Diff of the two buildlogs: -- --- b1/build.log 2024-10-11 23:13:23.093518877 +0000 +++ b2/build.log 2024-10-11 23:19:15.766556192 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 11 11:03:10 -12 2024 -I: pbuilder-time-stamp: 1728687790 +I: Current time: Fri Nov 14 19:36:25 +14 2025 +I: pbuilder-time-stamp: 1763098585 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -43,52 +43,84 @@ dpkg-source: info: applying adding_opens_arg_for_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/733974/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 14 05:36 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6f35b144232e4c0ba8149597a89ffe09' - 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='733974' - PS1='# ' - PS2='> ' + INVOCATION_ID=57834cd097a548aa8464a3e7aa0343bc + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1730115 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/pbuilderrc_YU8P --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/pbuilderrc_HiaN --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ONmzhG9r/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/733974/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -668,7 +700,7 @@ Get: 462 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-3 [28.3 MB] Get: 463 http://deb.debian.org/debian trixie/main amd64 r-cran-rjava amd64 1.0-11-1 [702 kB] Get: 464 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] -Fetched 404 MB in 40s (10.0 MB/s) +Fetched 404 MB in 9s (46.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19787 files and directories currently installed.) @@ -2189,8 +2221,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Oct 11 23:07:04 UTC 2024. -Universal Time is now: Fri Oct 11 23:07:04 UTC 2024. +Local time is now: Fri Nov 14 05:39:16 UTC 2025. +Universal Time is now: Fri Nov 14 05:39:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2) ... @@ -2779,7 +2811,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-11_source.changes +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1730115/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-11_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-11 dpkg-buildpackage: info: source distribution unstable @@ -2922,206 +2958,122 @@ [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... -[WARNING] Loading source files for package org.campagnelab.goby.compression... -[WARNING] Loading source files for package org.campagnelab.goby.methylation... -[WARNING] Loading source files for package org.campagnelab.goby.readers... -[WARNING] Loading source files for package org.campagnelab.goby.readers.sam... -[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... -[WARNING] Loading source files for package org.campagnelab.goby.xml... -[WARNING] Loading source files for package org.campagnelab.goby... -[WARNING] Loading source files for package org.campagnelab.goby.R... -[WARNING] Loading source files for package org.campagnelab.goby.parsers... -[WARNING] Loading source files for package org.campagnelab.goby.reads... -[WARNING] Loading source files for package org.campagnelab.goby.counts... -[WARNING] Loading source files for package org.campagnelab.goby.counts.compound... +[WARNING] Loading source files for package org.campagnelab.goby.util... +[WARNING] Loading source files for package org.campagnelab.goby.util.commits... +[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... +[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... +[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... +[WARNING] Loading source files for package org.campagnelab.goby.util.pool... +[WARNING] Loading source files for package org.campagnelab.goby.stats... +[WARNING] Loading source files for package org.campagnelab.goby.exception... [WARNING] Loading source files for package org.campagnelab.goby.modes... -[WARNING] Loading source files for package org.campagnelab.goby.modes.core... [WARNING] Loading source files for package org.campagnelab.goby.modes.formats... [WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... -[WARNING] Loading source files for package org.campagnelab.goby.exception... -[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... +[WARNING] Loading source files for package org.campagnelab.goby.modes.core... +[WARNING] Loading source files for package org.campagnelab.goby.compression... +[WARNING] Loading source files for package org.campagnelab.goby.xml... +[WARNING] Loading source files for package org.campagnelab.goby.cli... +[WARNING] Loading source files for package org.campagnelab.goby.alignments... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... +[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... +[WARNING] Loading source files for package org.campagnelab.goby... +[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... +[WARNING] Loading source files for package org.campagnelab.goby.readers.sam... +[WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... +[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... -[WARNING] Loading source files for package org.campagnelab.goby.util... -[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... -[WARNING] Loading source files for package org.campagnelab.goby.util.commits... -[WARNING] Loading source files for package org.campagnelab.goby.util.pool... -[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... -[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... -[WARNING] Loading source files for package org.campagnelab.goby.stats... -[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... -[WARNING] Loading source files for package org.campagnelab.goby.config... -[WARNING] Loading source files for package org.campagnelab.goby.alignments... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... +[WARNING] Loading source files for package org.campagnelab.goby.counts... +[WARNING] Loading source files for package org.campagnelab.goby.counts.compound... [WARNING] Loading source files for package org.campagnelab.goby.predictions... -[WARNING] Loading source files for package org.campagnelab.goby.cli... +[WARNING] Loading source files for package org.campagnelab.goby.config... +[WARNING] Loading source files for package org.campagnelab.goby.methylation... +[WARNING] Loading source files for package org.campagnelab.goby.parsers... +[WARNING] Loading source files for package org.campagnelab.goby.R... +[WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Loading source files for package org.campagnelab.dl.varanalysis.protobuf... [WARNING] Constructing Javadoc information... -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlRootElement; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol -[WARNING] @XmlRootElement -[WARNING] ^ -[WARNING] symbol: class XmlRootElement -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.REXP; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.RVector; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol -[WARNING] private static Result evaluateFisherExpression(final Rengine rengine, -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class FisherExact -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol -[WARNING] private Rengine rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol +[WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine -[WARNING] location: class GobyRengine -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol -[WARNING] public Rengine getRengine() { +[WARNING] location: class FisherExactRCalculator +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist +[WARNING] import DistLib.hypergeometric; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class GobyRengine -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol -[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { -[WARNING] ^ -[WARNING] symbol: class RMainLoopCallbacks -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol -[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol -[WARNING] public void rBusy(final Rengine rengine, final int which) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol -[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol -[WARNING] public void rShowMessage(final Rengine rengine, final String message) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol -[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol -[WARNING] public void rFlushConsole(final Rengine rengine) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol -[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol -[WARNING] public void rLoadHistory(final Rengine re, final String filename) { -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist +[WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol -[WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ -[WARNING] symbol: class RMainLoopCallbacks -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol -[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.Unmarshaller; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol -[WARNING] public void rBusy(final Rengine rengine, final int which) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol +[WARNING] private ParallelTeam team; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol -[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { +[WARNING] symbol: class ParallelTeam +[WARNING] location: class StatsMode +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol -[WARNING] public void rShowMessage(final Rengine rengine, final String message) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBException; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol -[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.Marshaller; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol -[WARNING] public void rFlushConsole(final Rengine rengine) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol -[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol +[WARNING] @XmlRootElement [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol -[WARNING] public void rLoadHistory(final Rengine re, final String filename) { +[WARNING] symbol: class XmlRootElement +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol +[WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist +[WARNING] symbol: class JAXBException +[WARNING] location: class MethylStatsMode +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist -[WARNING] import edu.rit.pj.ParallelTeam; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist +[WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBContext; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist +[WARNING] import org.apache.commons.exec.DefaultExecutor; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBException; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist +[WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.Unmarshaller; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol -[WARNING] private ParallelTeam team; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] symbol: class ParallelTeam -[WARNING] location: class StatsMode [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ @@ -3193,66 +3145,23 @@ [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist -[WARNING] import org.apache.commons.exec.CommandLine; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist -[WARNING] import org.apache.commons.exec.DefaultExecutor; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist -[WARNING] import org.apache.commons.exec.PumpStreamHandler; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBContext; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBException; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.Marshaller; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol -[WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException { -[WARNING] ^ -[WARNING] symbol: class JAXBException -[WARNING] location: class MethylStatsMode -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist -[WARNING] import DistLib.hypergeometric; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol -[WARNING] Rengine rEngine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class FisherExactRCalculator -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.IntegerForLoop; @@ -3277,12 +3186,139 @@ [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol +[WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks { +[WARNING] ^ +[WARNING] symbol: class RMainLoopCallbacks +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol +[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol +[WARNING] public void rBusy(final Rengine rengine, final int which) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol +[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol +[WARNING] public void rShowMessage(final Rengine rengine, final String message) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol +[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol +[WARNING] public void rFlushConsole(final Rengine rengine) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol +[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol +[WARNING] public void rLoadHistory(final Rengine re, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RLoggerMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol +[WARNING] private Rengine rengine; +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class GobyRengine +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol +[WARNING] public Rengine getRengine() { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class GobyRengine +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.REXP; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.RVector; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol +[WARNING] private static Result evaluateFisherExpression(final Rengine rengine, +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class FisherExact +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol +[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { +[WARNING] ^ +[WARNING] symbol: class RMainLoopCallbacks +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol +[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol +[WARNING] public void rBusy(final Rengine rengine, final int which) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol +[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol +[WARNING] public void rShowMessage(final Rengine rengine, final String message) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol +[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol +[WARNING] public void rFlushConsole(final Rengine rengine) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol +[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol +[WARNING] public void rLoadHistory(final Rengine re, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ @@ -4052,506 +4088,305 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaDataOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntryOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollectionOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html... 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Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.Builder.html... @@ -4586,58 +4421,259 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollectionOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... +[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... +[WARNING] Generating 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Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html... @@ -4778,47 +4814,47 @@ [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings [WARNING] Loading source files for package samples... -[WARNING] Loading source files for package org.campagnelab.goby.compression... -[WARNING] Loading source files for package org.campagnelab.goby.methylation... -[WARNING] Loading source files for package org.campagnelab.goby.readers... -[WARNING] Loading source files for package org.campagnelab.goby.readers.sam... -[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... -[WARNING] Loading source files for package org.campagnelab.goby.xml... -[WARNING] Loading source files for package org.campagnelab.goby... -[WARNING] Loading source files for package org.campagnelab.goby.R... -[WARNING] Loading source files for package org.campagnelab.goby.parsers... -[WARNING] Loading source files for package org.campagnelab.goby.reads... -[WARNING] Loading source files for package org.campagnelab.goby.counts... -[WARNING] Loading source files for package org.campagnelab.goby.counts.compound... +[WARNING] Loading source files for package org.campagnelab.goby.util... +[WARNING] Loading source files for package org.campagnelab.goby.util.commits... +[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... +[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... +[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... +[WARNING] Loading source files for package org.campagnelab.goby.util.pool... +[WARNING] Loading source files for package org.campagnelab.goby.stats... +[WARNING] Loading source files for package org.campagnelab.goby.exception... 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[WARNING] Loading source files for package org.campagnelab.goby.predictions... -[WARNING] Loading source files for package org.campagnelab.goby.cli... +[WARNING] Loading source files for package org.campagnelab.goby.config... +[WARNING] Loading source files for package org.campagnelab.goby.methylation... +[WARNING] Loading source files for package org.campagnelab.goby.parsers... +[WARNING] Loading source files for package org.campagnelab.goby.R... +[WARNING] Loading source files for package org.campagnelab.goby.reads... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 21.0.5-ea+8-Debian-1 @@ -5681,557 +5717,557 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/serialized-form.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html... -[WARNING] Generating 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returning an instance of {@link +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html... +[WARNING] Generating 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Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. +[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, +[WARNING] ^ +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html... +[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html... 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-[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. -[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. -[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, -[WARNING] ^ -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore +[WARNING] * Dequeues a document from the queue, returning an instance of {@link +[WARNING] ^ +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... @@ -6329,14 +6365,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.087 s] -[INFO] Goby I/O ........................................... SUCCESS [ 41.431 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 45.618 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.165 s] +[INFO] Goby I/O ........................................... SUCCESS [ 17.252 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 18.774 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:27 min -[INFO] Finished at: 2024-10-11T11:09:35-12:00 +[INFO] Total time: 36.653 s +[INFO] Finished at: 2025-11-14T19:40:31+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -6469,570 +6505,215 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite -field CHROM value: 0 -field POS value: 145497099 -field ID value: . -field REF value: A -field ALT value: G -field QUAL value: 17.1 -field FILTER value: . -field INFO[DP] value: 2 -field INFO[DP4] value: 0,0,2,0 -field INFO[MQ] value: 25 -field INFO[FQ] value: -30.8 -field INFO[AF1] value: 0.9999 -field INFO[CI95] value: 0.5,1 -field INFO[PV4] value: -field INFO[INDEL] value: INDEL -field INFO[PC2] value: 3,3 -field INFO[PCHI2] value: 0.752 -field INFO[QCHI2] value: 1 -field INFO[RP] value: -field FORMAT[GT] value: -field FORMAT[GQ] value: -field FORMAT[GL] value: -field FORMAT[DP] value: -field FORMAT[SP] value: -field FORMAT[PL] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 -field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 -field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 -field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 -field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 -field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 -field CHROM gfi:0 value: 0 -field POS gfi:1 value: 145497099 -field ID gfi:2 value: . -field REF gfi:3 value: A -field ALT gfi:4 value: G -field QUAL gfi:5 value: 17.1 -field FILTER gfi:6 value: . -field FORMAT[GT] gfi:7 value: -field FORMAT[GQ] gfi:8 value: -field FORMAT[GL] gfi:9 value: -field FORMAT[DP] gfi:10 value: -field FORMAT[SP] gfi:11 value: -field FORMAT[PL] gfi:12 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 -field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 -field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 -field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 -field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 -field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 +19:40:43.184 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 +19:40:43.189 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory] -11:10:23.168 WARN MessageChunksWriter - Using chunk-size=10000 -Total logical entries written: 1 -Total bytes written: 0 -Average bytes/logical entry: 0.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 45 -11:10:23.384 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. -11:10:24.286 INFO RLoggerMainLoopCallback - +Creating base test directory: test-results/stats +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +19:40:43.346 INFO RLoggerMainLoopCallback - -11:10:24.287 INFO RLoggerMainLoopCallback - R version 4.4.1 (2024-06-14) -- "Race for Your Life" +19:40:43.347 INFO RLoggerMainLoopCallback - R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu -11:10:24.287 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. +19:40:43.347 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. -11:10:24.287 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. +19:40:43.347 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. -11:10:24.287 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or +19:40:43.347 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. -11:10:24.730 WARN MessageChunksWriter - Using chunk-size=9 -11:10:24.747 WARN MessageChunksWriter - Using chunk-size=9 -Total logical entries written: 39 -Total bytes written: 660 -Average bytes/logical entry: 16.923077 -Number of bits/base 3.6590436 -11:10:24.761 WARN MessageChunksWriter - Using chunk-size=9 -Total logical entries written: 39 -Total bytes written: 685 -Average bytes/logical entry: 17.564102 -Number of bits/base 3.797644 -11:10:24.778 WARN MessageChunksWriter - Using chunk-size=9 -Total logical entries written: 39 -Total bytes written: 660 -Average bytes/logical entry: 16.923077 -Number of bits/base 3.6590436 ->1 -NNTGAATGAGACCTA +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] +[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest +[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. +##fileformat=VCFv4.1 +##Goby=UNKNOWN +##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB -qPhred=1 -qPhred=2 -qPhred=3 -qPhred=4 -qPhred=5 -qPhred=6 -qPhred=7 -qPhred=8 -qPhred=9 -qPhred=10 -qPhred=11 -qPhred=12 -qPhred=13 -qPhred=14 -qPhred=15 -qPhred=16 -qPhred=17 -qPhred=18 -qPhred=19 -qPhred=20 -qPhred=21 -qPhred=22 -qPhred=23 -qPhred=24 -qPhred=25 -qPhred=26 -qPhred=27 -qPhred=28 -qPhred=29 -qPhred=30 -qPhred=31 -qPhred=32 -qPhred=33 -qPhred=34 -qPhred=35 -qPhred=36 -qPhred=37 -qPhred=38 -qPhred=39 -qPhred=40 -qPhred=41 -qPhred=42 -qPhred=43 -qPhred=44 -qPhred=45 -qPhred=46 -qPhred=47 -qPhred=48 -qPhred=49 -qPhred=50 -qPhred=51 -qPhred=52 -qPhred=53 -qPhred=54 -qPhred=55 -qPhred=56 -qPhred=57 -qPhred=58 -qPhred=59 -qPhred=60 -qPhred=61 - 0 -AAC 3 -ACC 6 -ATC 9 -AGC 12 -AAC 15 -ACC 18 -ATC 21 -AGC 24 -AAC 27 -ACC 30 -ATC 33 -AGC 36 -AAC 39 -ACC 42 -ATC 45 -AGC 48 -AAC 51 -ACC 54 -ATC 57 -AGC 60 -AAC 63 -ACC 66 -ATC 69 -AGC 72 -AAC 75 -ACC 78 -ATC 81 -AGCloading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=6 count=1 -(0,1) -loading transition for reader[0] position=1 length=3 count=3 -(0,1)(1,4) -loading transition for reader[0] position=4 length=2 count=0 -(0,1)(1,4)(4,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -(0,0) -loading transition for reader[0] position=1 length=1 count=1 -(0,0)(1,1) -loading transition for reader[0] position=2 length=4 count=0 -(0,0)(1,1)(2,0) -loading transition for reader[1] position=4 length=10 count=1 -(0,0)(1,1)(2,0)(4,1) -loading transition for reader[0] position=6 length=2 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2) -loading transition for reader[0] position=8 length=1 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) -loading transition for reader[0] position=9 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) -loading transition for reader[0] position=10 length=2 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) -loading transition for reader[0] position=12 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) -loading transition for reader[0] position=13 length=3 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) -loading transition for reader[0] position=16 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -loading transition for reader[0] position=1 length=1 count=1 -loading transition for reader[0] position=2 length=4 count=0 -loading transition for reader[1] position=4 length=10 count=1 -loading transition for reader[0] position=6 length=2 count=1 -loading transition for reader[0] position=8 length=1 count=0 -loading transition for reader[0] position=9 length=1 count=1 -loading transition for reader[0] position=10 length=2 count=0 -loading transition for reader[0] position=12 length=1 count=1 -loading transition for reader[0] position=13 length=3 count=0 -loading transition for reader[0] position=16 length=1 count=1 - peak : start :5 count :13 length :100010 - peak : start :100020 count :10 length :1 -11:10:34.016 WARN WiggleWindow - Not writing 101 7 -11:10:34.016 WARN WiggleWindow - Not writing 111 7 -11:10:34.016 WARN WiggleWindow - Not writing 131 8 -11:10:34.016 WARN WiggleWindow - Not writing 141 8 -11:10:34.017 WARN WiggleWindow - Not writing 151 8 - appending (count=0,length=1) - appending (count=4,length=3) - appending (count=1,length=3) - appending (count=0,length=2) - appending (count=3,length=1) - appending (count=1,length=1) - appending (count=0,length=1) - appending (count=4,length=3) - appending (count=0,length=5) - appending (count=3,length=1) - appending (count=0,length=2) - appending (count=2,length=1) - appending (count=0,length=2) - appending (count=3,length=1) - appending (count=2,length=1) - appending (count=0,length=1) - appending (count=10,length=4) - appending (count=1,length=0) - appending (count=2,length=8) -Hello - appending (count=10,length=4) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=6 count=1 -(0,1) -loading transition for reader[0] position=1 length=3 count=3 -(0,1)(1,4) -loading transition for reader[0] position=4 length=2 count=0 -(0,1)(1,4)(4,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -(0,0) -loading transition for reader[0] position=1 length=1 count=1 -(0,0)(1,1) -loading transition for reader[0] position=2 length=4 count=0 -(0,0)(1,1)(2,0) -loading transition for reader[1] position=4 length=10 count=1 -(0,0)(1,1)(2,0)(4,1) -loading transition for reader[0] position=6 length=2 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2) -loading transition for reader[0] position=8 length=1 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) -loading transition for reader[0] position=9 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) -loading transition for reader[0] position=10 length=2 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) -loading transition for reader[0] position=12 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) -loading transition for reader[0] position=13 length=3 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) -loading transition for reader[0] position=16 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -loading transition for reader[0] position=1 length=1 count=1 -loading transition for reader[0] position=2 length=4 count=0 -loading transition for reader[1] position=4 length=10 count=1 -loading transition for reader[0] position=6 length=2 count=1 -loading transition for reader[0] position=8 length=1 count=0 -loading transition for reader[0] position=9 length=1 count=1 -loading transition for reader[0] position=10 length=2 count=0 -loading transition for reader[0] position=12 length=1 count=1 -loading transition for reader[0] position=13 length=3 count=0 -loading transition for reader[0] position=16 length=1 count=1 -loading transition for reader[0] position=0 length=1 count=0 -(0,0) -loading transition for reader[0] position=1 length=3 count=1 -(0,0)(1,1) -Appending count: 46391 length: 9 -Appending count: 49211 length: 8 -Appending count: 32047 length: 4 -Appending count: 15652 length: 3 -Appending count: 23870 length: 2 -Appending count: 44943 length: 7 -Appending count: 3824 length: 8 -Appending count: 44456 length: 7 -Appending count: 17404 length: 9 -Appending count: 11411 length: 6 -Appending count: 43431 length: 5 -Appending count: 49261 length: 5 -Appending count: 33159 length: 2 -Appending count: 20708 length: 9 -Appending count: 38802 length: 2 -Appending count: 40979 length: 7 -Appending count: 40292 length: 7 -Appending count: 35637 length: 5 -Appending count: 6814 length: 3 -Appending count: 11882 length: 5 -Appending count: 44812 length: 2 -Appending count: 17783 length: 3 -Appending count: 48863 length: 1 -Appending count: 24760 length: 4 -Appending count: 4185 length: 10 -Appending count: 21361 length: 7 -Appending count: 44024 length: 10 -Appending count: 30274 length: 3 -Appending count: 23369 length: 3 -Appending count: 30376 length: 5 - position= 0 count= 46391 - position= 1 count= 46391 - position= 2 count= 46391 - position= 3 count= 46391 - position= 4 count= 46391 - position= 5 count= 46391 - position= 6 count= 46391 - position= 7 count= 46391 - position= 8 count= 46391 - position= 9 count= 49211 - position= 10 count= 49211 - position= 11 count= 49211 - position= 12 count= 49211 - position= 13 count= 49211 - position= 14 count= 49211 - position= 15 count= 49211 - position= 16 count= 49211 - position= 17 count= 32047 - position= 18 count= 32047 - position= 19 count= 32047 - position= 20 count= 32047 - position= 21 count= 15652 - position= 22 count= 15652 - position= 23 count= 15652 - position= 24 count= 23870 - position= 25 count= 23870 - position= 26 count= 44943 - position= 27 count= 44943 - position= 28 count= 44943 - position= 29 count= 44943 - position= 30 count= 44943 - position= 31 count= 44943 - position= 32 count= 44943 - position= 33 count= 3824 - position= 34 count= 3824 - position= 35 count= 3824 - position= 36 count= 3824 - position= 37 count= 3824 - position= 38 count= 3824 - position= 39 count= 3824 - position= 40 count= 3824 - position= 41 count= 44456 - position= 42 count= 44456 - position= 43 count= 44456 - position= 44 count= 44456 - position= 45 count= 44456 - position= 46 count= 44456 - position= 47 count= 44456 - position= 48 count= 17404 - position= 49 count= 17404 - position= 50 count= 17404 - position= 51 count= 17404 - position= 52 count= 17404 - position= 53 count= 17404 - position= 54 count= 17404 - position= 55 count= 17404 - position= 56 count= 17404 - position= 57 count= 11411 - position= 58 count= 11411 - position= 59 count= 11411 - position= 60 count= 11411 - position= 61 count= 11411 - position= 62 count= 11411 - position= 63 count= 43431 - position= 64 count= 43431 - position= 65 count= 43431 - position= 66 count= 43431 - position= 67 count= 43431 - position= 68 count= 49261 - position= 69 count= 49261 - position= 70 count= 49261 - position= 71 count= 49261 - position= 72 count= 49261 - position= 73 count= 33159 - position= 74 count= 33159 - position= 75 count= 20708 - position= 76 count= 20708 - position= 77 count= 20708 - position= 78 count= 20708 - position= 79 count= 20708 - position= 80 count= 20708 - position= 81 count= 20708 - position= 82 count= 20708 - position= 83 count= 20708 - position= 84 count= 38802 - position= 85 count= 38802 - position= 86 count= 40979 - position= 87 count= 40979 - position= 88 count= 40979 - position= 89 count= 40979 - position= 90 count= 40979 - position= 91 count= 40979 - position= 92 count= 40979 - position= 93 count= 40292 - position= 94 count= 40292 - position= 95 count= 40292 - position= 96 count= 40292 - position= 97 count= 40292 - position= 98 count= 40292 - position= 99 count= 40292 - position= 100 count= 35637 - position= 101 count= 35637 - position= 102 count= 35637 - position= 103 count= 35637 - position= 104 count= 35637 - position= 105 count= 6814 - position= 106 count= 6814 - position= 107 count= 6814 - position= 108 count= 11882 - position= 109 count= 11882 - position= 110 count= 11882 - position= 111 count= 11882 - position= 112 count= 11882 - position= 113 count= 44812 - position= 114 count= 44812 - position= 115 count= 17783 - position= 116 count= 17783 - position= 117 count= 17783 - position= 118 count= 48863 - position= 119 count= 24760 - position= 120 count= 24760 - position= 121 count= 24760 - position= 122 count= 24760 - position= 123 count= 4185 - position= 124 count= 4185 - position= 125 count= 4185 - position= 126 count= 4185 - position= 127 count= 4185 - position= 128 count= 4185 - position= 129 count= 4185 - position= 130 count= 4185 - position= 131 count= 4185 - position= 132 count= 4185 - position= 133 count= 21361 - position= 134 count= 21361 - position= 135 count= 21361 - position= 136 count= 21361 - position= 137 count= 21361 - position= 138 count= 21361 - position= 139 count= 21361 - position= 140 count= 44024 - position= 141 count= 44024 - position= 142 count= 44024 - position= 143 count= 44024 - position= 144 count= 44024 - position= 145 count= 44024 - position= 146 count= 44024 - position= 147 count= 44024 - position= 148 count= 44024 - position= 149 count= 44024 - position= 150 count= 30274 - position= 151 count= 30274 - position= 152 count= 30274 - position= 153 count= 23369 - position= 154 count= 23369 - position= 155 count= 23369 - position= 156 count= 30376 - position= 157 count= 30376 - position= 158 count= 30376 - position= 159 count= 30376 - position= 160 count= 30376 -Scanning target file.. -Target file had 1 entries. -Wrote 1 target ids to alignment header. -Setting quality threshold to 0.05 -Total logical entries written: 2 -Total bytes written: 0 -Average bytes/logical entry: 0.0 -Min query index: 0 -Max query index: 0 -Number of queries: 3 -Number of targets: 3 -Removed by quality filter: 0 -Not best score: 1 -Number of alignments written: 2 -query_index: 0 -target_index: 0 -position: 14977972 -score: 780.0 -matching_reverse_strand: false -multiplicity: 1 -number_of_mismatches: 1 -number_of_indels: 0 -query_length: 142 -query_aligned_length: 134 -target_aligned_length: 134 -sequence_variations { - to: "T" - from: "A" - position: 6 - to_quality: "/" - read_index: 14 -} -fragment_index: 0 -query_index_occurrences: 2 -ambiguity: 1 +19:40:43.547 INFO BullardUpperQuartileNormalization - normalization denominator 50148.5 for sample B-7 +19:40:43.547 INFO BullardUpperQuartileNormalization - normalization denominator 51306.8 for sample B-3 +19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 102954 for sample A-3 +19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 104044 for sample A-12 +19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 53282.8 for sample B-15 +19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 50693.6 for sample B-14 +19:40:43.548 INFO BullardUpperQuartileNormalization - normalization denominator 49739.7 for sample B-11 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 103568 for sample A-17 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 51306.8 for sample B-2 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50966.1 for sample B-10 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 102409 for sample A-16 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50421.0 for sample B-8 +19:40:43.549 INFO BullardUpperQuartileNormalization - normalization denominator 50421.0 for sample B-4 +19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 98661.7 for sample A-2 +19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 101387 for sample A-0 +19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 50898.0 for sample B-6 +19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 101046 for sample A-9 +19:40:43.550 INFO BullardUpperQuartileNormalization - normalization denominator 103840 for sample A-8 +19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 100501 for sample A-5 +19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 99615.6 for sample A-4 +19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 103159 for sample A-6 +19:40:43.551 INFO BullardUpperQuartileNormalization - normalization denominator 98661.7 for sample A-7 +19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 51715.6 for sample B-5 +19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 99683.8 for sample A-10 +19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 102614 for sample A-14 +19:40:43.552 INFO BullardUpperQuartileNormalization - normalization denominator 48785.8 for sample B-9 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 101387 for sample A-1 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 50352.9 for sample B-0 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 50898.0 for sample B-12 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 52737.7 for sample B-13 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 103772 for sample A-19 +19:40:43.553 INFO BullardUpperQuartileNormalization - normalization denominator 100297 for sample A-18 +19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 102818 for sample A-15 +19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 50352.9 for sample B-1 +19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 102409 for sample A-13 +19:40:43.554 INFO BullardUpperQuartileNormalization - normalization denominator 104930 for sample A-11 +19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51715.6 for sample B-16 +19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51988.2 for sample B-17 +19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 50966.1 for sample B-19 +19:40:43.555 INFO BullardUpperQuartileNormalization - normalization denominator 51034.3 for sample B-18 +19:40:43.609 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +19:40:43.645 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +19:40:43.645 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +19:40:43.657 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +19:40:43.657 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +19:40:43.765 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +19:40:43.801 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. +19:40:43.801 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +19:40:43.894 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +19:40:43.904 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. +list3:element-id p-value p-value-BH-FDR-q-value +[ 0 [2.354054E-7, 1.177027E-5] ] +[ 1 [2.10159E-5, 4.294736666666667E-4] ] +[ 2 [2.576842E-5, 4.294736666666667E-4] ] +[ 3 [9.814783E-5, 9.471342857142858E-4] ] +[ 4 [1.05261E-4, 9.471342857142858E-4] ] +[ 5 [1.241481E-4, 9.471342857142858E-4] ] +[ 6 [1.325988E-4, 9.471342857142858E-4] ] +[ 7 [1.568503E-4, 9.803143750000002E-4] ] +[ 8 [2.254557E-4, 0.0012525316666666666] ] +[ 9 [3.79538E-4, 0.00189769] ] +[ 10 [6.114943E-4, 0.0027795195454545455] ] +[ 11 [0.001613954, 0.006724808333333334] ] +[ 12 [0.00330243, 0.012636935714285714] ] +[ 13 [0.003538342, 0.012636935714285714] ] +[ 14 [0.005236997, 0.017456656666666667] ] +[ 15 [0.006831909, 0.020762429411764708] ] +[ 16 [0.007059226, 0.020762429411764708] ] +[ 17 [0.008805129, 0.024458691666666667] ] +[ 18 [0.00940104, 0.02473957894736842] ] +[ 19 [0.01129798, 0.028244949999999998] ] +[ 20 [0.02115017, 0.050357547619047614] ] +[ 21 [0.04922736, 0.11188036363636364] ] +[ 22 [0.06053298, 0.1304633125] ] +[ 23 [0.06262239, 0.1304633125] ] +[ 24 [0.07395153, 0.14790306] ] +[ 25 [0.08281103, 0.15925198076923075] ] +[ 26 [0.08633331, 0.1598765] ] +[ 27 [0.1190654, 0.21261678571428572] ] +[ 28 [0.1890796, 0.32599931034482754] ] +[ 29 [0.2058494, 0.3430823333333333] ] +[ 30 [0.2209214, 0.3563248387096774] ] +[ 31 [0.2856, 0.44625000000000004] ] +[ 32 [0.3048895, 0.4619537878787878] ] +[ 33 [0.4660682, 0.6835770833333333] ] +[ 34 [0.4830809, 0.6835770833333333] ] +[ 35 [0.4921755, 0.6835770833333333] ] +[ 36 [0.5319453, 0.718845] ] +[ 37 [0.575155, 0.7414352564102564] ] +[ 38 [0.5783195, 0.7414352564102564] ] +[ 39 [0.6185894, 0.7626062790697675] ] +[ 40 [0.636362, 0.7626062790697675] ] +[ 41 [0.6448587, 0.7626062790697675] ] +[ 42 [0.6558414, 0.7626062790697675] ] +[ 43 [0.6885884, 0.7824868181818182] ] +[ 44 [0.7189864, 0.7988737777777778] ] +[ 45 [0.8179539, 0.8802645744680851] ] +[ 46 [0.8274487, 0.8802645744680851] ] +[ 47 [0.89713, 0.9304775510204082] ] +[ 48 [0.911868, 0.9304775510204082] ] +[ 49 [0.943789, 0.943789] ] -Processing test-data/sample-qual-scores/30reads.fa -Processed 0 read entries. -Min quality score: 2147483647 -Max quality score: -2147483648 -Avg quality score: 0 -Probable quality encoding scheme: fasta -Processing test-data/sample-qual-scores/30reads.fq -Processed 30 read entries. -Min quality score: 69 -Max quality score: 98 -Avg quality score: 94 -Probable quality encoding scheme: Illumina/Solexa +element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B +[ id-1 [0.9949106468576894, 0.49973229823135434, -0.007361132169582257, -1.0007726308812397, 0.0, 0.0] ] + +truncated fdr=3.53108e-05 original=3.53108e-05 +truncated fdr=0.00128842 original=0.00128842 +truncated fdr=0.00128842 original=0.00128842 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00294094 original=0.00294094 +truncated fdr=0.00375760 original=0.00375760 +truncated fdr=0.00569307 original=0.00569307 +truncated fdr=0.00833856 original=0.00833856 +truncated fdr=0.0201744 original=0.0201744 +truncated fdr=0.0379108 original=0.0379108 +truncated fdr=0.0379108 original=0.0379108 +truncated fdr=0.0523700 original=0.0523700 +truncated fdr=0.0622873 original=0.0622873 +truncated fdr=0.0622873 original=0.0622873 +truncated fdr=0.0733761 original=0.0733761 +truncated fdr=0.0742187 original=0.0742187 +truncated fdr=0.0847349 original=0.0847349 +truncated fdr=0.151073 original=0.151073 +truncated fdr=0.335641 original=0.335641 +truncated fdr=0.391390 original=0.391390 +truncated fdr=0.391390 original=0.391390 +truncated fdr=0.443709 original=0.443709 +truncated fdr=0.477756 original=0.477756 +truncated fdr=0.479630 original=0.479630 +truncated fdr=0.637850 original=0.637850 +truncated fdr=0.977998 original=0.977998 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +Creating base test directory: test-results/stats-writer +allele: A ref: [CC] alt: [T]19:40:56.111 WARN MessageChunksWriter - Using chunk-size=10000 Associating basename: basen0 to group: A Associating basename: basen1 to group: A Associating basename: basen2 to group: A @@ -7058,36 +6739,37 @@ Filtering reads that have these criteria: q<30 #count(allele) < (2 *#filtered) +19:40:56.430 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:36.655 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.500 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:36.660 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.503 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:36.664 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.505 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:36.666 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.507 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:36.670 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.509 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:36.673 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.511 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:36.675 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:56.513 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:36.678 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:56.514 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:36.680 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:56.517 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:36.682 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:56.518 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7117,34 +6799,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:36.869 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.663 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:36.871 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.665 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:36.873 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.666 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:36.875 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.668 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:36.877 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.669 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:36.879 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.671 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:36.881 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:56.672 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:36.883 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:56.675 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:36.885 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:56.676 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:36.888 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:56.678 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7174,34 +6856,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.038 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.749 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.040 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.750 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.043 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.751 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.045 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.753 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.047 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.755 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.053 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.756 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.057 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:56.758 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.061 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:56.759 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.063 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:56.760 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.066 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:56.762 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7231,34 +6913,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.171 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.824 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.175 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.825 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.177 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.826 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.179 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.827 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.181 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.829 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.183 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.830 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.185 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:56.832 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.186 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:56.833 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.188 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:56.834 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.190 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:56.835 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7288,34 +6970,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.324 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.930 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.326 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.931 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.329 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.933 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.331 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.934 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.335 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.935 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.337 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.936 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.339 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:56.938 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.342 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:56.939 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.344 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:56.940 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.346 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:56.942 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7345,34 +7027,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.458 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:56.991 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.460 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:56.992 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.462 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:56.993 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.464 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:56.995 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.466 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:56.997 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.468 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:56.999 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.471 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.001 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.473 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.002 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.475 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.004 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.477 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.005 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7402,34 +7084,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.588 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.062 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.590 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.063 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.592 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.064 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.594 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.065 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.597 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.066 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.599 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.067 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.600 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.068 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.602 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.070 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.605 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.071 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.607 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.072 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7459,34 +7141,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.692 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.115 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.693 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.116 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.695 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.117 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.696 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.118 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.698 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.119 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.699 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.120 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.701 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.121 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.702 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.122 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.704 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.123 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.705 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.124 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7516,34 +7198,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.787 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.164 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.789 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.165 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.790 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.166 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.792 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.167 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.793 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.168 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.795 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.169 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.797 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.170 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.798 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.171 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.800 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.172 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.801 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.173 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7573,34 +7255,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:37.888 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.213 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:37.890 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.214 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:37.892 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.215 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:37.893 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.216 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:37.895 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.217 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:37.897 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.218 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:37.899 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.219 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:37.901 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.220 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:37.903 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.221 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:37.904 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.222 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7630,34 +7312,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:38.030 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.270 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:38.032 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.272 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:38.033 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.273 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:38.035 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.273 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:38.036 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.274 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:38.038 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.275 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:38.040 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.276 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:38.041 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.277 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:38.042 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.278 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:38.044 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.279 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -7686,34 +7368,34 @@ [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -11:10:38.144 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +19:40:57.327 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -11:10:38.146 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +19:40:57.328 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -11:10:38.149 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +19:40:57.329 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -11:10:38.152 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +19:40:57.330 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -11:10:38.153 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +19:40:57.331 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -11:10:38.154 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +19:40:57.332 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -11:10:38.156 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +19:40:57.333 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -11:10:38.158 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +19:40:57.334 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -11:10:38.159 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +19:40:57.334 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -11:10:38.161 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +19:40:57.335 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 @@ -7751,6 +7433,12 @@ info: + /N q=40 s=1 list: pos=-1 #bases: 33 #indels: 0 filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences + 1/1 ..T + Loading test-data/fdr-mode/file1.vcf Loading test-data/fdr-mode/file2.vcf Loading test-data/fdr-mode/file3.vcf @@ -7774,670 +7462,121 @@ Combining test-data/fdr-mode/file1.vcf Combining test-data/fdr-mode/file2.vcf Combining test-data/fdr-mode/file3.vcf -TTC[27]->CGT[27] / qual=1:2:3 -A[15]->G[20] / qual=20 -A[15]->G[20] / qual=20 -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences - 1/1 ..T - -[ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits -[ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 4 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 1 -[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits -[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 - {1} {0}decoding: 4 - {0} {0}decoding: 4 - {0} {0}decoding: 4 - {0}decoding: 4 - {0}decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 -decoding: 4 - {0} {0} {0} {0} {0}decoding: 1 - {0} {0} {0} {0}decoding: 2 - {0} {0} {0} {0} {0}decoding: 3 -decoding: 4 - {0} {0} {0} {0}decoding: 3 - {0} {0} {0}decoding: 1 - {0} {0} {0} {0}decoding: 2 - {0} {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0} {0} {0}decoding: 3 - {0} {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0}decoding: 1 -[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits -[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 4 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 1 -[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 -Annotations loaded -Annotations loaded -Annotations loaded -Annotations loaded -Annotations loaded -Total logical entries written: 4 +Scanning target file.. +Target file had 1 entries. +Wrote 1 target ids to alignment header. +Setting quality threshold to 0.05 +Total logical entries written: 2 Total bytes written: 0 Average bytes/logical entry: 0.0 -Min query index: 1 -Max query index: 1 -Number of queries: 1 -Number of targets: 2 -Total logical entries written: 4 -Total bytes written: 62 -Average bytes/logical entry: 15.5 -Min query index: 1 -Max query index: 1 -Number of queries: 1 -Number of targets: 2 -count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} -count keys [0, 3, 5, 11, 13] --1 0.0 -0 0.0 -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 -29 0.0 -30 0.0 -overlapping count 3, 4 0.0 -overlapping count 15, 17 0.0 -overlapping count 9, 18 2.0 -overlapping count 3, 8 2.0 -overlapping count 11, 12 0.0 -overlapping count 9, 10 1.0 -overlapping count 8, 9 0.0 -overlapping count 8, 8 0.0 -overlapping count 5, 6 0.0 -overlapping count 3, 3 0.0 -overlapping count 3, 12 5.0 -overlapping count -1, 2 0.0 -overlapping count 0, 45 6.0 -overlapping count 13, 15 0.0 --1 0.0 -0 0.0 -1 0.0 -2 0.0 -3 2.0 -4 2.0 -5 3.0 -6 3.0 -7 3.0 -8 3.0 -9 3.0 -10 3.0 -11 2.0 -12 2.0 -13 0.0 -14 0.0 -15 1.0 -16 1.0 -17 1.0 -18 1.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 -29 0.0 -30 0.0 -overlapping count 3, 4 2.0 -overlapping count 2, 3 2.0 -overlapping count 3, 8 4.0 -overlapping count 11, 12 2.0 -overlapping count 9, 10 3.0 -overlapping count 8, 9 4.0 -overlapping count 8, 8 3.0 -overlapping count 5, 6 3.0 -overlapping count 3, 3 2.0 -overlapping count 3, 12 5.0 -overlapping count -1, 2 0.0 -overlapping count 0, 45 6.0 -overlapping count 13, 15 1.0 -11:12:08.660 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 -11:12:08.661 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds -11:12:08.721 INFO BullardUpperQuartileNormalization - normalization denominator 54080.2 for sample B-7 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53206.8 for sample B-3 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 109107 for sample A-3 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 110999 for sample A-12 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 54880.9 for sample B-15 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53570.7 for sample B-14 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 53934.6 for sample B-11 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-17 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 55754.3 for sample B-2 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 55390.4 for sample B-10 -11:12:08.722 INFO BullardUpperQuartileNormalization - normalization denominator 108888 for sample A-16 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 55463.1 for sample B-8 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 56045.4 for sample B-4 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108524 for sample A-2 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108379 for sample A-0 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 55681.5 for sample B-6 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-9 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 110708 for sample A-8 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 108597 for sample A-5 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 111145 for sample A-4 -11:12:08.723 INFO BullardUpperQuartileNormalization - normalization denominator 110562 for sample A-6 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 109179 for sample A-7 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 52842.8 for sample B-5 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 106923 for sample A-10 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 107214 for sample A-14 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54007.4 for sample B-9 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 109834 for sample A-1 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 56045.4 for sample B-0 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54444.1 for sample B-12 -11:12:08.724 INFO BullardUpperQuartileNormalization - normalization denominator 54735.3 for sample B-13 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 106268 for sample A-19 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 108597 for sample A-18 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 108233 for sample A-15 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55681.5 for sample B-1 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 107433 for sample A-13 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 110198 for sample A-11 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 53716.3 for sample B-16 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 54662.5 for sample B-17 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55972.6 for sample B-19 -11:12:08.725 INFO BullardUpperQuartileNormalization - normalization denominator 55972.6 for sample B-18 -11:12:08.820 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -11:12:08.876 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -11:12:08.876 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -11:12:08.899 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -11:12:08.899 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -11:12:09.070 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -11:12:09.127 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. -11:12:09.127 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -11:12:09.278 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -11:12:09.312 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. -list3:element-id p-value p-value-BH-FDR-q-value -[ 0 [2.354054E-7, 1.177027E-5] ] -[ 1 [2.10159E-5, 4.294736666666667E-4] ] -[ 2 [2.576842E-5, 4.294736666666667E-4] ] -[ 3 [9.814783E-5, 9.471342857142858E-4] ] -[ 4 [1.05261E-4, 9.471342857142858E-4] ] -[ 5 [1.241481E-4, 9.471342857142858E-4] ] -[ 6 [1.325988E-4, 9.471342857142858E-4] ] -[ 7 [1.568503E-4, 9.803143750000002E-4] ] -[ 8 [2.254557E-4, 0.0012525316666666666] ] -[ 9 [3.79538E-4, 0.00189769] ] -[ 10 [6.114943E-4, 0.0027795195454545455] ] -[ 11 [0.001613954, 0.006724808333333334] ] -[ 12 [0.00330243, 0.012636935714285714] ] -[ 13 [0.003538342, 0.012636935714285714] ] -[ 14 [0.005236997, 0.017456656666666667] ] -[ 15 [0.006831909, 0.020762429411764708] ] -[ 16 [0.007059226, 0.020762429411764708] ] -[ 17 [0.008805129, 0.024458691666666667] ] -[ 18 [0.00940104, 0.02473957894736842] ] -[ 19 [0.01129798, 0.028244949999999998] ] -[ 20 [0.02115017, 0.050357547619047614] ] -[ 21 [0.04922736, 0.11188036363636364] ] -[ 22 [0.06053298, 0.1304633125] ] -[ 23 [0.06262239, 0.1304633125] ] -[ 24 [0.07395153, 0.14790306] ] -[ 25 [0.08281103, 0.15925198076923075] ] -[ 26 [0.08633331, 0.1598765] ] -[ 27 [0.1190654, 0.21261678571428572] ] -[ 28 [0.1890796, 0.32599931034482754] ] -[ 29 [0.2058494, 0.3430823333333333] ] -[ 30 [0.2209214, 0.3563248387096774] ] -[ 31 [0.2856, 0.44625000000000004] ] -[ 32 [0.3048895, 0.4619537878787878] ] -[ 33 [0.4660682, 0.6835770833333333] ] -[ 34 [0.4830809, 0.6835770833333333] ] -[ 35 [0.4921755, 0.6835770833333333] ] -[ 36 [0.5319453, 0.718845] ] -[ 37 [0.575155, 0.7414352564102564] ] -[ 38 [0.5783195, 0.7414352564102564] ] -[ 39 [0.6185894, 0.7626062790697675] ] -[ 40 [0.636362, 0.7626062790697675] ] -[ 41 [0.6448587, 0.7626062790697675] ] -[ 42 [0.6558414, 0.7626062790697675] ] -[ 43 [0.6885884, 0.7824868181818182] ] -[ 44 [0.7189864, 0.7988737777777778] ] -[ 45 [0.8179539, 0.8802645744680851] ] -[ 46 [0.8274487, 0.8802645744680851] ] -[ 47 [0.89713, 0.9304775510204082] ] -[ 48 [0.911868, 0.9304775510204082] ] -[ 49 [0.943789, 0.943789] ] - -element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B -[ id-1 [0.9988225176027525, 0.5039216928000868, -0.001699748923964364, -0.9887285321667536, 0.0, 0.0] ] - -truncated fdr=3.53108e-05 original=3.53108e-05 -truncated fdr=0.00128842 original=0.00128842 -truncated fdr=0.00128842 original=0.00128842 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00294094 original=0.00294094 -truncated fdr=0.00375760 original=0.00375760 -truncated fdr=0.00569307 original=0.00569307 -truncated fdr=0.00833856 original=0.00833856 -truncated fdr=0.0201744 original=0.0201744 -truncated fdr=0.0379108 original=0.0379108 -truncated fdr=0.0379108 original=0.0379108 -truncated fdr=0.0523700 original=0.0523700 -truncated fdr=0.0622873 original=0.0622873 -truncated fdr=0.0622873 original=0.0622873 -truncated fdr=0.0733761 original=0.0733761 -truncated fdr=0.0742187 original=0.0742187 -truncated fdr=0.0847349 original=0.0847349 -truncated fdr=0.151073 original=0.151073 -truncated fdr=0.335641 original=0.335641 -truncated fdr=0.391390 original=0.391390 -truncated fdr=0.391390 original=0.391390 -truncated fdr=0.443709 original=0.443709 -truncated fdr=0.477756 original=0.477756 -truncated fdr=0.479630 original=0.479630 -truncated fdr=0.637850 original=0.637850 -truncated fdr=0.977998 original=0.977998 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. -##fileformat=VCFv4.1 -##Goby=UNKNOWN -##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB - -Creating base test directory: test-results/stats-writer -allele: A ref: [CC] alt: [T]Creating base test directory: test-results/stats -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] -[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest -[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -Setting quality threshold to 0.02 -[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. -Processing queryIndex=8 with description '8 perfect start of ref' -Processing queryIndex=9 with description '9 perfect start of ref reverse strand' -Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' -Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' -Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' -Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' -Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' -Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' -Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' -Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' -Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' -Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' -Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' -Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' -Processing queryIndex=0 with description '0 perfect match' -Processing queryIndex=1 with description '1 perfect match on reverse strand' -Processing queryIndex=2 with description '2 mutation' -Processing queryIndex=3 with description '3 mutation on reverse strand' -Processing queryIndex=4 with description '4 insertion' -Processing queryIndex=6 with description '6 deletion' -Processing queryIndex=7 with description '7 deletion on reverse strand' -Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' -Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' -Processing queryIndex=5 with description '5 insertion on reverse strand' -Processing queryIndex=10 with description '10 perfect end of ref' -Processing queryIndex=11 with description '11 perfect end of ref reverse strand' -11:12:24.625 WARN MessageChunksWriter - Using chunk-size=1 -11:12:24.632 WARN MessageChunksWriter - Using chunk-size=1 -11:12:24.798 WARN MessageChunksWriter - Using chunk-size=1 -11:12:24.890 WARN MessageChunksWriter - Using chunk-size=1 -read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT -expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT -recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT -read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =TAAAACCTAAAAAAAAAAAAAAACCCC -expected =TAAAA--TAAAAAAAAAAAAAAACCCC -recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC -read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA -expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA -recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA -read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT -expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT -recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT +Min query index: 0 +Max query index: 0 +Number of queries: 3 +Number of targets: 3 +Removed by quality filter: 0 +Not best score: 1 +Number of alignments written: 2 query_index: 0 target_index: 0 -position: 0 -query_position: 0 -matching_reverse_strand: false -query_length: 75 -query_aligned_length: 75 -target_aligned_length: 75 -mapping_quality: 255 -pair_flags: 0 -fragment_index: 0 -ambiguity: 1 - -query_index: 1 -target_index: 0 -position: 1 -query_position: 0 -matching_reverse_strand: false -query_length: 75 -query_aligned_length: 75 -target_aligned_length: 75 -mapping_quality: 255 -pair_flags: 0 -fragment_index: 0 -ambiguity: 1 - -11:12:25.084 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.087 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.097 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.178 WARN MessageChunksWriter - Using chunk-size=1000 -0 -23 -11:12:25.776 WARN MessageChunksWriter - Using chunk-size=1000 - -11:12:25.781 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.782 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.783 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:25.866 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.081 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.257 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.455 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.580 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.581 WARN MessageChunksWriter - Using chunk-size=1000 -entry.position(): 1 -entry.position(): 2 -entry.position(): 3 -entry.position(): 5 -entry.position(): 6 -entry.position(): 7 -entry.position(): 8 -entry.position(): 9 -entry.position(): 10 -entry.position(): 10 -entry.position(): 12 -entry.position(): 99 -11:12:26.649 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.778 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:26.960 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.133 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.317 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.484 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.587 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits. -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1 -11:12:27.589 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits. -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2 -11:12:27.591 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits. -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3 -11:12:27.595 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.732 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:27.733 WARN MessageChunksWriter - Using chunk-size=1000 -entry:query_index: 0 -target_index: 0 -position: 5 -score: 5.0 -matching_reverse_strand: false -query_length: 20 -query_aligned_length: 20 -target_aligned_length: 20 -sequence_variations { - to: "CTAG" - from: "----" - position: 10 - read_index: 10 -} - -entry:query_index: 1 -target_index: 0 -position: 5 -matching_reverse_strand: false -query_length: 20 -query_aligned_length: 20 -target_aligned_length: 20 -sequence_variations { - to: "CTAG" - from: "----" - position: 10 - to_quality: "((((" - read_index: 10 -} - -entry: query_index: 0 -target_index: 0 -position: 0 -matching_reverse_strand: false -query_length: 10 -query_aligned_length: 10 -sequence_variations { - to: "AAA" - from: "---" - position: 3 - read_index: 3 -} - -processing entry on target 0 at position 0 -processing entry on target 0 at position 5 -processing entry on target 1 at position 0 -processing entry on target 1 at position 5 -processing entry on target 4 at position 0 -processing entry on target 4 at position 5 -entry:query_index: 0 -target_index: 0 -position: 10 -matching_reverse_strand: false -query_length: 50 -query_aligned_length: 50 -sequence_variations { - to: "AAA" - from: "---" - position: 20 - read_index: 20 -} - -entry:query_index: 1 -target_index: 0 -position: 1 +position: 14977972 +score: 780.0 matching_reverse_strand: false -query_length: 50 -query_aligned_length: 50 +multiplicity: 1 +number_of_mismatches: 1 +number_of_indels: 0 +query_length: 142 +query_aligned_length: 134 +target_aligned_length: 134 sequence_variations { to: "T" from: "A" - position: 20 - read_index: 20 + position: 6 + to_quality: "/" + read_index: 14 } +fragment_index: 0 +query_index_occurrences: 2 +ambiguity: 1 -11:12:27.916 WARN MessageChunksWriter - Using chunk-size=2 -Total logical entries written: 0 -Total bytes written: 31 -Average bytes/logical entry: Infinity -Min query index: 2147483647 -Max query index: -2147483648 -Number of queries: 2 -Number of targets: 0 -97 -11:12:27.927 WARN MessageChunksWriter - Using chunk-size=2 -Total logical entries written: 6 -Total bytes written: 162 -Average bytes/logical entry: 27.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 3 -11:12:27.935 WARN MessageChunksWriter - Using chunk-size=2 -Total logical entries written: 6 -Total bytes written: 162 -Average bytes/logical entry: 27.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 3 -11:12:27.943 WARN MessageChunksWriter - Using chunk-size=2 -Total logical entries written: 6 -Total bytes written: 162 -Average bytes/logical entry: 27.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 3 -11:12:27.949 WARN MessageChunksWriter - Using chunk-size=2 -Total logical entries written: 6 -Total bytes written: 162 -Average bytes/logical entry: 27.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 3 -11:12:28.051 WARN MessageChunksWriter - Using chunk-size=1000 -Total logical entries written: 20000 -Total bytes written: 77210 -Average bytes/logical entry: 3.8605 -Min query index: 0 -Max query index: 1999 -Number of queries: 2000 -Number of targets: 10 -11:12:28.317 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:28.551 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:28.553 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:28.770 WARN MessageChunksWriter - Using chunk-size=1000 +Processing test-data/sample-qual-scores/30reads.fa +Processed 0 read entries. +Min quality score: 2147483647 +Max quality score: -2147483648 +Avg quality score: 0 +Probable quality encoding scheme: fasta +Processing test-data/sample-qual-scores/30reads.fq +Processed 30 read entries. +Min quality score: 69 +Max quality score: 98 +Avg quality score: 94 +Probable quality encoding scheme: Illumina/Solexa +TTC[27]->CGT[27] / qual=1:2:3 +A[15]->G[20] / qual=20 +A[15]->G[20] / qual=20 +Setting quality threshold to 0.02 +19:40:58.337 WARN MessageChunksWriter - Using chunk-size=1 +19:40:58.342 WARN MessageChunksWriter - Using chunk-size=1 +19:40:58.345 WARN MessageChunksWriter - Using chunk-size=1 +19:40:58.348 WARN MessageChunksWriter - Using chunk-size=1 +[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. +19:40:58.372 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.380 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +Scanned 5 entries +19:40:58.387 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.388 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +Scanned 2 entries +19:40:58.391 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.393 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.397 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.398 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.402 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.403 WARN MessageChunksWriter - Using chunk-size=1000 +0 +2 +19:40:58.407 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.408 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102 +19:40:58.413 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.414 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.418 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.419 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.423 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.424 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +Scanned 5 entries +19:40:58.432 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.474 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.475 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.504 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:28.805 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:28.807 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:28.817 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.005 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.005 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.533 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.534 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.542 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.572 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.573 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:29.005 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.573 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 111ms; used/avail/free/total/max mem: 687.57M/20.54G/50.63M/738.20M/21.22G -11:12:29.123 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 81.13M/21.01G/86.64M/167.77M/21.09G +19:40:58.579 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 @@ -8518,36 +7657,36 @@ multiplicity: 1 query_length: 35 -11:12:29.285 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.291 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.342 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.342 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.343 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.343 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.615 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.618 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.648 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:29.343 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.343 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.649 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 40ms; used/avail/free/total/max mem: 51.13M/21.17G/703.84M/754.97M/21.22G -11:12:29.387 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.407 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:29.655 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:29.945 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:30.219 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:30.540 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 131.46M/20.96G/36.31M/167.77M/21.09G +19:40:58.652 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.670 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.698 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.723 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.724 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.749 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:30.853 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:31.162 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.773 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.774 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 151.79M/21.07G/603.18M/754.97M/21.22G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 104.76M/20.98G/79.79M/184.55M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -8676,25 +7815,25 @@ multiplicity: 1 query_length: 35 -11:12:31.499 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:31.793 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:32.080 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:32.379 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.850 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.873 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.874 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.899 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:32.605 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:32.816 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:32.959 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. -11:12:32.966 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. -11:12:32.966 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.922 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.923 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.925 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:32.966 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +19:40:58.930 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 210.52M/21.01G/544.46M/754.97M/21.22G -11:12:32.968 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 81.52M/21.01G/103.03M/184.55M/21.09G +19:40:58.931 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % found entry: query_index: 0 target_index: 1 @@ -8720,64 +7859,64 @@ multiplicity: 1 query_length: 35 -11:12:33.030 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:33.481 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:33.719 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:33.950 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.937 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.959 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.960 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:58.982 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:34.168 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:34.301 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:34.304 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:34.306 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.004 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.005 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.007 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.008 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.009 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.009 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:34.309 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.010 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 36ms; used/avail/free/total/max mem: 235.75M/20.99G/519.22M/754.97M/21.22G -11:12:34.349 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:34.351 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -11:12:34.355 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:34.409 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:34.525 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:34.925 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 108.00M/20.98G/76.55M/184.55M/21.09G +19:40:59.011 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.018 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.021 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.043 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.044 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.066 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:35.071 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:35.199 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.088 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.089 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) -11:12:35.203 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.091 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. Found input file with 2 target(s) -11:12:35.203 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.091 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. ... max number of reads was 10 First pass: determine which reads should be kept in the merged alignment. Scanning align-105 Scanning align-106 Found 40 logical alignment entries. Prepare merged too many hits information. -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:35.207 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.093 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.094 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 24ms; used/avail/free/total/max mem: 260.84M/20.96G/494.13M/754.97M/21.22G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 50.53M/21.04G/134.02M/184.55M/21.09G Second pass: writing the merged alignment. -11:12:35.234 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:35.235 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +19:40:59.095 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.096 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. Wrote 20 skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000% Total logical entries written: 20 Total bytes written: 0 @@ -8787,25 +7926,25 @@ Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 -11:12:35.241 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:35.532 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:35.761 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:35.885 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.099 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.121 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.122 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.144 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:36.172 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:36.270 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:36.273 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:36.348 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -11:12:36.349 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.166 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.167 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.168 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.169 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.169 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:36.349 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +19:40:59.170 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 286.05M/20.94G/468.92M/754.97M/21.22G -11:12:36.352 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 75.08M/21.01G/109.47M/184.55M/21.09G +19:40:59.171 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1 position: 11 @@ -8886,19 +8025,19 @@ multiplicity: 1 query_length: 35 -11:12:36.542 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:36.755 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:36.757 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:36.841 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.175 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.197 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.198 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.220 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:36.959 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:37.086 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.243 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.244 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 175ms [2 items, 11.49 items/s, 87.00 ms/item]; used/avail/free/total/max mem: 344.73M/20.88G/410.24M/754.97M/21.22G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 50.24M/21.04G/704.73M/754.97M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -9027,30 +8166,30 @@ multiplicity: 1 query_length: 35 -11:12:37.700 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:37.878 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:37.947 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.112 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.332 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.354 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.355 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.379 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -11:12:38.282 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.283 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.289 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.294 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.333 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.334 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.334 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.334 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.403 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.403 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.407 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.410 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -11:12:38.334 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.334 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.439 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 437.02M/20.79G/317.96M/754.97M/21.22G -11:12:38.339 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -11:12:38.361 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 140.38M/20.95G/614.60M/754.97M/21.09G +19:40:59.442 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +19:40:59.455 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 @@ -9211,46 +8350,7 @@ multiplicity: 1 query_length: 35 -11:12:38.422 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.426 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -Scanned 5 entries -11:12:38.438 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.441 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -Scanned 2 entries -11:12:38.450 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.454 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.465 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.467 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.477 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.481 WARN MessageChunksWriter - Using chunk-size=1000 -0 -2 -11:12:38.492 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.495 WARN MessageChunksWriter - Using chunk-size=1000 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102 -11:12:38.504 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.506 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.516 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.518 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.527 WARN MessageChunksWriter - Using chunk-size=1000 -11:12:38.530 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -Scanned 5 entries -11:12:38.541 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.489 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9258,7 +8358,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.549 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.492 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9266,7 +8366,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.554 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.495 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9274,7 +8374,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.558 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.497 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9282,7 +8382,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.562 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.499 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9290,7 +8390,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.566 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.501 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9298,7 +8398,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -11:12:38.571 WARN MessageChunksWriter - Using chunk-size=2 +19:40:59.504 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -9306,12 +8406,947 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 +Processing queryIndex=8 with description '8 perfect start of ref' +Processing queryIndex=9 with description '9 perfect start of ref reverse strand' +Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' +Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' +Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' +Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' +Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' +Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' +Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' +Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' +Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' +Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' +Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' +Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' +Processing queryIndex=0 with description '0 perfect match' +Processing queryIndex=1 with description '1 perfect match on reverse strand' +Processing queryIndex=2 with description '2 mutation' +Processing queryIndex=3 with description '3 mutation on reverse strand' +Processing queryIndex=4 with description '4 insertion' +Processing queryIndex=6 with description '6 deletion' +Processing queryIndex=7 with description '7 deletion on reverse strand' +Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' +Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' +Processing queryIndex=5 with description '5 insertion on reverse strand' +Processing queryIndex=10 with description '10 perfect end of ref' +Processing queryIndex=11 with description '11 perfect end of ref reverse strand' +query_index: 0 +target_index: 0 +position: 0 +query_position: 0 +matching_reverse_strand: false +query_length: 75 +query_aligned_length: 75 +target_aligned_length: 75 +mapping_quality: 255 +pair_flags: 0 +fragment_index: 0 +ambiguity: 1 + +query_index: 1 +target_index: 0 +position: 1 +query_position: 0 +matching_reverse_strand: false +query_length: 75 +query_aligned_length: 75 +target_aligned_length: 75 +mapping_quality: 255 +pair_flags: 0 +fragment_index: 0 +ambiguity: 1 + +entry:query_index: 0 +target_index: 0 +position: 5 +score: 5.0 +matching_reverse_strand: false +query_length: 20 +query_aligned_length: 20 +target_aligned_length: 20 +sequence_variations { + to: "CTAG" + from: "----" + position: 10 + read_index: 10 +} + +entry:query_index: 1 +target_index: 0 +position: 5 +matching_reverse_strand: false +query_length: 20 +query_aligned_length: 20 +target_aligned_length: 20 +sequence_variations { + to: "CTAG" + from: "----" + position: 10 + to_quality: "((((" + read_index: 10 +} + +entry: query_index: 0 +target_index: 0 +position: 0 +matching_reverse_strand: false +query_length: 10 +query_aligned_length: 10 +sequence_variations { + to: "AAA" + from: "---" + position: 3 + read_index: 3 +} + +processing entry on target 0 at position 0 +processing entry on target 0 at position 5 +processing entry on target 1 at position 0 +processing entry on target 1 at position 5 +processing entry on target 4 at position 0 +processing entry on target 4 at position 5 +entry:query_index: 0 +target_index: 0 +position: 10 +matching_reverse_strand: false +query_length: 50 +query_aligned_length: 50 +sequence_variations { + to: "AAA" + from: "---" + position: 20 + read_index: 20 +} + +entry:query_index: 1 +target_index: 0 +position: 1 +matching_reverse_strand: false +query_length: 50 +query_aligned_length: 50 +sequence_variations { + to: "T" + from: "A" + position: 20 + read_index: 20 +} + +19:40:59.617 WARN MessageChunksWriter - Using chunk-size=1000 + +19:40:59.621 WARN MessageChunksWriter - Using chunk-size=1000 +Total logical entries written: 20000 +Total bytes written: 77210 +Average bytes/logical entry: 3.8605 +Min query index: 0 +Max query index: 1999 +Number of queries: 2000 +Number of targets: 10 +19:40:59.701 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.703 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.709 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.711 WARN MessageChunksWriter - Using chunk-size=1000 +0 +23 +19:40:59.722 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.724 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.725 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.731 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.732 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.733 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.739 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.739 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.740 WARN MessageChunksWriter - Using chunk-size=1000 +entry.position(): 1 +entry.position(): 2 +entry.position(): 3 +entry.position(): 5 +entry.position(): 6 +entry.position(): 7 +entry.position(): 8 +entry.position(): 9 +entry.position(): 10 +entry.position(): 10 +entry.position(): 12 +entry.position(): 99 +19:40:59.747 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.747 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.748 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.754 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.755 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.755 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.758 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1 +19:40:59.759 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2 +19:40:59.760 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3 +[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3 +19:40:59.762 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.763 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.764 WARN MessageChunksWriter - Using chunk-size=1000 +19:40:59.866 WARN MessageChunksWriter - Using chunk-size=2 +Total logical entries written: 0 +Total bytes written: 31 +Average bytes/logical entry: Infinity +Min query index: 2147483647 +Max query index: -2147483648 +Number of queries: 2 +Number of targets: 0 +97 +19:40:59.873 WARN MessageChunksWriter - Using chunk-size=2 +Total logical entries written: 6 +Total bytes written: 162 +Average bytes/logical entry: 27.0 +Min query index: 0 +Max query index: 0 +Number of queries: 1 +Number of targets: 3 +19:40:59.878 WARN MessageChunksWriter - Using chunk-size=2 +Total logical entries written: 6 +Total bytes written: 162 +Average bytes/logical entry: 27.0 +Min query index: 0 +Max query index: 0 +Number of queries: 1 +Number of targets: 3 +19:40:59.881 WARN MessageChunksWriter - Using chunk-size=2 +Total logical entries written: 6 +Total bytes written: 162 +Average bytes/logical entry: 27.0 +Min query index: 0 +Max query index: 0 +Number of queries: 1 +Number of targets: 3 +19:40:59.883 WARN MessageChunksWriter - Using chunk-size=2 +Total logical entries written: 6 +Total bytes written: 162 +Average bytes/logical entry: 27.0 +Min query index: 0 +Max query index: 0 +Number of queries: 1 +Number of targets: 3 +read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT +expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT +recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT +read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =TAAAACCTAAAAAAAAAAAAAAACCCC +expected =TAAAA--TAAAAAAAAAAAAAAACCCC +recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC +read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA +expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA +recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA +read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT +expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT +recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT +Total logical entries written: 1 +Total bytes written: 0 +Average bytes/logical entry: 0.0 +Min query index: 0 +Max query index: 0 +Number of queries: 1 +Number of targets: 45 +field CHROM value: 0 +field POS value: 145497099 +field ID value: . +field REF value: A +field ALT value: G +field QUAL value: 17.1 +field FILTER value: . +field INFO[DP] value: 2 +field INFO[DP4] value: 0,0,2,0 +field INFO[MQ] value: 25 +field INFO[FQ] value: -30.8 +field INFO[AF1] value: 0.9999 +field INFO[CI95] value: 0.5,1 +field INFO[PV4] value: +field INFO[INDEL] value: INDEL +field INFO[PC2] value: 3,3 +field INFO[PCHI2] value: 0.752 +field INFO[QCHI2] value: 1 +field INFO[RP] value: +field FORMAT[GT] value: +field FORMAT[GQ] value: +field FORMAT[GL] value: +field FORMAT[DP] value: +field FORMAT[SP] value: +field FORMAT[PL] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 +field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 +field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 +field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 +field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 +field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 +field CHROM gfi:0 value: 0 +field POS gfi:1 value: 145497099 +field ID gfi:2 value: . +field REF gfi:3 value: A +field ALT gfi:4 value: G +field QUAL gfi:5 value: 17.1 +field FILTER gfi:6 value: . +field FORMAT[GT] gfi:7 value: +field FORMAT[GQ] gfi:8 value: +field FORMAT[GL] gfi:9 value: +field FORMAT[DP] gfi:10 value: +field FORMAT[SP] gfi:11 value: +field FORMAT[PL] gfi:12 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 +field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 +field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 +field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 +field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 +field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 +[ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits +[ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 4 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 1 +[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits +[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 + {1} {0}decoding: 4 + {0} {0}decoding: 4 + {0} {0}decoding: 4 + {0}decoding: 4 + {0}decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 +decoding: 4 + {0} {0} {0} {0} {0}decoding: 1 + {0} {0} {0} {0}decoding: 2 + {0} {0} {0} {0} {0}decoding: 3 +decoding: 4 + {0} {0} {0} {0}decoding: 3 + {0} {0} {0}decoding: 1 + {0} {0} {0} {0}decoding: 2 + {0} {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0} {0} {0}decoding: 3 + {0} {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0}decoding: 1 +[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits +[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 4 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 1 +Total logical entries written: 4 +Total bytes written: 0 +Average bytes/logical entry: 0.0 +Min query index: 1 +Max query index: 1 +Number of queries: 1 +Number of targets: 2 +Total logical entries written: 4 +Total bytes written: 62 +Average bytes/logical entry: 15.5 +Min query index: 1 +Max query index: 1 +Number of queries: 1 +Number of targets: 2 +Annotations loaded +Annotations loaded +Annotations loaded +Annotations loaded +Annotations loaded +count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} +count keys [0, 3, 5, 11, 13] +-1 0.0 +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 +14 0.0 +15 0.0 +16 0.0 +17 0.0 +18 0.0 +19 0.0 +20 0.0 +21 0.0 +22 0.0 +23 0.0 +24 0.0 +25 0.0 +26 0.0 +27 0.0 +28 0.0 +29 0.0 +30 0.0 +overlapping count 3, 4 0.0 +overlapping count 15, 17 0.0 +overlapping count 9, 18 2.0 +overlapping count 3, 8 2.0 +overlapping count 11, 12 0.0 +overlapping count 9, 10 1.0 +overlapping count 8, 9 0.0 +overlapping count 8, 8 0.0 +overlapping count 5, 6 0.0 +overlapping count 3, 3 0.0 +overlapping count 3, 12 5.0 +overlapping count -1, 2 0.0 +overlapping count 0, 45 6.0 +overlapping count 13, 15 0.0 +-1 0.0 +0 0.0 +1 0.0 +2 0.0 +3 2.0 +4 2.0 +5 3.0 +6 3.0 +7 3.0 +8 3.0 +9 3.0 +10 3.0 +11 2.0 +12 2.0 +13 0.0 +14 0.0 +15 1.0 +16 1.0 +17 1.0 +18 1.0 +19 0.0 +20 0.0 +21 0.0 +22 0.0 +23 0.0 +24 0.0 +25 0.0 +26 0.0 +27 0.0 +28 0.0 +29 0.0 +30 0.0 +overlapping count 3, 4 2.0 +overlapping count 2, 3 2.0 +overlapping count 3, 8 4.0 +overlapping count 11, 12 2.0 +overlapping count 9, 10 3.0 +overlapping count 8, 9 4.0 +overlapping count 8, 8 3.0 +overlapping count 5, 6 3.0 +overlapping count 3, 3 2.0 +overlapping count 3, 12 5.0 +overlapping count -1, 2 0.0 +overlapping count 0, 45 6.0 +overlapping count 13, 15 1.0 +[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 + appending (count=0,length=1) + appending (count=4,length=3) + appending (count=1,length=3) + appending (count=0,length=2) + appending (count=3,length=1) + appending (count=1,length=1) + appending (count=0,length=1) + appending (count=4,length=3) + appending (count=0,length=5) + appending (count=3,length=1) + appending (count=0,length=2) + appending (count=2,length=1) + appending (count=0,length=2) + appending (count=3,length=1) + appending (count=2,length=1) + appending (count=0,length=1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=6 count=1 +(0,1) +loading transition for reader[0] position=1 length=3 count=3 +(0,1)(1,4) +loading transition for reader[0] position=4 length=2 count=0 +(0,1)(1,4)(4,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +(0,0) +loading transition for reader[0] position=1 length=1 count=1 +(0,0)(1,1) +loading transition for reader[0] position=2 length=4 count=0 +(0,0)(1,1)(2,0) +loading transition for reader[1] position=4 length=10 count=1 +(0,0)(1,1)(2,0)(4,1) +loading transition for reader[0] position=6 length=2 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2) +loading transition for reader[0] position=8 length=1 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) +loading transition for reader[0] position=9 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) +loading transition for reader[0] position=10 length=2 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) +loading transition for reader[0] position=12 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) +loading transition for reader[0] position=13 length=3 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) +loading transition for reader[0] position=16 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +loading transition for reader[0] position=1 length=1 count=1 +loading transition for reader[0] position=2 length=4 count=0 +loading transition for reader[1] position=4 length=10 count=1 +loading transition for reader[0] position=6 length=2 count=1 +loading transition for reader[0] position=8 length=1 count=0 +loading transition for reader[0] position=9 length=1 count=1 +loading transition for reader[0] position=10 length=2 count=0 +loading transition for reader[0] position=12 length=1 count=1 +loading transition for reader[0] position=13 length=3 count=0 +loading transition for reader[0] position=16 length=1 count=1 +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=6 count=1 +(0,1) +loading transition for reader[0] position=1 length=3 count=3 +(0,1)(1,4) +loading transition for reader[0] position=4 length=2 count=0 +(0,1)(1,4)(4,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +(0,0) +loading transition for reader[0] position=1 length=1 count=1 +(0,0)(1,1) +loading transition for reader[0] position=2 length=4 count=0 +(0,0)(1,1)(2,0) +loading transition for reader[1] position=4 length=10 count=1 +(0,0)(1,1)(2,0)(4,1) +loading transition for reader[0] position=6 length=2 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2) +loading transition for reader[0] position=8 length=1 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) +loading transition for reader[0] position=9 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) +loading transition for reader[0] position=10 length=2 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) +loading transition for reader[0] position=12 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) +loading transition for reader[0] position=13 length=3 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) +loading transition for reader[0] position=16 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +loading transition for reader[0] position=1 length=1 count=1 +loading transition for reader[0] position=2 length=4 count=0 +loading transition for reader[1] position=4 length=10 count=1 +loading transition for reader[0] position=6 length=2 count=1 +loading transition for reader[0] position=8 length=1 count=0 +loading transition for reader[0] position=9 length=1 count=1 +loading transition for reader[0] position=10 length=2 count=0 +loading transition for reader[0] position=12 length=1 count=1 +loading transition for reader[0] position=13 length=3 count=0 +loading transition for reader[0] position=16 length=1 count=1 +loading transition for reader[0] position=0 length=1 count=0 +(0,0) +loading transition for reader[0] position=1 length=3 count=1 +(0,0)(1,1) +Appending count: 43113 length: 9 +Appending count: 6504 length: 1 +Appending count: 49428 length: 1 +Appending count: 28366 length: 6 +Appending count: 4957 length: 5 +Appending count: 19942 length: 4 +Appending count: 31963 length: 5 +Appending count: 6545 length: 9 +Appending count: 31011 length: 8 +Appending count: 24656 length: 1 +Appending count: 30730 length: 5 +Appending count: 33918 length: 8 +Appending count: 35015 length: 6 +Appending count: 14759 length: 8 +Appending count: 41591 length: 8 +Appending count: 36918 length: 3 +Appending count: 21210 length: 2 +Appending count: 30619 length: 8 +Appending count: 29739 length: 9 +Appending count: 8300 length: 9 +Appending count: 17774 length: 1 +Appending count: 16626 length: 1 +Appending count: 25425 length: 8 +Appending count: 41492 length: 7 +Appending count: 4916 length: 9 +Appending count: 48770 length: 4 +Appending count: 40261 length: 2 +Appending count: 28376 length: 7 +Appending count: 35125 length: 1 +Appending count: 27842 length: 5 + position= 0 count= 43113 + position= 1 count= 43113 + position= 2 count= 43113 + position= 3 count= 43113 + position= 4 count= 43113 + position= 5 count= 43113 + position= 6 count= 43113 + position= 7 count= 43113 + position= 8 count= 43113 + position= 9 count= 6504 + position= 10 count= 49428 + position= 11 count= 28366 + position= 12 count= 28366 + position= 13 count= 28366 + position= 14 count= 28366 + position= 15 count= 28366 + position= 16 count= 28366 + position= 17 count= 4957 + position= 18 count= 4957 + position= 19 count= 4957 + position= 20 count= 4957 + position= 21 count= 4957 + position= 22 count= 19942 + position= 23 count= 19942 + position= 24 count= 19942 + position= 25 count= 19942 + position= 26 count= 31963 + position= 27 count= 31963 + position= 28 count= 31963 + position= 29 count= 31963 + position= 30 count= 31963 + position= 31 count= 6545 + position= 32 count= 6545 + position= 33 count= 6545 + position= 34 count= 6545 + position= 35 count= 6545 + position= 36 count= 6545 + position= 37 count= 6545 + position= 38 count= 6545 + position= 39 count= 6545 + position= 40 count= 31011 + position= 41 count= 31011 + position= 42 count= 31011 + position= 43 count= 31011 + position= 44 count= 31011 + position= 45 count= 31011 + position= 46 count= 31011 + position= 47 count= 31011 + position= 48 count= 24656 + position= 49 count= 30730 + position= 50 count= 30730 + position= 51 count= 30730 + position= 52 count= 30730 + position= 53 count= 30730 + position= 54 count= 33918 + position= 55 count= 33918 + position= 56 count= 33918 + position= 57 count= 33918 + position= 58 count= 33918 + position= 59 count= 33918 + position= 60 count= 33918 + position= 61 count= 33918 + position= 62 count= 35015 + position= 63 count= 35015 + position= 64 count= 35015 + position= 65 count= 35015 + position= 66 count= 35015 + position= 67 count= 35015 + position= 68 count= 14759 + position= 69 count= 14759 + position= 70 count= 14759 + position= 71 count= 14759 + position= 72 count= 14759 + position= 73 count= 14759 + position= 74 count= 14759 + position= 75 count= 14759 + position= 76 count= 41591 + position= 77 count= 41591 + position= 78 count= 41591 + position= 79 count= 41591 + position= 80 count= 41591 + position= 81 count= 41591 + position= 82 count= 41591 + position= 83 count= 41591 + position= 84 count= 36918 + position= 85 count= 36918 + position= 86 count= 36918 + position= 87 count= 21210 + position= 88 count= 21210 + position= 89 count= 30619 + position= 90 count= 30619 + position= 91 count= 30619 + position= 92 count= 30619 + position= 93 count= 30619 + position= 94 count= 30619 + position= 95 count= 30619 + position= 96 count= 30619 + position= 97 count= 29739 + position= 98 count= 29739 + position= 99 count= 29739 + position= 100 count= 29739 + position= 101 count= 29739 + position= 102 count= 29739 + position= 103 count= 29739 + position= 104 count= 29739 + position= 105 count= 29739 + position= 106 count= 8300 + position= 107 count= 8300 + position= 108 count= 8300 + position= 109 count= 8300 + position= 110 count= 8300 + position= 111 count= 8300 + position= 112 count= 8300 + position= 113 count= 8300 + position= 114 count= 8300 + position= 115 count= 17774 + position= 116 count= 16626 + position= 117 count= 25425 + position= 118 count= 25425 + position= 119 count= 25425 + position= 120 count= 25425 + position= 121 count= 25425 + position= 122 count= 25425 + position= 123 count= 25425 + position= 124 count= 25425 + position= 125 count= 41492 + position= 126 count= 41492 + position= 127 count= 41492 + position= 128 count= 41492 + position= 129 count= 41492 + position= 130 count= 41492 + position= 131 count= 41492 + position= 132 count= 4916 + position= 133 count= 4916 + position= 134 count= 4916 + position= 135 count= 4916 + position= 136 count= 4916 + position= 137 count= 4916 + position= 138 count= 4916 + position= 139 count= 4916 + position= 140 count= 4916 + position= 141 count= 48770 + position= 142 count= 48770 + position= 143 count= 48770 + position= 144 count= 48770 + position= 145 count= 40261 + position= 146 count= 40261 + position= 147 count= 28376 + position= 148 count= 28376 + position= 149 count= 28376 + position= 150 count= 28376 + position= 151 count= 28376 + position= 152 count= 28376 + position= 153 count= 28376 + position= 154 count= 35125 + position= 155 count= 27842 + position= 156 count= 27842 + position= 157 count= 27842 + position= 158 count= 27842 + position= 159 count= 27842 + appending (count=10,length=4) + appending (count=1,length=0) + appending (count=2,length=8) +Hello + appending (count=10,length=4) +19:41:42.591 WARN WiggleWindow - Not writing 101 7 +19:41:42.592 WARN WiggleWindow - Not writing 111 7 +19:41:42.592 WARN WiggleWindow - Not writing 131 8 +19:41:42.592 WARN WiggleWindow - Not writing 141 8 +19:41:42.592 WARN WiggleWindow - Not writing 151 8 + peak : start :5 count :13 length :100010 + peak : start :100020 count :10 length :1 original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 140.207 s - in TestSuite -11:12:39.428 INFO GobyRengine - Shutdown hook is terminating R +qPhred=1 +qPhred=2 +qPhred=3 +qPhred=4 +qPhred=5 +qPhred=6 +qPhred=7 +qPhred=8 +qPhred=9 +qPhred=10 +qPhred=11 +qPhred=12 +qPhred=13 +qPhred=14 +qPhred=15 +qPhred=16 +qPhred=17 +qPhred=18 +qPhred=19 +qPhred=20 +qPhred=21 +qPhred=22 +qPhred=23 +qPhred=24 +qPhred=25 +qPhred=26 +qPhred=27 +qPhred=28 +qPhred=29 +qPhred=30 +qPhred=31 +qPhred=32 +qPhred=33 +qPhred=34 +qPhred=35 +qPhred=36 +qPhred=37 +qPhred=38 +qPhred=39 +qPhred=40 +qPhred=41 +qPhred=42 +qPhred=43 +qPhred=44 +qPhred=45 +qPhred=46 +qPhred=47 +qPhred=48 +qPhred=49 +qPhred=50 +qPhred=51 +qPhred=52 +qPhred=53 +qPhred=54 +qPhred=55 +qPhred=56 +qPhred=57 +qPhred=58 +qPhred=59 +qPhred=60 +qPhred=61 + 0 +AAC 3 +ACC 6 +ATC 9 +AGC 12 +AAC 15 +ACC 18 +ATC 21 +AGC 24 +AAC 27 +ACC 30 +ATC 33 +AGC 36 +AAC 39 +ACC 42 +ATC 45 +AGC 48 +AAC 51 +ACC 54 +ATC 57 +AGC 60 +AAC 63 +ACC 66 +ATC 69 +AGC 72 +AAC 75 +ACC 78 +ATC 81 +AGC19:41:46.289 WARN MessageChunksWriter - Using chunk-size=9 +19:41:46.291 WARN MessageChunksWriter - Using chunk-size=9 +Total logical entries written: 39 +Total bytes written: 660 +Average bytes/logical entry: 16.923077 +Number of bits/base 3.6590436 +19:41:46.292 WARN MessageChunksWriter - Using chunk-size=9 +Total logical entries written: 39 +Total bytes written: 685 +Average bytes/logical entry: 17.564102 +Number of bits/base 3.797644 +19:41:46.294 WARN MessageChunksWriter - Using chunk-size=9 +Total logical entries written: 39 +Total bytes written: 660 +Average bytes/logical entry: 16.923077 +Number of bits/base 3.6590436 +>1 +NNTGAATGAGACCTA + +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 64.137 s - in TestSuite +19:41:46.600 INFO GobyRengine - Shutdown hook is terminating R [INFO] [INFO] Results: [INFO] @@ -9320,14 +9355,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.080 s] -[INFO] Goby I/O ........................................... SUCCESS [ 15.437 s] -[INFO] Goby Full Distribution ............................. SUCCESS [02:53 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.034 s] +[INFO] Goby I/O ........................................... SUCCESS [ 5.552 s] +[INFO] Goby Full Distribution ............................. SUCCESS [01:14 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 03:09 min -[INFO] Finished at: 2024-10-11T11:12:47-12:00 +[INFO] Total time: 01:19 min +[INFO] Finished at: 2025-11-14T19:41:52+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -9398,14 +9433,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.607 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.074 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.058 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.601 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.047 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.178 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.052 s -[INFO] Finished at: 2024-10-11T11:12:50-12:00 +[INFO] Total time: 0.948 s +[INFO] Finished at: 2025-11-14T19:41:54+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore Analysing pom.xml... @@ -9416,12 +9451,12 @@ > dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine -Oct 11, 2024 11:12:57 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Nov 14, 2025 7:42:00 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 -Oct 11, 2024 11:13:03 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Nov 14, 2025 7:42:05 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian @@ -9448,13 +9483,13 @@ dh_missing dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined -dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined +dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined +dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'. @@ -9466,12 +9501,14 @@ 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/1730115/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1730115/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/733974 and its subdirectories -I: Current time: Fri Oct 11 11:13:22 -12 2024 -I: pbuilder-time-stamp: 1728688402 +I: removing directory /srv/workspace/pbuilder/1730115 and its subdirectories +I: Current time: Fri Nov 14 19:42:14 +14 2025 +I: pbuilder-time-stamp: 1763098934