR - WARNING 2022-08-27 11:19:12 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. - WARNING 2022-08-27 11:19:12 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2021-07-26 07:42:17 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=12, counter=0. + WARNING 2021-07-26 07:42:17 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 2022-08-27 11:19:31 ReferenceSource Sequence not found: chrSheila + WARNING 2021-07-26 07:42:31 ReferenceSource Sequence not found: chrSheila Gradle suite > Gradle test > htsjdk.samtools.CRAMEdgeCasesTest.testNullsAndBeyondRef STANDARD_ERROR - WARNING 2022-08-27 11:19:32 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. - WARNING 2022-08-27 11:19:32 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2021-07-26 07:42:31 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=3, counter=0. + WARNING 2021-07-26 07:42:31 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 2022-08-27 11:19:32 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. - WARNING 2022-08-27 11:19:32 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2021-07-26 07:42:31 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=37, counter=0. + WARNING 2021-07-26 07:42:31 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... @@ -4585,64 +4656,64 @@ Resetting tmpdir Gradle suite > Gradle test > htsjdk.samtools.DownsamplingIteratorTests.testBasicFunction STANDARD_ERROR - Could not delete file /tmp/pbuilder1/DiskBackedQueueTest/diskbackedqueue.7844246113262342277.tmp + Could not delete file /tmp/pbuilder2/DiskBackedQueueTest/diskbackedqueue.4744906534772630598.tmp Gradle is still running, please be patient... Gradle suite > Gradle test > htsjdk.samtools.reference.FastaSequenceIndexCreatorTest.testBuildFromFasta[0](src/test/resources/htsjdk/samtools/reference/Homo_sapiens_assembly18.trimmed.fasta) STANDARD_ERROR - WARNING 2022-08-27 11:43:32 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:33 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream + WARNING 2021-07-26 08:04:50 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 2022-08-27 11:43:39 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:57 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 2022-08-27 11:43:39 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:57 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 2022-08-27 11:43:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2022-08-27 11:43:40 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:58 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:58 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 2022-08-27 11:43:41 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2022-08-27 11:43:41 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:59 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:59 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 2022-08-27 11:43:41 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 - WARNING 2022-08-27 11:43:41 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:59 Gff3Codec ignoring directive ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118200 + WARNING 2021-07-26 08:04:59 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 2022-08-27 11:43:43 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombLongEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2021-07-26 08:05:01 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 2022-08-27 11:43:43 ExperimentalEncoding Using the experimental encoding htsjdk.samtools.cram.encoding.core.experimental.GolombRiceIntegerEncoding which is untested and scheduled for removal from the CRAM spec + WARNING 2021-07-26 08:05:01 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 file5404268326336143163.bad + Could not delete file file3132537865745657023.bad Gradle suite > Gradle test > htsjdk.samtools.util.IntervalTreeTest.performanceTest STANDARD_OUT - Time to construct a tree with 50000 nodes: 162 milliseconds - Queried for the same 100-length mapping 66198022 times in 10 seconds. + Time to construct a tree with 50000 nodes: 285 milliseconds + Queried for the same 100-length mapping 67746384 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 @@ -4651,96 +4722,96 @@ 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 310 because intersection length 49 < minMatchSize 133.0 (0.35 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 53 because intersection length 91 < minMatchSize 133.0 (0.65 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 814 < minMatchSize 843.5999999999999 (0.9166667 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 144 < minMatchSize 152.95 (0.89440995 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 6 because intersection length 160 < minMatchSize 167.2 (0.90909094 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 7 because intersection length 146 < minMatchSize 170.04999999999998 (0.8156425 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 30171758 because intersection length 64 < minMatchSize 155.79999999999998 (0.3902439 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 31548103 because intersection length 8 < minMatchSize 155.79999999999998 (0.048780486 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 16 because intersection length 414 < minMatchSize 498.75 (0.7885714 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 363 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 18 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) - INFO 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 1571 because intersection length 36 < minMatchSize 50.349999999999994 (0.6792453 < 0.95) + INFO 2021-07-26 08:05:22 LiftOver Interval null failed to match chain 363 because intersection length 17 < minMatchSize 50.349999999999994 (0.3207547 < 0.95) + INFO 2021-07-26 08:05:22 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 18 because intersection length 53 < minMatchSize 66.5 (0.75714284 < 0.95) + INFO 2021-07-26 08:05:22 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) @@ -4900,7 +4971,7 @@ 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 2022-08-27 11:44:04 LiftOver Interval null failed to match chain 3 because intersection length 16 < minMatchSize 16.15 (0.9411765 < 0.95) + INFO 2021-07-26 08:05:22 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 @@ -4922,135 +4993,135 @@ e Gradle suite > Gradle test > htsjdk.samtools.MergingSamRecordIteratorTest.testVanillaUnsortedMultiIterator STANDARD_OUT + b d e c - b a Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[0](@HD VN:1.0 SO:UNSORTED ) STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. + WARNING 2021-07-26 08:07:15 SAMTextHeaderCodec Found non-conforming header SO tag: UNSORTED. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[1](@HD VN:1.0 SO:FALSE ) STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. + WARNING 2021-07-26 08:07:15 SAMTextHeaderCodec Found non-conforming header SO tag: FALSE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[2](@HD VN:1.0 SO:COORDINATE ) STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. + WARNING 2021-07-26 08:07:15 SAMTextHeaderCodec Found non-conforming header SO tag: COORDINATE. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[3](@HD VN:1.0 SO:uNknOWn ) STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. + WARNING 2021-07-26 08:07:15 SAMTextHeaderCodec Found non-conforming header SO tag: uNknOWn. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileHeaderTest.testValidationStringencyLenientAndSilent[4](@HD VN:1.0 SO:cOoRdinate ) STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. + WARNING 2021-07-26 08:07:15 SAMTextHeaderCodec Found non-conforming header SO tag: cOoRdinate. Treating as 'unknown'. Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.specialFileWriterTest STANDARD_ERROR - WARNING 2022-08-27 11:45:53 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null - WARNING 2022-08-27 11:45:53 SAMFileWriterFactory Cannot create index for BAM because output file is not a regular file: file:///dev/null + WARNING 2021-07-26 08:07:15 SAMFileWriterFactory Cannot create MD5 file for BAM because output file is not a regular file: file:///dev/null + WARNING 2021-07-26 08:07:15 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 2022-08-27 11:45:53 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.9541458267589113855..cram - INFO 2022-08-27 11:45:53 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2022-08-27 11:45:53 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2022-08-27 11:45:53 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/tmp.16815748065974162063..cram + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeSamOrBamForCramExtension STANDARD_ERROR - INFO 2022-08-27 11:45:53 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension18301173423463690600.cram + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeSamOrBamForCramExtension10221407795563607228.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.5574478875418562050.bam, Error parsing SAM header. @RG line missing SM tag. Line: + Ignoring SAM validation error: ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File /tmp/tmp.13393923130200799421.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 2022-08-27 11:45:54 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension16887386650983308086.cram - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Reference fasta is not provided when writing CRAM file file:///tmp/testMakeWriterForCramExtension17866838981290568631.cram + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Will attempt to use a default reference or download as set by defaults: + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Default REFERENCE_FASTA (-Dsamjdk.reference_fasta): null + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Default USE_CRAM_REF_DOWNLOAD (-Dsamjdk.use_cram_ref_download): false Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForNoExtension STANDARD_ERROR - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension16834371313158885389 + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForNoExtension15821985733389772639 Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterForUnknownFileExtension STANDARD_ERROR - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension412100709963814710.png + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/testMakeWriterForUnknownFileExtension17351844250885782648.png Gradle suite > Gradle test > htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriterPath[0](sam) STANDARD_ERROR - INFO 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://a3ed5351-342e-4695-a6c7-2bf19ab4a42e/work/testMakeWriterPathsam + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://387ad13b-3acb-4995-9392-e93534f997f6/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 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://71002a47-691a-4fe8-b6f7-af4b71960117/work/testMakeWriterPathbam + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ade0452c-8340-4ec8-a75a-7b5c11b0ee9b/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 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ece574df-c94d-42c5-8bb8-bb1ab110ada5/work/testMakeWriterPathcram + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://779624c0-c011-40ed-a171-18923bdbb17b/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 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://f18b12df-dc96-4e2f-b059-7754922b1eb4/work/testMakeWriterPathsam + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://2e1179c5-61f2-47ee-a0ce-204bf782c13c/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 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://ea30547d-3879-4c31-bb05-1b22bcd07a9b/work/testMakeWriterPathbam + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://39454adc-ef1d-4578-a607-ce556ceb474d/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 2022-08-27 11:45:54 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://c70855e7-d9e5-4f5c-95ab-d87620e64bfe/work/testMakeWriterPathcram + INFO 2021-07-26 08:07:16 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: jimfs://6dff0e07-2e39-4025-9757-c7d430003ca9/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 2022-08-27 11:45:56 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1 and tag M5 has the two values: dummy and dummy2. + ERROR 2021-07-26 08:07:19 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 2022-08-27 11:45:57 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 2022-08-27 11:45:57 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 2021-07-26 08:07:20 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 2021-07-26 08:07:20 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 2022-08-27 11:46:08 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory - INFO 2022-08-27 11:46:08 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory - INFO 2022-08-27 11:46:08 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar - INFO 2022-08-27 11:46:08 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam + INFO 2021-07-26 08:07:28 CustomReaderFactory Attempting to open https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam with custom factory + INFO 2021-07-26 08:07:28 CustomReaderFactory Attempting to load factory class htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory + INFO 2021-07-26 08:07:28 CustomReaderFactory Created custom factory for https://www.googleapis.com/genomics/v1beta/reads/ from htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory loaded from this jar + INFO 2021-07-26 08:07:28 SamReaderFactoryTest Opening customr reader for src/test/resources/htsjdk/samtools/uncompressed.sam Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.exhaustInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.openPath STANDARD_ERROR - INFO 2022-08-27 11:46:08 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... + INFO 2021-07-26 08:07:28 SamReaderFactoryTest Reading from src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam ... Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryInputResourcePermutation SKIPPED Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.queryStreamingPathBamWithFileIndex STANDARD_ERROR - INFO 2022-08-27 11:46:10 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 2022-08-27 11:46:10 SamReaderFactoryTest Finished queries in 245ms + INFO 2021-07-26 08:07:29 SamReaderFactoryTest Query from data=PATH:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam;index=FILE:src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai ... + INFO 2021-07-26 08:07:29 SamReaderFactoryTest Finished queries in 180ms Gradle suite > Gradle test > htsjdk.samtools.SamReaderFactoryTest.testSamReaderFromMalformedSeekableStream STANDARD_ERROR - WARNING 2022-08-27 11:46:10 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2021-07-26 08:07:30 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 2022-08-27 11:46:10 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2021-07-26 08:07:30 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 2022-08-27 11:46:10 SamReaderFactory Unable to detect file format from input URL or stream, assuming SAM format. + WARNING 2021-07-26 08:07:30 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 2022-08-27 11:46:13 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2022-08-27 11:46:13 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2021-07-26 08:07:32 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2021-07-26 08:07:32 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 2022-08-27 11:46:13 BAMRecordCodec Reference length is too large for BAM bin field. - WARNING 2022-08-27 11:46:13 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. + WARNING 2021-07-26 08:07:32 BAMRecordCodec Reference length is too large for BAM bin field. + WARNING 2021-07-26 08:07:32 BAMRecordCodec Reads on references longer than 536870912bp will have bin set to 0. Gradle suite > Gradle test > htsjdk.utils.SamtoolsTestUtilsTest.testCRAMConversion SKIPPED @@ -5063,53 +5134,53 @@ Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceBlocksTest.testSliceBlocksRoundTrip SKIPPED Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SliceTests STANDARD_ERROR - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:15 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:34 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 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 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 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:46:16 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@fae66e09] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@a1a5772] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@ebf82111] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cdd5eab0] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@afb3b44f] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@91917dee] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@736f478d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@554d112c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@372adacb] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1908a46a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:35 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 2022-08-27 11:46:17 Slice Slice mapped outside of reference: seqID=SINGLE_REFERENCE: 0, start=1, span=20, counter=0. + WARNING 2021-07-26 08:07:36 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 @@ -5133,96 +5204,96 @@ Resetting tmpdir Resetting tmpdir -Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[0](A, 0, 0, 0, 0, 0, [B@4df0b2a4) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[0](A, 0, 0, 0, 0, 0, [B@6c70ae78) 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@62b64b3a) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[1](A, 0, 0, 0, 1, 0, [B@11b42502) 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@44372339) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[2](A, 0, 1, 2, 3, 4, [B@44beee96) 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@105af74d) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[3](A, 0, 4, 3, 2, 1, [B@3c34f376) 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@37e52a6b) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[4](C, 0, 0, 0, 0, 0, [B@6a145ef) 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@1c14e958) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[5](C, 0, 0, 0, 1, 0, [B@531d3d12) 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@7fc02d9f) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[6](C, 1, 0, 2, 3, 4, [B@2c88c399) 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@3be639c) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[7](C, 4, 0, 3, 2, 1, [B@10293b01) 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@5b8f661c) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[8](G, 0, 0, 0, 0, 0, [B@98ca696) 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@4b79bcc2) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[9](G, 0, 0, 0, 1, 0, [B@49ecc089) 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@26a9ed7f) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[10](G, 1, 2, 0, 3, 4, [B@5713ccc3) 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@47a97680) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[11](G, 4, 3, 0, 2, 1, [B@4825f377) 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@1ea56c91) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[12](T, 0, 0, 0, 0, 0, [B@1f7816b) 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@51294c51) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[13](T, 0, 0, 0, 0, 1, [B@15c32b6f) 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@66f92a1f) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[14](T, 1, 2, 3, 0, 4, [B@39138d0b) 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@616dc2be) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[15](T, 4, 3, 2, 0, 1, [B@11b99870) 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@6abc9293) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[16](N, 0, 0, 0, 0, 0, [B@f9f59ef) 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@7622e008) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[17](N, 0, 0, 0, 1, 0, [B@5fe70cf5) 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@43d14f39) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[18](N, 1, 2, 3, 4, 0, [B@3967683e) 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@5d53445e) STANDARD_OUT +Gradle suite > Gradle test > htsjdk.samtools.cram.structure.SubstitutionMatrixTest.testSingleReferenceBaseSubstitution[19](N, 4, 3, 2, 1, 0, [B@115afc79) 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[354](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. - WARNING 2022-08-27 11:50:18 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. +Gradle suite > Gradle test > htsjdk.TestDataProviders.testDataProviderswithDP[39](private java.lang.Object[][] htsjdk.samtools.cram.structure.SliceTests.sliceStateTestCases(), class htsjdk.samtools.cram.structure.SliceTests) STANDARD_ERROR + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@1bec6934] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@2b20529d] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@cfe1c3c] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@eedbe5db] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@d0b9af7a] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@b2977919] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@947542b8] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@76530c57] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@5830d5f6] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 CRAMCompressionRecord CRAMRecord [htsjdk.samtools.cram.structure.CRAMCompressionRecord@3a0e9f95] has an valid alignment start but not a valid reference index. + WARNING 2021-07-26 08:07:52 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 (2.186 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/test +Finished generating test XML results (1.315 secs) into: /build/htsjdk-2.23.0+dfsg/build/test-results/test Generating HTML test report... -Finished generating test html results (2.204 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/test -:test (Thread[main,5,main]) completed. Took 38 mins 31.936 secs. +Finished generating test html results (2.028 secs) into: /build/htsjdk-2.23.0+dfsg/build/reports/tests/test +:test (Thread[Task worker for ':',5,main]) completed. Took 37 mins 29.223 secs. -BUILD SUCCESSFUL in 39m 19s +BUILD SUCCESSFUL in 39m 7s 6 actionable tasks: 5 executed, 1 up-to-date -make[1]: Leaving directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=gradle dh_prep -O--buildsystem=gradle @@ -5255,13 +5326,13 @@ dh_link -O--buildsystem=gradle rm -f debian/libhtsjdk-java-doc.debhelper.log debian/libhtsjdk-java.debhelper.log debian/rules override_jh_installlibs -make[1]: Entering directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt binnengegaan jh_installlibs --version-strip='[+]dfsg[.0-9]*' install -d debian/libhtsjdk-java/usr/share/java install -p -m0644 ./build/libs/htsjdk-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar rm -f debian/libhtsjdk-java/usr/share/java/htsjdk.jar ln -s htsjdk-2.23.0.jar debian/libhtsjdk-java/usr/share/java/htsjdk.jar -make[1]: Leaving directory '/build/htsjdk-2.23.0+dfsg' +make[1]: Map '/build/htsjdk-2.23.0+dfsg' wordt verlaten jh_classpath -O--buildsystem=gradle jh_manifest -plibhtsjdk-java "--classpath=/usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar /usr/share/java/libjaxb-api.jar /usr/share/java/jaxb-impl.jar" debian/libhtsjdk-java/usr/share/java/htsjdk.jar Updating symlinked /build/htsjdk-2.23.0+dfsg/debian/libhtsjdk-java/usr/share/java/htsjdk-2.23.0.jar (via debian/libhtsjdk-java/usr/share/java/htsjdk.jar) @@ -5326,55 +5397,42 @@ 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/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/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/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/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/SAMSequenceDictionaryCodec.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/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/SamReaderFactory.Option.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/SamReaderFactory.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/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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/S 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/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeBuilder.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/CommonInfo.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/Genotype.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/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::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/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 @@ -5382,66 +5440,63 @@ 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 Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IntegerTypeGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.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.PLAccessor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc - 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::Strip Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc - 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/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/external/ExternalEncoding.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/varia 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 + 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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exa 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/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/CoreCodec.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 @@ -5456,188 +5511,150 @@ 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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/GZIPExternalCompressor.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/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.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/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing 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 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/common/MutableInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc + 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/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:: 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-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPClient.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 + 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/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/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/TagFilter.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/MappingQualityFilter.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/JavascriptSamRecordFilter.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/filter/IntervalKeepPairFilter.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/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 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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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/LocusComparator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Locus.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/LocationAware.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Locatable.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Iterables.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IterableOnceIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/IterableAdapter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ProcessExecutor.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/IterableOnceIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/Iso8601Date.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/IOUtil.html using 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 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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+ 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 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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/BinWithOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/CoordinateSortedPairInfoMap.Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMStreamWriter.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/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/AbstractBAMFileIndex.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/IndexMerger.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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexer.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/sra/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAUnalignmentIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRALazyRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/sra/SRAIndexedSequenceFile.html using File::StripNondeterminism::handlers::javadoc 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/sra/SRAUnalignmentIterator.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 @@ -5648,72 +5665,151 @@ 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/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/metrics/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjd 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/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/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/TribbleIndexCreator.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/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 - 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/gff/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/SequenceRegion.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Writer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3FeatureImpl.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.Gff3Directive.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.DecodeDepth.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3BaseData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Feature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/gff/Gff3Constants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/UnsortedFileException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/exception/CodecLineParsingException.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjNondeterminism::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/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::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.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.htmmple/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/CountRecords.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc + 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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFInfoHeaderLine.html using File::StripNondeterminism::handlers::javadoc + 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::javadoc + 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 + 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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCodec.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/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-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/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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/ + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc + 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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/index-all.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/member-search-index.zip using File::StripNondeterminism::handlers::zip + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/type-search-index.zip using File::StripNondeterminism::handlers::zip + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/package-search-index.zip using File::StripNondeterminism::handlers::zip + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/constant-values.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_75_e6e6e6_1x400.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_222222_256x240.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_55_fbf9ee_1x400.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_cd0a0a_256x240.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_2e83ff_256x240.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_888888_256x240.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_highlight-soft_75_cccccc_1x100.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_75_dadada_1x400.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_95_fef1ec_1x400.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_454545_256x240.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_65_dadada_1x400.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/x.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/glass.png using File::StripNondeterminism::handlers::png + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/ClassFinder.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 @@ -5723,50 +5819,73 @@ 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/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/AbstractFeatureCodec.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/TribbleException.UnableToReadIndexFile.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/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/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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc - 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/htsNormalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/BZIP2ExternalCompressor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/compression/rans/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing 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 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/hnt/variantcontext/writer/BCF2FieldWriter.IGFGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GTWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.GenericSiteWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.FTGenotypesWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.StringOrCharacter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.IntArray.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.GenericInts.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Float.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.Flag.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.AtomicInt.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2FieldEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/BCF2Encoder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/VariantContextFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/SnpFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/HeterozygosityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/GenotypeQualityFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/FilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/CompoundFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/PassingVariantFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/filter/FilteringVariantContextIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/example/PrintVariantsExample.html using File::StripNondeterminism::handlers::javadoc + 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/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/BCF2Type.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/BCF2Utils.html using File::StripNondeterminism::handlers::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/variant/bcf2/BCF2Codec.LazyData.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/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-dojavadoc + 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 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/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/CramContainerHeaderIterator.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/build/CramContainerIterator.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/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 @@ -5774,6 +5893,7 @@ 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 @@ -5782,32 +5902,44 @@ 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/CRAMEncodingStrategy.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/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/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 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::StripNondete-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/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/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/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/FastqEncoder.html using File::StripNondeterminism::handlers::javadoc + Normalic/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/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 +zing 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/fastq/BasicFastqWriter.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/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 +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 @@ -5819,17 +5951,13 @@ 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 Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/DefaultBitInputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CramInt.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CountingInputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/BitOutputStream.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/BitInputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CRC32OutputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CRC32InputStream.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/io/CramIntArray.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/digest/ContentDigests.KNOWN_DIGESTS.html using File::StripNondeterminism::handlers::javadoc - 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/EncodingFactory.html using File::StripNondeterminism::handlers::javadoc @@ -5841,80 +5969,11 @@ 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 Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtoolsrminism::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/build/CramContainerIterator.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/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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/deprecated-list.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/allpackages-index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/index-all.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/member-search-index.zip using File::StripNondeterminism::handlers::zip - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/allclasses-index.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/type-search-index.zip using File::StripNondeterminism::handlers::zip - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/package-search-index.zip using File::StripNondeterminism::handlers::zip - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/overview-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/serialized-form.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/constant-values.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_75_e6e6e6_1x400.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_222222_256x240.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_55_fbf9ee_1x400.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_cd0a0a_256x240.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_2e83ff_256x240.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_888888_256x240.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_highlight-soft_75_cccccc_1x100.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_75_dadada_1x400.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_95_fef1ec_1x400.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-icons_454545_256x240.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/jquery/images/ui-bg_glass_65_dadada_1x400.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/x.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/resources/glass.png using File::StripNondeterminism::handlers::png - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/ValidationUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/utils/ClassFinder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFStandardHeaderLines.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFSimpleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFSampleHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFRecordCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPercentEncodedTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPedigreeHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFPassThruTextTransformer.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFMetaHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIteratorBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFIterator.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::javadoc - 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::javjdk/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/LongLineBufferedReader.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/readers/LineReader.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/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 -/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Substitution.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/SoftClip.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Scores.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/RefSkip.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/ReadFeature.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/ReadBase.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Padding.html using File::StripNondeterminism::handlers::javadoc @@ -5923,56 +5982,26 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/HardClip.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Deletion.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/Bases.html using File::StripNondeterminism::handlers::javadoc -dk/tribble/example/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/ProfileIndexReading.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/IndicesAreEqual.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/IndexToTable.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/ExampleBinaryCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/example/CountRecords.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/bed/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/SimpleBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.Exon2.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDFeature.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/BEDCodec.StartOffset.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/bed/FullBEDFeature.Exon.html using File::StripNondeterminism::handlers::javadoc - 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 - 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 - 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/shk/samtools/metrics/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-tree.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/cram/encoding/reader/package-summary.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/l 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 @@ -5984,6 +6013,8 @@ 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 @@ -6001,40 +6032,150 @@ 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/sharapi/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/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/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/ExternalByteEncoding.html using File::StripNondeterminism::handlers::javadoc +tsjdk/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/Tribble.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/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 + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/tribble/readers/PositionalBufferedStream.html using File::StripNondeterminism::handlers::javadoc + 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/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/psamtools/SamFileValidator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileSource.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFiles.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SamFileHeaderMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileHeader.SortOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileHeader.PgIdGenerator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileHeader.GroupOrder.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMFileHeader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/ReservedTagConstants.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/QueryInterval.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/NotPrimarySkippingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/MergingSamRecordIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMBinaryTagAndValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/LinearIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/SAMBinaryTagAndUnsignedArrayValue.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/GenomicIndexUtil.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/FileTruncatedException.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DuplicateSetIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DuplicateSet.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DuplicateScoringStrategy.ScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DuplicateScoringStrategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DownsamplingIteratorFactory.Strategy.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DownsamplingIteratorFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DownsamplingIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DiskBasedBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/DefaultSAMRecordFactory.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMStreamWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMStartingAtIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMSBIIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMRecordCodec.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BamIndexValidator.IndexValidationStringency.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BamIndexValidator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexMetaData.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexMerger.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndexer.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMFileWriter.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMFileSpan.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMFileReader.BAMQueryFilteringIterator.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BAMFileReader.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/BamFileIoUtils.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/AlignmentBlock.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/AbstractSAMHeaderRecord.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/AbstractBAMFileIndex.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/Defaults.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/e/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/WholeGenomeReferenceSequenceMask.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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/PeekIterator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/PeekableIterator.html usare/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/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 -javadoc +ackage-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 +minism::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/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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/EdgingRecordAndOffset.Type.html using 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/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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/DateParser.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CustomGzipOutputStream.html using File::StripNondeterminism::handlers::javadoc + Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CoordSpanInputSteam.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CoordMath.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ComparableTuple.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/CollectionUtil.Partitioner.html using 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/IntervalUtil.html using 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/IntervalTreeMap.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 @@ -6042,6 +6183,8 @@ 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 @@ -6052,98 +6195,26 @@ Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AsciiWriter.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractRecordAndOffset.AlignmentType.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractRecordAndOffset.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/CollectionUtil.DefaultingMap.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/AbstractProgressLogger.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractLocusIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractLocusInfo.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractIterator.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractAsyncWriter.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/AbstractProgressLogger.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/IOUtil.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::StripNondetermilibhtsjdk-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/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 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 +nism::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/IntervalCodec.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/Interval.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/zip/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/zip/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/zip/InflaterFactory.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/zip/DeflaterFactory.html using File::StripNondeterminism::handlers::javadoc - 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-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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPReply.html using File::StripNondeterminism::handlers::javadoc - Normalizing debiing 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 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 debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/LocusImpl.html using File::StripNondeterminism::handlers::javadoc -an/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/samtools/util/ftp/FTPClient.html using File::StripNondeterminism::handlers::javadoc - 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 -adoc - 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/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/VCFInfoHeaderLine.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 - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFContigHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFConstants.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.SupportedHeaderLineType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCompoundHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFCodec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCFAltHeaderLine.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/VCF3Codec.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/vcf/AbstractVCFCodec.html using File::StripNondeterminism::handlers::javadoc - 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/utils/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/VCFHeaderReader.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/SAMSequenceDictionaryExtractor.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/GeneralUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/utils/BinomialCoefficientUtil.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/package-tree.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/package-summary.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextUtils.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextComparator.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.Validation.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.Type.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/StructuralVariantType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyParser.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/JexlMissingValueTreatment.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeType.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypesContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.GenotypeLikelihoodsAllelePair.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeLikelihoods.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/GenotypeJEXLContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/FastGenotype.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/VariantContextUtils.JexlVCMatchExp.html using File::StripNondeterminism::handlers::javadoc - 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/GenotypeBuilder.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/LazyGenotypesContext.LazyData.html using File::StripNondeterminism::handlers::javadoc - Normalizing debian/libhtsjdk-java-doc/usr/share/doc/libhtsjdk-java-doc/api/htsjdk/variant/variantcontext/Genotype.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/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::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 dh_compress -O--buildsystem=gradle cd debian/libhtsjdk-java cd debian/libhtsjdk-java-doc @@ -6154,11 +6225,11 @@ gzip -9nf usr/share/doc/libhtsjdk-java-doc/changelog.Debian cd '/build/htsjdk-2.23.0+dfsg' dh_fixperms -O--buildsystem=gradle - find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + find debian/libhtsjdk-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhtsjdk-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/libhtsjdk-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libhtsjdk-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhtsjdk-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhtsjdk-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 @@ -6183,8 +6254,8 @@ 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: pakket 'libhtsjdk-java' wordt gebouwd in '../libhtsjdk-java_2.23.0+dfsg-2_all.deb'. +dpkg-deb: pakket 'libhtsjdk-java-doc' wordt gebouwd in '../libhtsjdk-java-doc_2.23.0+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../htsjdk_2.23.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6192,12 +6263,14 @@ 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/25642/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25642/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/9676 and its subdirectories -I: Current time: Sat Aug 27 11:52:22 -12 2022 -I: pbuilder-time-stamp: 1661644342 +I: removing directory /srv/workspace/pbuilder/25642 and its subdirectories +I: Current time: Mon Jul 26 08:13:57 +14 2021 +I: pbuilder-time-stamp: 1627236837