Diff of the two buildlogs: -- --- b1/build.log 2024-05-26 07:14:03.791891111 +0000 +++ b2/build.log 2024-05-26 07:23:06.800799056 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 25 18:57:33 -12 2024 -I: pbuilder-time-stamp: 1716706653 +I: Current time: Sun Jun 29 03:37:18 +14 2025 +I: pbuilder-time-stamp: 1751117838 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying lowering_heap_allocation.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2592240/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2870149/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 28 13:37 /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/2870149/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2870149/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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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='076c344d97ec42d2b741705350683466' - 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='2592240' - PS1='# ' - PS2='> ' + INVOCATION_ID=e456ba2d62614e91985b07eef1f3916c + 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=2870149 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.JzreLDA3/pbuilderrc_hFXo --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.JzreLDA3/b1 --logfile b1/build.log snpeff_5.2.b+dfsg-1.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.JzreLDA3/pbuilderrc_3GaJ --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.JzreLDA3/b2 --logfile b2/build.log snpeff_5.2.b+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2592240/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 26 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2870149/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -570,7 +602,7 @@ Get: 412 http://deb.debian.org/debian trixie/main amd64 maven all 3.8.7-2 [19.3 kB] Get: 413 http://deb.debian.org/debian trixie/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 414 http://deb.debian.org/debian trixie/main amd64 maven-debian-helper all 2.6.4 [108 kB] -Fetched 353 MB in 13s (28.1 MB/s) +Fetched 353 MB in 6s (60.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19700 files and directories currently installed.) @@ -1912,8 +1944,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun May 26 07:03:19 UTC 2024. -Universal Time is now: Sun May 26 07:03:19 UTC 2024. +Local time is now: Sat Jun 28 13:39:05 UTC 2025. +Universal Time is now: Sat Jun 28 13:39:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2449,7 +2481,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snpeff-5.2.b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpeff_5.2.b+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2870149/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2870149/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snpeff-5.2.b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snpeff_5.2.b+dfsg-1_source.changes dpkg-buildpackage: info: source package snpeff dpkg-buildpackage: info: source version 5.2.b+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2482,7 +2518,7 @@ sed "s/Gpr\.compile.*/\"$(date --utc --date="@1701186978" +"%Y-%m-%d %H:%M" )\";/" SnpEff.java.old > src/main/java/org/snpeff/SnpEff.java dh_auto_configure mh_patchpoms -plibsnpeff-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian/maven-repo -Failed to parse /build/reproducible-path/snpeff-5.2.b+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /build/reproducible-path/snpeff-5.2.b+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -2498,7 +2534,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.repo.POMTransformer.main(POMTransformer.java:779) -Failed to parse /build/reproducible-path/snpeff-5.2.b+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /build/reproducible-path/snpeff-5.2.b+dfsg/debian/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -2556,55 +2592,55 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings +[WARNING] Loading source files for package org.snpeff.complexity... +[WARNING] Loading source files for package org.snpeff.overlap... +[WARNING] Loading source files for package org.snpeff... +[WARNING] Loading source files for package org.snpeff.gtex... +[WARNING] Loading source files for package org.snpeff.ped... +[WARNING] Loading source files for package org.snpeff.snpEffect... +[WARNING] Loading source files for package org.snpeff.snpEffect.factory... +[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... +[WARNING] Loading source files for package org.snpeff.collections... +[WARNING] Loading source files for package org.snpeff.motif... +[WARNING] Loading source files for package org.snpeff.util... +[WARNING] Loading source files for package org.snpeff.nextProt... +[WARNING] Loading source files for package org.snpeff.stats... +[WARNING] Loading source files for package org.snpeff.stats.plot... +[WARNING] Loading source files for package org.snpeff.fastq... [WARNING] Loading source files for package org.snpeff.fileIterator... [WARNING] Loading source files for package org.snpeff.fileIterator.parser... [WARNING] Loading source files for package org.snpeff.fileIterator.microCosm... -[WARNING] Loading source files for package org.snpeff.collections... -[WARNING] Loading source files for package org.snpeff.interval... -[WARNING] Loading source files for package org.snpeff.interval.codonChange... -[WARNING] Loading source files for package org.snpeff.interval.tree... -[WARNING] Loading source files for package org.snpeff.genotypes... -[WARNING] Loading source files for package org.snpeff... -[WARNING] Loading source files for package org.snpeff.serializer... -[WARNING] Loading source files for package org.snpeff.spliceSites... -[WARNING] Loading source files for package org.snpeff.coverage... -[WARNING] Loading source files for package org.snpeff.gsa... -[WARNING] Loading source files for package org.snpeff.gtex... -[WARNING] Loading source files for package org.snpeff.genBank... -[WARNING] Loading source files for package org.snpeff.align... -[WARNING] Loading source files for package org.snpeff.overlap... +[WARNING] Loading source files for package org.snpeff.nmer... [WARNING] Loading source files for package org.snpeff.sam... +[WARNING] Loading source files for package org.snpeff.probablility... +[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... +[WARNING] Loading source files for package org.snpeff.vcf... +[WARNING] Loading source files for package org.snpeff.genotypes... [WARNING] Loading source files for package org.snpeff.outputFormatter... [WARNING] Loading source files for package org.snpeff.codons... -[WARNING] Loading source files for package org.snpeff.complexity... -[WARNING] Loading source files for package org.snpeff.nextProt... -[WARNING] Loading source files for package org.snpeff.filter... +[WARNING] Loading source files for package org.snpeff.geneOntology... +[WARNING] Loading source files for package org.snpeff.align... [WARNING] Loading source files for package org.snpeff.svg... -[WARNING] Loading source files for package org.snpeff.ped... +[WARNING] Loading source files for package org.snpeff.binseq.indexer... [WARNING] Loading source files for package org.snpeff.binseq... [WARNING] Loading source files for package org.snpeff.binseq.coder... [WARNING] Loading source files for package org.snpeff.binseq.comparator... -[WARNING] Loading source files for package org.snpeff.binseq.indexer... +[WARNING] Loading source files for package org.snpeff.genBank... +[WARNING] Loading source files for package org.snpeff.gsa... [WARNING] Loading source files for package org.snpeff.geneSets.algorithm... [WARNING] Loading source files for package org.snpeff.geneSets... -[WARNING] Loading source files for package org.snpeff.geneOntology... +[WARNING] Loading source files for package org.snpeff.osCmd... +[WARNING] Loading source files for package org.snpeff.logStatsServer... [WARNING] Loading source files for package org.snpeff.reactome... [WARNING] Loading source files for package org.snpeff.reactome.events... -[WARNING] Loading source files for package org.snpeff.osCmd... -[WARNING] Loading source files for package org.snpeff.motif... -[WARNING] Loading source files for package org.snpeff.util... -[WARNING] Loading source files for package org.snpeff.stats... -[WARNING] Loading source files for package org.snpeff.stats.plot... +[WARNING] Loading source files for package org.snpeff.spliceSites... [WARNING] Loading source files for package org.snpeff.pdb... -[WARNING] Loading source files for package org.snpeff.vcf... -[WARNING] Loading source files for package org.snpeff.nmer... -[WARNING] Loading source files for package org.snpeff.fastq... -[WARNING] Loading source files for package org.snpeff.snpEffect... -[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... -[WARNING] Loading source files for package org.snpeff.snpEffect.factory... -[WARNING] Loading source files for package org.snpeff.probablility... -[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... -[WARNING] Loading source files for package org.snpeff.logStatsServer... +[WARNING] Loading source files for package org.snpeff.interval... +[WARNING] Loading source files for package org.snpeff.interval.tree... +[WARNING] Loading source files for package org.snpeff.interval.codonChange... +[WARNING] Loading source files for package org.snpeff.serializer... +[WARNING] Loading source files for package org.snpeff.coverage... +[WARNING] Loading source files for package org.snpeff.filter... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 @@ -3445,442 +3481,442 @@ [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/package-tree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BinSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VariantFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FastaFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BlastResultFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/LineSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FastqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/complexity/class-use/SequenceComplexity.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/SequenceRotator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/Overlap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/BasesChangeCounter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/OverlapDnaSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Zzz.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Qseq2Fastq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Pcingola.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/PromoterSequences.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationConsensusMultipleBed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.OutputFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.InputFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.GeneDatabaseFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileSplitBytType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileConsensus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Fastq2Fastq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/GtexExperiment.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/Gtex.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/IdMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/Sex.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedGenotype.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedPedigree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/TfamEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedFamily.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PlinkMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/LossOfFunction.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffects.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffectStructural.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotatorChain.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.FunctionalClass.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.EffectImpact.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.Coding.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/Config.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/SnpEffectPredictor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/HgvsProtein.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/HgvsDna.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/Hgvs.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffectFusion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/IntHisto.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/ErrorWarningType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/EffectType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/PurityChange.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGtf22.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenBank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenesFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryKnownGene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactory.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryFeatures.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryEmbl.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRand.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff3.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRefSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff2.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuild.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdPdb.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCount.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdLen.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGsa.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGenes2Bed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDownload.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdTranslocationsReport.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.DumpFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdEff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDatabases.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdClosest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuildNextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdAcat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdShow.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdProtein.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/CommandLine.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/ArrayUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/AutoHashMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/HashLongLongArray.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/BitUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/OpenBitSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/MultivalueHashMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/Pwm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/MotifLogo.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/PwmAndSeqs.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/Jaspar.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/GprSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Download.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/IubString.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/CombinatorialIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Log.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Log.FatalErrorBehabiour.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/KeyValue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Timer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Gpr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/GprHtml.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Iterator2Iterable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Tuple.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Diff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtMarkerFactory.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoform.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtDb.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlNode.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/Location.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtSequenceConservation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlIsoform.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlAnnotation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoformInteraction.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtHandler.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/CvTerm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantEffectStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/MineMarkerIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/BooleanMutable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CountByType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/MineTwoMarkerIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CounterDouble.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/Average.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/Counter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHH.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCpG.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHG.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/SamplingStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/AlleleCountStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpected.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/GenotypeStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/TranslocationReport.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ChrPosStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ReadsOnMarkersModel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/GeneCountByTypeTable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/IntStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CoverageByType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/PosStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/HomHetStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VcfStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CountByKey.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantTypeStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/FloatStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/TsTvStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/AverageInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GooglePlotInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionNumExonsChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleHistogram.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleBarChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleLineChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleChartVenn.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGenePercentBar.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GooglePlot.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqSplit.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmerMedian.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmerAdrian.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTools.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/LineFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VcfHapMapFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqIdFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/RegulationGffFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MotifFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/GenericMarkerFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/SamFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/RegulationFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/Gff3FileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MatrixEntryFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MotifFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FastaFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MatrixEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/NullReader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/SeekableBufferedReader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BinSeqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/LineSeqFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/GuessTableTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BlastResultEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VcfHapMapFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/GenericMarkerFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VariantTxtFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/LineClassFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqPeFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/NullReader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MatrixEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FastqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BlastResultFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/RegulationBedFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VariantFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BigBedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/SamFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BedFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqIdFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/VcfFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/SeekableBufferedReader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/RegulationBedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/BlastResultEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqPeFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/RegulationGffFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/MatrixEntryFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/TableFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/DnaSeqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/LineClassFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/class-use/Gff3FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/parser/class-use/Parser.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/microCosm/class-use/MicroCosmEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fileIterator/microCosm/class-use/MicroCosmFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/MultivalueHashMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/AutoHashMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/HashLongLongArray.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/ArrayUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/BitUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/collections/class-use/OpenBitSet.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSite.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GenericMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Custom.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/NextProt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/RareAminoAcid.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/CytoBands.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr3prime.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteBranchU12.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinProteinInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Transcript.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/BioType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ExonSpliceCharacterizer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Regulation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Upstream.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalSetIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteBranch.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantWithScore.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteRegion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantNonRef.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Motif.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Exon.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Exon.ExonSpliceType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gtf2Marker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerWithFrame.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Markers.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GffType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ChromosomeSimpleName.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntergenicConserved.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntronConserved.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantBnd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Variant.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Variant.VariantType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Genome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalAndSubIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gene.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gene.GeneType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Marker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Intron.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Downstream.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/CircularCorrection.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinStructuralInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalComparatorByStart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerParentId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteDonor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GffMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/TranscriptSupportLevel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalComparatorByEnd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Chromosome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr5prime.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MicroRnaBindingSite.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Cds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/FrameType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Intergenic.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteAcceptor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Interval.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Genes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMixed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInterval.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeSnp.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeStructural.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeIns.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMnp.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInv.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChange.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDup.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeArray.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeOri.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalNodeOri.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/Itree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalNode.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalForest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genotypes/class-use/GenotypeVector.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genotypes/class-use/Genotypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.InputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/SnpEff.GeneDatabaseFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Qseq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/PromoterSequences.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Pcingola.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileSplitBytType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Zzz.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationFileConsensus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/Fastq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/class-use/RegulationConsensusMultipleBed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/MarkerSerializer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/TxtSerializable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/AcgtTree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/SnpEffCmdSpliceAnalysis.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/SpliceTypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/TranscriptSet.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountReadsOnMarkers.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountReads.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CoverageChr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/Coverage.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountFragments.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/MarkerTypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ScoreList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ScoreList.ScoreSummary.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/PvaluesList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ChrPosScoreList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/Gtex.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/IdMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gtex/class-use/GtexExperiment.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/FeaturesFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Embl.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/FeatureCoordinates.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/GenBank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/GenBankFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Feature.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Feature.Type.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/EmblFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Features.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/StringDiff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/VariantRealign.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/SmithWaterman.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/NeedlemanWunschOverlap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/VcfRefAltAlign.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/NeedlemanWunsch.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/OverlapDnaSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/Overlap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/BasesChangeCounter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/overlap/class-use/SequenceRotator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/Nmer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/NmerCountWc.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/NmerCount.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeaderRecord.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeaderRecordSq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/sam/class-use/SamHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/Binomial.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RandMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/CochranArmitageTest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementSimulate.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/FisherExactTest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumPdf.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/Hypergeometric.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementPdf.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/NormalDistribution.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMapRank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfConsequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfConsequenceHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.VcfInfoNumber.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/Pedigree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfGenotype.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEntry.AlleleFrequencyType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/EffFormatVersion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfLof.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VariantVcfEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/LineChrPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfInfoType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfNmd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEffect.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.LineAndPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.FileRegion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/PedigreeEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genotypes/class-use/GenotypeVector.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genotypes/class-use/Genotypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/outputFormatter/class-use/OutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/outputFormatter/class-use/BedOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/outputFormatter/class-use/VcfOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/outputFormatter/class-use/BedAnnotationOutputFormatter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/outputFormatter/class-use/OutputFormatter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/codons/class-use/CodonTables.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/codons/class-use/FindRareAaIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/codons/class-use/CodonTables.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/codons/class-use/CodonTable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/complexity/class-use/SequenceComplexity.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtMarkerFactory.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtHandler.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoformInteraction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtDb.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/Location.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlNode.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtXmlAnnotation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/CvTerm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nextProt/class-use/NextProtSequenceConservation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/VariantEffectFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/Filter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgExon.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgNextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/GoTerms.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/GoTerm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/CompareByValue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/SmithWaterman.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/NeedlemanWunsch.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/VcfRefAltAlign.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/NeedlemanWunschOverlap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/StringDiff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/class-use/VariantRealign.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgGene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgScale.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgSpacer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/Svg.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgTranscript.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgScale.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgTranslocation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgIntron.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgBnd.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgCds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgGene.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedPedigree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedGenotype.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PlinkMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/Sex.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/TfamEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/ped/class-use/PedFamily.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequenceByte.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/GenomicSequences.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/BinarySequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequencePe.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgNextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgBnd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/svg/class-use/SvgExon.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapRessult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/SuffixIndexerNmer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterCompareAllAll.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterDnaId.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/SequenceIndexer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/IdGenerator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaNSequence.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequenceWithId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequenceId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaNSequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/GenomicSequences.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/BinarySequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequenceByte.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequencePe.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequence.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/class-use/DnaSequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/coder/class-use/Coder.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/coder/class-use/DnaQualityCoder.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/coder/class-use/DnaCoder.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/coder/class-use/Coder.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/DnaQualSubsequenceComparator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/SequenceReference.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/DnaSubsequenceComparator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/DnaQualSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/SubsequenceComparator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterDnaId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/SequenceIndexer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterCompareAllAll.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/OverlapRessult.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/indexer/class-use/SuffixIndexerNmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/comparator/class-use/SequenceReference.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/EmblFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/FeatureCoordinates.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Features.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/GenBank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Feature.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Feature.Type.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/GenBankFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/FeaturesFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/genBank/class-use/Embl.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ChrPosScoreList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/PvaluesList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ScoreList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/gsa/class-use/ScoreList.ScoreSummary.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueGreedyAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueGreedyAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/NoneAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedyVariableSize.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedy.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueGreedyAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedyVariableSize.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.EnrichmentAlgorithmType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSet.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/CompareByValue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSets.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSetsRanked.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSetsRanked.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/GeneSets.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneSets/class-use/Result.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/CompareByValue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/GoTerm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/geneOntology/class-use/GoTerms.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/OsCmdQueue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/LineFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/StreamGobbler.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/OsCmdRunner.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/Progress.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/ExecuteOsCommand.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/VersionCheck.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/LogStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/LogStats.RequestResult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/GeneIds.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Reactome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Monitor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Entity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Entity.TransferFunction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/GeneIds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Polymerisation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Reaction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Reaction.RegulationType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Complex.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Event.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Depolymerisation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Monitor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/class-use/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Pathway.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Complex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/BlackBoxEvent.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Polymerisation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Depolymerisation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Event.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/CatalystActivity.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/OsCmdRunner.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/OsCmdQueue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/StreamGobbler.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/ExecuteOsCommand.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/Progress.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/osCmd/class-use/LineFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/MotifLogo.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/Pwm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/PwmAndSeqs.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/motif/class-use/Jaspar.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Download.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Timer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Tuple.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Diff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/IubString.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/GprSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Iterator2Iterable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Log.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Log.FatalErrorBehabiour.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/Gpr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/KeyValue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/CombinatorialIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/util/class-use/GprHtml.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/FloatStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/HomHetStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CounterDouble.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CoverageByType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/BooleanMutable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CountByType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/AlleleCountStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCpG.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/TsTvStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHG.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHH.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/Counter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/GeneCountByTypeTable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VcfStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantTypeStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/MineTwoMarkerIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ChrPosStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/TranslocationReport.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/PosStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/Average.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/AverageInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/GenotypeStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/CountByKey.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ReadsOnMarkersModel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/MineMarkerIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/ObservedOverExpected.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/IntStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/VariantEffectStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/class-use/SamplingStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GooglePlotInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleBarChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionNumExonsChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GooglePlot.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleHistogram.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGenePercentBar.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleChartVenn.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleLineChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/PdbUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Reaction.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/reactome/events/class-use/Reaction.RegulationType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/AcgtTree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/TranscriptSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/SpliceTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/spliceSites/class-use/SnpEffCmdSpliceAnalysis.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/IdMapperEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/IdMapper.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/PdbUtil.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/PdbFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/DistanceResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/ProteinInteractions.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfNmd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VariantVcfEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfConsequenceHeader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEffect.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/EffFormatVersion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfConsequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfLof.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.VcfInfoNumber.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.LineAndPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.FileRegion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/Pedigree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/PedigreeEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfEntry.AlleleFrequencyType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/LineChrPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfGenotype.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeaderEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfHeader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/vcf/class-use/VcfInfoType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/NmerCount.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/Nmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/nmer/class-use/NmerCountWc.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmerAdrian.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTools.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqTrimmerMedian.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/fastq/class-use/FastqSplit.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotatorChain.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/LossOfFunction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/ErrorWarningType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/PurityChange.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/IntHisto.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/SnpEffectPredictor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/EffectType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/Config.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/HgvsProtein.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.FunctionalClass.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.EffectImpact.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.Coding.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/Hgvs.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffectFusion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/HgvsDna.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffectStructural.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VariantEffects.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.DumpFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGenes2Bed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/CommandLine.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDownload.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdEff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdPdb.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDatabases.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdShow.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdLen.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCount.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdClosest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGsa.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuildNextProt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdAcat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuild.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdProtein.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdTranslocationsReport.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRefSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryKnownGene.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenesFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenBank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryEmbl.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactory.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff3.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRand.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryFeatures.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff2.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGtf22.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/CochranArmitageTest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/FisherExactTest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementPdf.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/Hypergeometric.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/NormalDistribution.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RandMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/Binomial.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumPdf.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementSimulate.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMapRank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/LogStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/LogStats.RequestResult.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/logStatsServer/class-use/VersionCheck.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/IdMapper.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/pdb/class-use/DistanceResult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalAndSubIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/CircularCorrection.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Intergenic.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ExonSpliceCharacterizer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gene.GeneType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MicroRnaBindingSite.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinProteinInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteBranch.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Genome.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntergenicConserved.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Upstream.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantBnd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr3prime.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Exon.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Exon.ExonSpliceType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GenericMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalComparatorByEnd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/TranscriptSupportLevel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerParentId.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/MarkerWithFrame.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteDonor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalComparatorByStart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Transcript.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Motif.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ChromosomeSimpleName.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/NextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Gtf2Marker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Chromosome.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Variant.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Variant.VariantType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Interval.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Downstream.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteRegion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSite.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteAcceptor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/ProteinStructuralInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/RareAminoAcid.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Marker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Regulation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Markers.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantNonRef.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Intron.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/SpliceSiteBranchU12.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Cds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/BioType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntronConserved.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Utr5prime.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Custom.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/Genes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GffType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/VariantWithScore.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/FrameType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/GffMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/CytoBands.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/class-use/IntervalSetIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/Itree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeArray.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeOri.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalForest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalNodeOri.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalNode.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/tree/class-use/IntervalTree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInterval.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInv.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeSnp.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeIns.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMixed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDup.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeStructural.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMnp.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/interval/codonChange/class-use/CodonChange.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/MarkerSerializer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/serializer/class-use/TxtSerializable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountReadsOnMarkers.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountFragments.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/Coverage.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CountReads.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/CoverageChr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/coverage/class-use/MarkerTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/VariantEffectFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/filter/class-use/Filter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/align/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/apidocs/org/snpeff/binseq/package-use.html... @@ -3966,55 +4002,55 @@ [INFO] Adding the --ignore-source-errors option [INFO] Configuration changed, re-generating javadoc. [WARNING] Javadoc Warnings +[WARNING] Loading source files for package org.snpeff.complexity... +[WARNING] Loading source files for package org.snpeff.overlap... +[WARNING] Loading source files for package org.snpeff... +[WARNING] Loading source files for package org.snpeff.gtex... +[WARNING] Loading source files for package org.snpeff.ped... +[WARNING] Loading source files for package org.snpeff.snpEffect... +[WARNING] Loading source files for package org.snpeff.snpEffect.factory... +[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... +[WARNING] Loading source files for package org.snpeff.collections... +[WARNING] Loading source files for package org.snpeff.motif... +[WARNING] Loading source files for package org.snpeff.util... +[WARNING] Loading source files for package org.snpeff.nextProt... +[WARNING] Loading source files for package org.snpeff.stats... +[WARNING] Loading source files for package org.snpeff.stats.plot... +[WARNING] Loading source files for package org.snpeff.fastq... [WARNING] Loading source files for package org.snpeff.fileIterator... [WARNING] Loading source files for package org.snpeff.fileIterator.parser... [WARNING] Loading source files for package org.snpeff.fileIterator.microCosm... -[WARNING] Loading source files for package org.snpeff.collections... -[WARNING] Loading source files for package org.snpeff.interval... -[WARNING] Loading source files for package org.snpeff.interval.codonChange... -[WARNING] Loading source files for package org.snpeff.interval.tree... -[WARNING] Loading source files for package org.snpeff.genotypes... -[WARNING] Loading source files for package org.snpeff... -[WARNING] Loading source files for package org.snpeff.serializer... -[WARNING] Loading source files for package org.snpeff.spliceSites... -[WARNING] Loading source files for package org.snpeff.coverage... -[WARNING] Loading source files for package org.snpeff.gsa... -[WARNING] Loading source files for package org.snpeff.gtex... -[WARNING] Loading source files for package org.snpeff.genBank... -[WARNING] Loading source files for package org.snpeff.align... -[WARNING] Loading source files for package org.snpeff.overlap... +[WARNING] Loading source files for package org.snpeff.nmer... [WARNING] Loading source files for package org.snpeff.sam... +[WARNING] Loading source files for package org.snpeff.probablility... +[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... +[WARNING] Loading source files for package org.snpeff.vcf... +[WARNING] Loading source files for package org.snpeff.genotypes... [WARNING] Loading source files for package org.snpeff.outputFormatter... [WARNING] Loading source files for package org.snpeff.codons... -[WARNING] Loading source files for package org.snpeff.complexity... -[WARNING] Loading source files for package org.snpeff.nextProt... -[WARNING] Loading source files for package org.snpeff.filter... +[WARNING] Loading source files for package org.snpeff.geneOntology... +[WARNING] Loading source files for package org.snpeff.align... [WARNING] Loading source files for package org.snpeff.svg... -[WARNING] Loading source files for package org.snpeff.ped... +[WARNING] Loading source files for package org.snpeff.binseq.indexer... [WARNING] Loading source files for package org.snpeff.binseq... [WARNING] Loading source files for package org.snpeff.binseq.coder... [WARNING] Loading source files for package org.snpeff.binseq.comparator... -[WARNING] Loading source files for package org.snpeff.binseq.indexer... +[WARNING] Loading source files for package org.snpeff.genBank... +[WARNING] Loading source files for package org.snpeff.gsa... [WARNING] Loading source files for package org.snpeff.geneSets.algorithm... [WARNING] Loading source files for package org.snpeff.geneSets... -[WARNING] Loading source files for package org.snpeff.geneOntology... +[WARNING] Loading source files for package org.snpeff.osCmd... +[WARNING] Loading source files for package org.snpeff.logStatsServer... [WARNING] Loading source files for package org.snpeff.reactome... [WARNING] Loading source files for package org.snpeff.reactome.events... -[WARNING] Loading source files for package org.snpeff.osCmd... -[WARNING] Loading source files for package org.snpeff.motif... -[WARNING] Loading source files for package org.snpeff.util... -[WARNING] Loading source files for package org.snpeff.stats... -[WARNING] Loading source files for package org.snpeff.stats.plot... +[WARNING] Loading source files for package org.snpeff.spliceSites... [WARNING] Loading source files for package org.snpeff.pdb... -[WARNING] Loading source files for package org.snpeff.vcf... -[WARNING] Loading source files for package org.snpeff.nmer... -[WARNING] Loading source files for package org.snpeff.fastq... -[WARNING] Loading source files for package org.snpeff.snpEffect... -[WARNING] Loading source files for package org.snpeff.snpEffect.commandLine... -[WARNING] Loading source files for package org.snpeff.snpEffect.factory... -[WARNING] Loading source files for package org.snpeff.probablility... -[WARNING] Loading source files for package org.snpeff.probablility.bootstrap... -[WARNING] Loading source files for package org.snpeff.logStatsServer... +[WARNING] Loading source files for package org.snpeff.interval... +[WARNING] Loading source files for package org.snpeff.interval.tree... +[WARNING] Loading source files for package org.snpeff.interval.codonChange... +[WARNING] Loading source files for package org.snpeff.serializer... +[WARNING] Loading source files for package org.snpeff.coverage... +[WARNING] Loading source files for package org.snpeff.filter... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... [WARNING] Standard Doclet version 17.0.11+9-Debian-1 @@ -4855,442 +4891,442 @@ [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/package-tree.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/TableFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineClassFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MotifFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/FastqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/complexity/class-use/SequenceComplexity.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/BasesChangeCounter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/OverlapDnaSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/SequenceRotator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/Overlap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Pcingola.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Fastq2Fastq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationFileConsensus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationFileSplitBytType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationConsensusMultipleBed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.OutputFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.InputFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.GeneDatabaseFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/PromoterSequences.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Qseq2Fastq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Zzz.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/IdMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/Gtex.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/GtexExperiment.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/TfamEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedGenotype.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedFamily.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedPedigree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/Sex.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PlinkMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffects.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/HgvsDna.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/HgvsProtein.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.FunctionalClass.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.EffectImpact.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.Coding.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/Hgvs.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffectFusion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffectStructural.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/IntHisto.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/ErrorWarningType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotatorChain.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/SnpEffectPredictor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/PurityChange.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/EffectType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/LossOfFunction.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/Config.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRand.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenesFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRefSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryKnownGene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenBank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryEmbl.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGtf22.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff2.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryFeatures.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactory.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff3.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDatabases.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdTranslocationsReport.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGenes2Bed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCount.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuildNextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdProtein.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/CommandLine.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdClosest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdLen.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGsa.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDownload.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdAcat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdShow.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuild.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.DumpFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdEff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdPdb.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/HashLongLongArray.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/OpenBitSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/ArrayUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/AutoHashMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/BitUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/MultivalueHashMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/Jaspar.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/MotifLogo.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/Pwm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/PwmAndSeqs.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Download.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/KeyValue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Tuple.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Log.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Log.FatalErrorBehabiour.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/CombinatorialIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/GprHtml.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Iterator2Iterable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Gpr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/GprSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Timer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/IubString.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Diff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoform.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/CvTerm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoformInteraction.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtSequenceConservation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlNode.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtMarkerFactory.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlIsoform.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlAnnotation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/Location.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtDb.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtHandler.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/HomHetStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpected.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/GeneCountByTypeTable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/SamplingStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/Counter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CountByKey.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantTypeStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CoverageByType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/AlleleCountStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/BooleanMutable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/MineMarkerIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/GenotypeStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ReadsOnMarkersModel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/TranslocationReport.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantEffectStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/TsTvStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/FloatStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/Average.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHH.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCpG.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CountByType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/PosStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHG.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CounterDouble.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VcfStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/IntStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ChrPosStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/MineTwoMarkerIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/AverageInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleChartVenn.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleLineChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleBarChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionNumExonsChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionChart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGenePercentBar.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GooglePlotInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleHistogram.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GooglePlot.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTools.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqSplit.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmerAdrian.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmerMedian.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/SeekableBufferedReader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/FileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/NullReader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VariantTxtFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BinSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationGffFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/DnaSeqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationBedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/GuessTableTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MatrixEntryFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/DnaSeqIdFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VariantFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/NullReader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/SamFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BigBedFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MarkerFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/Gff3FileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/TableFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineClassFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/DnaSeqPeFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/FastaFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/GenericMarkerFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineSeqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MatrixEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BlastResultFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VcfFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MatrixEntryFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/DnaSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BlastResultEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VcfHapMapFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BlastResultFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/DnaSeqIdFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MarkerFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationBedFileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VariantFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineSeqFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/GenericMarkerFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/Gff3FileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BigBedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/LineFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MatrixEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/FastqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BlastResultEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/VariantTxtFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/RegulationGffFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/BinSeqFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/MotifFileIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/class-use/FileIterator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/parser/class-use/Parser.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/microCosm/class-use/MicroCosmEntry.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/microCosm/class-use/MicroCosmFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/ArrayUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/AutoHashMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/OpenBitSet.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/MultivalueHashMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/HashLongLongArray.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/collections/class-use/BitUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/CircularCorrection.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MicroRnaBindingSite.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Markers.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ChromosomeSimpleName.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Upstream.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Genes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gene.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gene.GeneType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Intergenic.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteBranchU12.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntergenicConserved.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntronConserved.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Custom.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinProteinInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerUtil.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantBnd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantNonRef.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerWithFrame.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Marker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSite.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalAndSubIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinStructuralInteractionLocus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Transcript.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantWithScore.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/TranscriptSupportLevel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerParentId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/FrameType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Regulation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Intron.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Cds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Variant.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Variant.VariantType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Chromosome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GenericMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Exon.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Exon.ExonSpliceType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GffType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/CytoBands.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Interval.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/BioType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalComparatorByStart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalSetIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteRegion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Downstream.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ExonSpliceCharacterizer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr5prime.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gtf2Marker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalComparatorByEnd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteAcceptor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr3prime.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteDonor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Motif.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteBranch.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/RareAminoAcid.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Genome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/NextProt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GffMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDup.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChange.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeIns.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeSnp.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMixed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMnp.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInv.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeStructural.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInterval.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/Itree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeOri.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalForest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalNodeOri.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalNode.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeArray.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genotypes/class-use/GenotypeVector.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genotypes/class-use/Genotypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationFileConsensus.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Qseq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationFileSplitBytType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.InputFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/SnpEff.GeneDatabaseFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Zzz.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/RegulationConsensusMultipleBed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/PromoterSequences.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Fastq2Fastq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/class-use/Pcingola.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/serializer/class-use/MarkerSerializer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/serializer/class-use/TxtSerializable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/AcgtTree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/TranscriptSet.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/SnpEffCmdSpliceAnalysis.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/SpliceTypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/MarkerTypes.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/Coverage.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountReadsOnMarkers.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountReads.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CoverageChr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountFragments.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ChrPosScoreList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ScoreList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ScoreList.ScoreSummary.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/PvaluesList.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/Gtex.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/GtexExperiment.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gtex/class-use/IdMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/FeaturesFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Features.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/FeatureCoordinates.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/EmblFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/GenBankFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/GenBank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Embl.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Feature.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Feature.Type.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/SmithWaterman.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/NeedlemanWunschOverlap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/VcfRefAltAlign.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/StringDiff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/VariantRealign.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/NeedlemanWunsch.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/OverlapDnaSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/BasesChangeCounter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/Overlap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/overlap/class-use/SequenceRotator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fileIterator/microCosm/class-use/MicroCosmEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/Nmer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/NmerCount.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/NmerCountWc.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamHeaderRecordSq.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamHeader.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamHeaderRecord.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/sam/class-use/SamHeaderRecordSq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/outputFormatter/class-use/BedAnnotationOutputFormatter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/CochranArmitageTest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumPdf.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementPdf.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/Hypergeometric.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RandMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/Binomial.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementSimulate.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/FisherExactTest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/NormalDistribution.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleInt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMapRank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfGenotype.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfLof.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfConsequenceHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VariantVcfEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/LineChrPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderFormat.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/Pedigree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.VcfInfoNumber.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEntry.AlleleFrequencyType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.LineAndPos.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.FileRegion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEffect.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfInfoType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfNmd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/EffFormatVersion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/PedigreeEntry.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfConsequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeader.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genotypes/class-use/GenotypeVector.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genotypes/class-use/Genotypes.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/outputFormatter/class-use/BedOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/outputFormatter/class-use/VcfOutputFormatter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/outputFormatter/class-use/BedAnnotationOutputFormatter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/outputFormatter/class-use/OutputFormatter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/codons/class-use/FindRareAaIntervals.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/codons/class-use/CodonTable.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/codons/class-use/CodonTables.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/codons/class-use/FindRareAaIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/complexity/class-use/SequenceComplexity.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtSequenceConservation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtMarkerFactory.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlAnnotation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/Location.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlNode.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/LocationTargetIsoformInteraction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/CvTerm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlIsoform.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtHandler.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtDb.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nextProt/class-use/NextProtXmlEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/filter/class-use/VariantEffectFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/filter/class-use/Filter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/GoTerm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/CompareByValue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/GoTerms.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/SmithWaterman.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/VariantRealign.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/StringDiff.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/NeedlemanWunschOverlap.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/NeedlemanWunsch.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/class-use/VcfRefAltAlign.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgGene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgNextProt.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgExon.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgSpacer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgCds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgTranslocation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgBnd.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgIntron.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgTranslocation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgCds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgSpacer.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgTranscript.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/Svg.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgNextProt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgGene.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgScale.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/SvgBnd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/Sex.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedGenotype.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedFileIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/TfamEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PlinkMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedFamily.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/ped/class-use/PedPedigree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequencePe.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaNSequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequenceByte.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/GenomicSequences.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/svg/class-use/Svg.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/SequenceIndexer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapRessult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterCompareAllAll.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/SuffixIndexerNmer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterDnaId.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequenceWithId.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/BinarySequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/GenomicSequences.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequenceId.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaNSequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/BinarySequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequence.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequenceByte.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/IdGenerator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaAndQualitySequenceWithId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/coder/class-use/Coder.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/class-use/DnaSequencePe.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/coder/class-use/DnaCoder.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/coder/class-use/DnaQualityCoder.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/SubsequenceComparator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/coder/class-use/Coder.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/DnaQualSubsequenceComparator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/DnaSubsequenceComparator.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/SequenceReference.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterDnaId.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/SuffixIndexerNmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/SequenceIndexer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapFilterCompareAllAll.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/indexer/class-use/OverlapRessult.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/NoneAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/DnaSubsequenceComparator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/comparator/class-use/SubsequenceComparator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Features.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/GenBank.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/FeaturesFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/FeatureCoordinates.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Embl.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Feature.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/Feature.Type.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/GenBankFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/genBank/class-use/EmblFile.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ChrPosScoreList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/PvaluesList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ScoreList.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/gsa/class-use/ScoreList.ScoreSummary.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedy.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithmGreedyVariableSize.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueGreedyAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/NoneAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/EnrichmentAlgorithm.EnrichmentAlgorithmType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/LeadingEdgeFractionAlgorithm.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueGreedyAlgorithm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueGreedyAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/FisherPValueAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/algorithm/class-use/RankSumPValueAlgorithm.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSets.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSetsRanked.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSet.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSets.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/GeneSet.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/CompareByValue.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneSets/class-use/Result.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/GoTerms.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/GoTerm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/geneOntology/class-use/CompareByValue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/StreamGobbler.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/ExecuteOsCommand.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/Progress.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/OsCmdQueue.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/LineFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/OsCmdRunner.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.RequestResult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/VersionCheck.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Reactome.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/GeneIds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Compartment.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Monitor.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Entity.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Entity.TransferFunction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/GeneIds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Reactome.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/class-use/Compartment.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Complex.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Depolymerisation.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/CatalystActivity.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Pathway.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Reaction.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Reaction.RegulationType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Event.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Pathway.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/BlackBoxEvent.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Depolymerisation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Complex.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Polymerisation.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/LineFilter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/OsCmdQueue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/Progress.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/StreamGobbler.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/OsCmdRunner.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/osCmd/class-use/ExecuteOsCommand.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/MotifLogo.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/PwmAndSeqs.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/Pwm.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/motif/class-use/Jaspar.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/KeyValue.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/GprSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/IubString.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Log.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Log.FatalErrorBehabiour.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Iterator2Iterable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/CombinatorialIterator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Tuple.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/GprHtml.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Download.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Diff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Timer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/util/class-use/Gpr.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantTypeStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/Counter.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/HomHetStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/TranslocationReport.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/SamplingStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCpG.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/FloatStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/AverageInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ChrPosStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VcfStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/Average.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/AlleleCountStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CoverageByType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHG.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/VariantEffectStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/MineTwoMarkerIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpectedCHH.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/GeneCountByTypeTable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ReadsOnMarkersModel.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CounterDouble.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/TsTvStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/PosStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/BooleanMutable.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/MineMarkerIntervals.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CountByType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/CountByKey.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/ObservedOverExpected.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/GenotypeStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/class-use/IntStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleBarChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionNumExonsChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GooglePlotInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleLineChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGenePercentBar.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleChartVenn.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleGeneRegionChart.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GooglePlot.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/stats/plot/class-use/GoogleHistogram.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/IdMapper.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/BlackBoxEvent.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/reactome/events/class-use/Event.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/SpliceTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/SnpEffCmdSpliceAnalysis.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/AcgtTree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/spliceSites/class-use/TranscriptSet.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/DistanceResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/PdbUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/IdMapper.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/PdbFile.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/ProteinInteractions.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/DistanceResult.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/IdMapperEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/pdb/class-use/PdbFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/EffFormatVersion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfLof.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfGenotype.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VariantVcfEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/Pedigree.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfConsequenceHeader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfInfoType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderInfo.VcfInfoNumber.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfNmd.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeader.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.LineAndPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/FileIndexChrPos.FileRegion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEntry.AlleleFrequencyType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfEffect.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/LineChrPos.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/PedigreeEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfConsequence.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/vcf/class-use/VcfHeaderEntry.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/NmerCount.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/Nmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/nmer/class-use/NmerCountWc.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqSplit.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmerMedian.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTools.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmer.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/fastq/class-use/FastqTrimmerAdrian.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/LossOfFunction.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/PurityChange.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/SnpEffectPredictor.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotator.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffectStructural.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/HgvsDna.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/IntHisto.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.FunctionalClass.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.EffectImpact.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffect.Coding.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/Hgvs.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffectFusion.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/ErrorWarningType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/EffectType.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/HgvsProtein.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/Config.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VariantEffects.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/class-use/VcfAnnotatorChain.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDump.DumpFormat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGsa.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdPdb.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/CommandLine.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdLen.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdEff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCount.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDatabases.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdDownload.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdCds.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdAcat.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdTranslocationsReport.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdClosest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdGenes2Bed.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuild.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdShow.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdProtein.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/commandLine/class-use/SnpEffCmdBuildNextProt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenesFile.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff2.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff3.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryKnownGene.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGenBank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRand.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryFeatures.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactory.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryEmbl.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGff.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryGtf22.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/snpEffect/factory/class-use/SnpEffPredictorFactoryRefSeq.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/Hypergeometric.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/FisherExactTest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumPdf.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/Binomial.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementSimulate.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RankSumNoReplacementPdf.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/CochranArmitageTest.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/RandMarker.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/class-use/NormalDistribution.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMap.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleMapRank.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/probablility/bootstrap/class-use/ReSampleInt.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/VersionCheck.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.html... -[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/logStatsServer/class-use/LogStats.RequestResult.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gene.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gene.GeneType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Intergenic.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/BioType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Interval.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr5prime.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Marker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/CircularCorrection.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteRegion.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinProteinInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/TranscriptSupportLevel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Regulation.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Genes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteDonor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerParentId.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Markers.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantWithScore.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Genome.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GffMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Downstream.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/RareAminoAcid.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalAndSubIntervals.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteBranchU12.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerSeq.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteAcceptor.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSiteBranch.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/NextProt.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Exon.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Exon.ExonSpliceType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Chromosome.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerWithFrame.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ExonSpliceCharacterizer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ProteinStructuralInteractionLocus.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantBnd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Cds.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntronConserved.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Variant.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Variant.VariantType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalSetIterator.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Intron.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Gtf2Marker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/CytoBands.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/VariantNonRef.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MarkerUtil.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalComparatorByEnd.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Upstream.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr3prime.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/MicroRnaBindingSite.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Motif.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/ChromosomeSimpleName.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Utr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Transcript.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/FrameType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GenericMarker.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntervalComparatorByStart.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/GffType.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/IntergenicConserved.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/Custom.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/class-use/SpliceSite.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeOri.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/Itree.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalNodeOri.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalForest.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalNode.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/tree/class-use/IntervalTreeArray.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMnp.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChange.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeIns.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeStructural.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeSnp.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInv.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeMixed.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDel.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeDup.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/interval/codonChange/class-use/CodonChangeInterval.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/serializer/class-use/TxtSerializable.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/serializer/class-use/MarkerSerializer.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountReads.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/MarkerTypes.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountFragments.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CountReadsOnMarkers.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/CoverageChr.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/coverage/class-use/Coverage.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/filter/class-use/VariantEffectFilter.html... +[WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/filter/class-use/Filter.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/align/package-use.html... [WARNING] Generating /build/reproducible-path/snpeff-5.2.b+dfsg/target/site/apidocs/org/snpeff/binseq/package-use.html... @@ -5352,8 +5388,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 46.231 s -[INFO] Finished at: 2024-05-25T19:05:11-12:00 +[INFO] Total time: 21.427 s +[INFO] Finished at: 2025-06-29T03:39:59+14:00 [INFO] ------------------------------------------------------------------------ dh_auto_test /usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/snpeff-5.2.b\+dfsg -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian -Dmaven.repo.local=/build/reproducible-path/snpeff-5.2.b\+dfsg/debian/maven-repo --batch-mode test @@ -5382,75 +5418,23 @@ [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -TestCasesProteinInteraction.test_02_split_codon_base(58): Test -TestCasesProteinInteraction.test_01_split_codon_base(26): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.164 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular -TestCasesCircular.test_circular_01(26): Test -TestCasesCircular.test_circular_02(54): Test -TestCasesCircular.test_circular_03(83): Test -TestCasesCircular.test_circular_04(103): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse -TestCasesEffectCollapse.test_01(68): Test -TestCasesEffectCollapse.test_02(74): Test -TestCasesEffectCollapse.test_03(80): Test -TestCasesEffectCollapse.test_04(86): Test -TestCasesEffectCollapse.test_05(92): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.478 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -TestCasesStructuralInv.test01_invGene(214): Test -TestCasesStructuralInv.test02(249): Test -TestCasesStructuralInv.test03(266): Test -TestCasesStructuralInv.test04(283): Test -TestCasesStructuralInv.test05(300): Test -TestCasesStructuralInv.test06(317): Test -TestCasesStructuralInv.test07(334): Test -TestCasesStructuralInv.test08(352): Test -TestCasesStructuralInv.test09(370): Test -TestCasesStructuralInv.test10(387): Test -TestCasesStructuralInv.test01_invTr(231): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.147 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.877 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant -TestCasesIntervalVariant.test_01(36): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.907 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron +TestCasesHgvsIntron.test_01_intron(23): Test +............................................................... +100 ............................................................ +200 ................................................................ +300 ......................................................... +400 ......................................................................................................................... +600 ......................................................................................................... +800 ....................................................... +900 .................................................................. +1000 ............................................................. +1100 .................................................................. +1200 ......................................................... +1300 ........................................................................................................... +1500 ....................................................... +1600 ............................................................... +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.589 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns TestCasesApplyIns.test_apply_variant_01(21): Test TestCasesApplyIns.test_apply_variant_02(32): Test @@ -5465,149 +5449,43 @@ TestCasesApplyIns.test_apply_variant_11(159): Test TestCasesApplyIns.test_apply_variant_12(178): Test TestCasesApplyIns.test_apply_variant_13(192): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.43 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test -TestCasesApplyMixed.test_apply_variant_06_longer(169): Test -TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test -TestCasesApplyMixed.test_apply_variant_04_longer(98): Test -TestCasesApplyMixed.test_apply_variant_09_longer(259): Test -TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test -TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test -TestCasesApplyMixed.test_apply_variant_02_longer(42): Test -TestCasesApplyMixed.test_apply_variant_07_longer(203): Test -TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test -TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test -TestCasesApplyMixed.test_apply_variant_05_longer(134): Test -TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test -TestCasesApplyMixed.test_apply_variant_03_longer(64): Test -TestCasesApplyMixed.test_apply_variant_08_longer(237): Test -TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test -TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test -TestCasesApplyMixed.test_apply_variant_01_longer(22): Test -[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.483 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf -TestCasesVcf.test_22_huge_headers(363): Test -TestCasesVcf.test_12_readHeader_NL(257): Test -TestCasesVcf.test_36_cleanupUnderscores(703): Test -TestCasesVcf.test_23_VcfUnsorted(379): Test -TestCasesVcf.test_00(40): Test -TestCasesVcf.test_01(54): Test -TestCasesVcf.test_29(568): Test -TestCasesVcf.test_16_indels(321): Test -TestCasesVcf.test_09_empty_ALT(195): Test -TestCasesVcf.test_27_vcfInfoHeaderReplace(489): Test -TestCasesVcf.test_18_vcf_tabix(348): Test -TestCasesVcf.test_26_vcfInfoHeaderAdd(456): Test -TestCasesVcf.test_14_VcfInfoKey(283): Test -TestCasesVcf.test_10_empty_QUAL(210): Test -TestCasesVcf.test_06_mixed_change(121): Test -TestCasesVcf.test_12_readHeader(237): Test -TestCasesVcf.test_15_Eff_format_version_guess(309): Test -TestCasesVcf.test_28_vcfInfoReplace(533): Test -TestCasesVcf.test_30_gVCF_NON_REF(590): Test -TestCasesVcf.test_05_choking_on_dot_slash_dot(89): Test -TestCasesVcf.test_08_alt_del(169): Test -TestCasesVcf.test_07_long_lines(143): Test -TestCasesVcf.test_11_empty(225): Test -TestCasesVcf.test_33_translocations(652): Test -TestCasesVcf.test_35_translocations_parsing(680): Test -TestCasesVcf.test_13_chrOri(268): Test -TestCasesVcf.test_04_del(72): Test -TestCasesVcf.test_14_VcfInfoValue(296): Test -[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 21.726 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString -TestCasesIubString.test_01(29): Test -TestCasesIubString.test_02(39): Test -TestCasesIubString.test_03(49): Test -TestCasesIubString.test_04(68): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -TestCasesSeekableReader.test_00(60): Test -ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf -TestCasesSeekableReader.test_01(74): Test -ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.347 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose -TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test -TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs -TestCasesHgvs.test_01(56): Test -TestCasesHgvs.test_02(69): Test -TestCasesHgvs.test_03(83): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.706 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome -TestCasesReactome.test_01(32): Test -TestCasesReactome.test_01(48): Out: 0.9051482536448667 -TestCasesReactome.test_02(57): Test -TestCasesReactome.test_02(75): Out: -0.8192933610763514 -TestCasesReactome.test_02(80): Out: 2.1152011710898737 -TestCasesReactome.test_03(89): Test -TestCasesReactome.test_03(105): Out: 0.86631007995171 -TestCasesReactome.test_03(110): Out: 2.1219547901144384 -TestCasesReactome.test_04(119): Test -TestCasesReactome.test_04(135): Out: 0.6973026352658382 -TestCasesReactome.test_04(140): Out: -0.5583420748968899 -TestCasesReactome.test_05(149): Test -TestCasesReactome.test_05(165): Out: -0.9154962776570641 -TestCasesReactome.test_05(170): Out: 0.34014843250566407 -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -TestCasesApplyMnp.test_apply_variant_01(22): Test -TestCasesApplyMnp.test_apply_variant_02(33): Test -TestCasesApplyMnp.test_apply_variant_03(44): Test -TestCasesApplyMnp.test_apply_variant_04(61): Test -TestCasesApplyMnp.test_apply_variant_05(79): Test -TestCasesApplyMnp.test_apply_variant_06(97): Test -TestCasesApplyMnp.test_apply_variant_07(115): Test -TestCasesApplyMnp.test_apply_variant_08(133): Test -TestCasesApplyMnp.test_apply_variant_09(144): Test -TestCasesApplyMnp.test_apply_variant_10(155): Test -TestCasesApplyMnp.test_apply_variant_11(176): Test -TestCasesApplyMnp.test_apply_variant_12(197): Test -TestCasesApplyMnp.test_apply_variant_13(219): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.421 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment -TestCasesVariantRealignment.test_07_savant(203): Test -TestCasesVariantRealignment.test_01(56): Test -TestCasesVariantRealignment.test_02(82): Test -TestCasesVariantRealignment.test_03(105): Test -TestCasesVariantRealignment.test_05_savant(157): Test -TestCasesVariantRealignment.test_04_Intron(131): Test -TestCasesVariantRealignment.test_06_savant(194): Test -TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test -TestCasesVariantRealignment.test_05_savant_opposite(174): Test -TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.206 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers -TestCasesNmers.test_03_Nmers(33): Test -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte -TestCasesDnaSequenceByte.test_01(18): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats -TestCasesIntStats.test_01(31): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.521 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.642 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +TestCasesMarkerUtils.test_collapseZeroGap(107): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +TestCasesSpliceSite.test_01(34): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant +TestCasesIntervalVariant.test_01(36): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.75 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBuild TestCasesBuild.test_01_chromoNamesDoNotMatch_Gff(18): Test TestCasesBuild.test_02_chromoNamesDoNotMatch_GffFasta(54): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.247 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -TestCasesStructuralDup.test01_dupGene(157): Test -TestCasesStructuralDup.test02(194): Test -TestCasesStructuralDup.test03(212): Test -TestCasesStructuralDup.test04(229): Test -TestCasesStructuralDup.test05(247): Test -TestCasesStructuralDup.test06(265): Test -TestCasesStructuralDup.test07(286): Test -TestCasesStructuralDup.test08(303): Test -TestCasesStructuralDup.test09(324): Test -TestCasesStructuralDup.test10(345): Test -TestCasesStructuralDup.test01_dupTr(175): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.072 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps -TestCasesMnps.test_01(187): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.836 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBuild +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +TestCasesHgvsExon.test_01_coding(27): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5619,22 +5497,24 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 25.591 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.032 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv +TestCasesStructuralInv.test01_invGene(214): Test +TestCasesStructuralInv.test02(249): Test +TestCasesStructuralInv.test03(266): Test +TestCasesStructuralInv.test04(283): Test +TestCasesStructuralInv.test05(300): Test +TestCasesStructuralInv.test06(317): Test +TestCasesStructuralInv.test07(334): Test +TestCasesStructuralInv.test08(352): Test +TestCasesStructuralInv.test09(370): Test +TestCasesStructuralInv.test10(387): Test +TestCasesStructuralInv.test01_invTr(231): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.063 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands [WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -TestCasesCodonTable.test_01(28): Test -TestCasesCodonTable.test_02(59): Test -00:02:02 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.448 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -TestCasesAnnParse.test_EffectType(29): Test -TestCasesAnnParse.test_old_SO(45): Test -TestCasesAnnParse.test_old_SO_vcf(53): Test -TestCasesAnnParse.testCase_tfbs_ablation(71): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.261 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds -TestCasesCds.test_CdsPos(35): Test +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns +TestCasesIns.test_01(38): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5646,10 +5526,41 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -TestCasesCds.test_cdsStartEnd_1(73): Test -TestCasesCds.test_cdsStartEnd_2(96): Test -WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.033 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.094 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +TestCasesVariantRealignment.test_07_savant(203): Test +TestCasesVariantRealignment.test_01(56): Test +TestCasesVariantRealignment.test_02(82): Test +TestCasesVariantRealignment.test_03(105): Test +TestCasesVariantRealignment.test_05_savant(157): Test +TestCasesVariantRealignment.test_04_Intron(131): Test +TestCasesVariantRealignment.test_06_savant(194): Test +TestCasesVariantRealignment.test_09_reallyLongRealign(224): Test +TestCasesVariantRealignment.test_05_savant_opposite(174): Test +TestCasesVariantRealignment.test_08_reallyLongRealign(213): Test +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.733 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesReactome +TestCasesReactome.test_01(32): Test +TestCasesReactome.test_01(48): Out: 0.9051482536448667 +TestCasesReactome.test_02(57): Test +TestCasesReactome.test_02(75): Out: -0.8192933610763514 +TestCasesReactome.test_02(80): Out: 2.1152011710898737 +TestCasesReactome.test_03(89): Test +TestCasesReactome.test_03(105): Out: 0.86631007995171 +TestCasesReactome.test_03(110): Out: 2.1219547901144384 +TestCasesReactome.test_04(119): Test +TestCasesReactome.test_04(135): Out: 0.6973026352658382 +TestCasesReactome.test_04(140): Out: -0.5583420748968899 +TestCasesReactome.test_05(149): Test +TestCasesReactome.test_05(165): Out: -0.9154962776570641 +TestCasesReactome.test_05(170): Out: 0.34014843250566407 +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesReactome +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIubString +TestCasesIubString.test_01(29): Test +TestCasesIubString.test_02(39): Test +TestCasesIubString.test_03(49): Test +TestCasesIubString.test_04(68): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIubString [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos TestCasesFileIndexChrPos.test_00_short_file(79): Test .................................................................................................... @@ -5699,28 +5610,107 @@ 700 .................................................................................................... 800 .................................................................................................... 900 ................................................................................................... -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.437 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence -TestCasesDnaNSequence.test_02_long_replaceBase(243): Test -TestCasesDnaNSequence.test_13_reverseWc(253): Test -TestCasesDnaNSequence.test_02_long_getBases(233): Test -TestCasesDnaNSequence.test_01_short_getBases(194): Test -TestCasesDnaNSequence.test_01_short(175): Test -TestCasesDnaNSequence.test_02_long(214): Test -TestCasesDnaNSequence.test_02_long_getBase(223): Test -TestCasesDnaNSequence.test_01_short_getBase(184): Test -TestCasesDnaNSequence.test_01_short_replaceBase(204): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.263 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -TestCasesSpliceRegion.test_01(33): Test -..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.417 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial -TestCasesBinomial.test_01(86): Test -TestCasesBinomial.test_02(191): Test -TestCasesBinomial.test_03(299): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -TestCasesHgvsExon.test_01_coding(27): Test +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.044 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +TestCasesHgvs.test_01(56): Test +TestCasesHgvs.test_02(69): Test +TestCasesHgvs.test_03(83): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.692 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvs +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.854 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +TestCasesApplyMixed.test_apply_variant_04_shorter(116): Test +TestCasesApplyMixed.test_apply_variant_06_longer(169): Test +TestCasesApplyMixed.test_apply_variant_06_shorter(186): Test +TestCasesApplyMixed.test_apply_variant_04_longer(98): Test +TestCasesApplyMixed.test_apply_variant_09_longer(259): Test +TestCasesApplyMixed.test_apply_variant_01_shorter(32): Test +TestCasesApplyMixed.test_apply_variant_08_shorter(248): Test +TestCasesApplyMixed.test_apply_variant_02_longer(42): Test +TestCasesApplyMixed.test_apply_variant_07_longer(203): Test +TestCasesApplyMixed.test_apply_variant_03_shorter(81): Test +TestCasesApplyMixed.test_apply_variant_05_shorter(152): Test +TestCasesApplyMixed.test_apply_variant_05_longer(134): Test +TestCasesApplyMixed.test_apply_variant_07_shorter(220): Test +TestCasesApplyMixed.test_apply_variant_03_longer(64): Test +TestCasesApplyMixed.test_apply_variant_08_longer(237): Test +TestCasesApplyMixed.test_apply_variant_02_shorter(53): Test +TestCasesApplyMixed.test_apply_variant_09_shorter(270): Test +TestCasesApplyMixed.test_apply_variant_01_longer(22): Test +[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.522 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.501 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +TestCasesApplyMnp.test_apply_variant_01(22): Test +TestCasesApplyMnp.test_apply_variant_02(33): Test +TestCasesApplyMnp.test_apply_variant_03(44): Test +TestCasesApplyMnp.test_apply_variant_04(61): Test +TestCasesApplyMnp.test_apply_variant_05(79): Test +TestCasesApplyMnp.test_apply_variant_06(97): Test +TestCasesApplyMnp.test_apply_variant_07(115): Test +TestCasesApplyMnp.test_apply_variant_08(133): Test +TestCasesApplyMnp.test_apply_variant_09(144): Test +TestCasesApplyMnp.test_apply_variant_10(155): Test +TestCasesApplyMnp.test_apply_variant_11(176): Test +TestCasesApplyMnp.test_apply_variant_12(197): Test +TestCasesApplyMnp.test_apply_variant_13(219): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.289 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +TestCasesProteinInteraction.test_02_split_codon_base(58): Test +TestCasesProteinInteraction.test_01_split_codon_base(26): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.521 s - in org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +TestCasesIntervalTree.test_01(141): Test +. +0 .................................................................................................... +10000 .................................................................................................... +20000 .................................................................................................... +30000 .................................................................................................... +40000 .................................................................................................... +50000 .................................................................................................... +60000 .................................................................................................... +70000 .................................................................................................... +80000 .................................................................................................... +90000 ................................................................................................... +TestCasesIntervalTree.test_02(164): Test +. +0 .................................................................................................... +1000 .................................................................................................... +2000 .................................................................................................... +3000 .................................................................................................... +4000 .................................................................................................... +5000 .................................................................................................... +6000 .................................................................................................... +7000 .................................................................................................... +8000 .................................................................................................... +9000 ................................................................................................... +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.308 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps +TestCasesSnps.test_01(43): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5732,35 +5722,36 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.054 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage -TestCasesCochranArmitage.test_01(18): Test -TestCasesCochranArmitage.test_02(28): Test -TestCasesCochranArmitage.test_03(37): Test -TestCasesCochranArmitage.test_04(46): Test -TestCasesCochranArmitage.test_05(57): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.911 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +TestCasesGenePvalueList.test_01(28): Test +TestCasesGenePvalueList.test_02(46): Test +TestCasesGenePvalueList.test_03(64): Test +TestCasesGenePvalueList.test_04(82): Test +TestCasesGenePvalueList.test_05(111): Test +TestCasesGenePvalueList.test_06(129): Test +TestCasesGenePvalueList.test_07(155): Test +TestCasesGenePvalueList.test_08(187): Test +TestCasesGenePvalueList.test_09(209): Test +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.714 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup TestCasesHgvsProtDup.test_01(31): Test TestCasesHgvsProtDup.test_02(70): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.788 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -TestCasesApplyDel.test_apply_variant_01(21): Test -TestCasesApplyDel.test_apply_variant_02(31): Test -TestCasesApplyDel.test_apply_variant_03(42): Test -TestCasesApplyDel.test_apply_variant_04(59): Test -TestCasesApplyDel.test_apply_variant_05(77): Test -TestCasesApplyDel.test_apply_variant_06(95): Test -TestCasesApplyDel.test_apply_variant_07(113): Test -TestCasesApplyDel.test_apply_variant_08(131): Test -TestCasesApplyDel.test_apply_variant_09(142): Test -TestCasesApplyDel.test_apply_variant_10(153): Test -TestCasesApplyDel.test_apply_variant_11(176): Test -TestCasesApplyDel.test_apply_variant_12(199): Test -TestCasesApplyDel.test_apply_variant_13(223): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.212 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSnps -TestCasesSnps.test_01(43): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign +TestCasesAlign.test_01(23): Test +TestCasesAlign.test_02(113): Test +TestCasesAlign.test_StringDiff_06(106): +Sequence 1 : acgtactgatagtcagtcatgctagtcXgtcgatctagtcgacatcatgctagcgatcatg + diff : | | | + Name2 : XcgtactgatagtcagtcatgctagtcagX + +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNmers +TestCasesNmers.test_03_Nmers(33): Test +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.004 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNmers +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCds +TestCasesCds.test_CdsPos(35): Test .................................................................................................... 100 .................................................................................................... 200 .................................................................................................... @@ -5772,7 +5763,181 @@ 800 .................................................................................................... 900 .................................................................................................... 1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.587 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSnps +TestCasesCds.test_cdsStartEnd_1(73): Test +TestCasesCds.test_cdsStartEnd_2(96): Test +WARNING_EXON_NOT_FOUND: WARNING: Cannot find first exonic position after 101 for transcript 'tr1' +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.77 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCds +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVcf +TestCasesVcf.test_22_huge_headers(363): Test +TestCasesVcf.test_12_readHeader_NL(257): Test +TestCasesVcf.test_36_cleanupUnderscores(703): Test +TestCasesVcf.test_23_VcfUnsorted(379): Test +TestCasesVcf.test_00(40): Test +TestCasesVcf.test_01(54): Test +TestCasesVcf.test_29(568): Test +TestCasesVcf.test_16_indels(321): Test +TestCasesVcf.test_09_empty_ALT(195): Test +TestCasesVcf.test_27_vcfInfoHeaderReplace(489): Test +TestCasesVcf.test_18_vcf_tabix(348): Test +TestCasesVcf.test_26_vcfInfoHeaderAdd(456): Test +TestCasesVcf.test_14_VcfInfoKey(283): Test +TestCasesVcf.test_10_empty_QUAL(210): Test +TestCasesVcf.test_06_mixed_change(121): Test +TestCasesVcf.test_12_readHeader(237): Test +TestCasesVcf.test_15_Eff_format_version_guess(309): Test +TestCasesVcf.test_28_vcfInfoReplace(533): Test +TestCasesVcf.test_30_gVCF_NON_REF(590): Test +TestCasesVcf.test_05_choking_on_dot_slash_dot(89): Test +TestCasesVcf.test_08_alt_del(169): Test +TestCasesVcf.test_07_long_lines(143): Test +TestCasesVcf.test_11_empty(225): Test +TestCasesVcf.test_33_translocations(652): Test +TestCasesVcf.test_35_translocations_parsing(680): Test +TestCasesVcf.test_13_chrOri(268): Test +TestCasesVcf.test_04_del(72): Test +TestCasesVcf.test_14_VcfInfoValue(296): Test +[INFO] Tests run: 33, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.592 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVcf +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +TestCasesStructuralDup.test01_dupGene(157): Test +TestCasesStructuralDup.test02(194): Test +TestCasesStructuralDup.test03(212): Test +TestCasesStructuralDup.test04(229): Test +TestCasesStructuralDup.test05(247): Test +TestCasesStructuralDup.test06(265): Test +TestCasesStructuralDup.test07(286): Test +TestCasesStructuralDup.test08(303): Test +TestCasesStructuralDup.test09(324): Test +TestCasesStructuralDup.test10(345): Test +TestCasesStructuralDup.test01_dupTr(175): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.402 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta +TestCasesFasta.test_01(23): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +TestCasesHgvsDnaDup.test_01(31): Test +TestCasesHgvsDnaDup.test_02(54): Test +TestCasesHgvsDnaDup.test_03(81): Test +TestCasesHgvsDnaDup.test_04(111): Test +TestCasesHgvsDnaDup.test_05(141): Test +TestCasesHgvsDnaDup.test_06(167): Test +TestCasesHgvsDnaDup.test_07(195): Test +TestCasesHgvsDnaDup.test_08(221): Test +TestCasesHgvsDnaDup.test_09(247): Test +TestCasesHgvsDnaDup.test_10(277): Test +TestCasesHgvsDnaDup.test_11(308): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.352 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +TestCasesCodonTable.test_01(28): Test +TestCasesCodonTable.test_02(59): Test +00:01:17 Codon table 'Blepharisma_Macronuclear' for genome 'test_ctab' +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +TestCasesApplySnp.test_apply_variant_01(21): Test +TestCasesApplySnp.test_apply_variant_02(31): Test +TestCasesApplySnp.test_apply_variant_04(41): Test +TestCasesApplySnp.test_apply_variant_05(59): Test +TestCasesApplySnp.test_apply_variant_06(77): Test +TestCasesApplySnp.test_apply_variant_08(95): Test +TestCasesApplySnp.test_apply_variant_09(106): Test +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.757 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +TestCasesFisherExactTest.test_05_fisher(313): Test +TestCasesFisherExactTest.test_0(97): Test +TestCasesFisherExactTest.test_03_fisher(103): Test +TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test +TestCasesFisherExactTest.test_04_fisher(208): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +TestCasesSequenceIndexer.test_01(69): Test +TestCasesSequenceIndexer.test_02(100): Test +TestCasesSequenceIndexer.test_03(125): Test +TestCasesSequenceIndexer.test_04(152): Test +TestCasesSequenceIndexer.test_05(182): Test +TestCasesSequenceIndexer.test_06(207): Test +TestCasesSequenceIndexer.test_07(225): Test +TestCasesSequenceIndexer.test_08(247): Test +TestCasesSequenceIndexer.test_09(267): Test +TestCasesSequenceIndexer.test_10(287): Test +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.543 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +TestCasesIntStats.test_01(31): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.278 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntStats +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +TestCasesEffectCollapse.test_01(68): Test +TestCasesEffectCollapse.test_02(74): Test +TestCasesEffectCollapse.test_03(80): Test +TestCasesEffectCollapse.test_04(86): Test +TestCasesEffectCollapse.test_05(92): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.308 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +TestCasesOverlap.test_binSeq_01(26): Test +TestCasesOverlap.test_binSeq_02(32): Test +TestCasesOverlap.test_binSeq_03(38): Test +TestCasesOverlap.test_binSeq_04(44): Test +TestCasesOverlap.test_binSeq_05(50): Test +TestCasesOverlap.test_binSeq_06(56): Test +TestCasesOverlap.test_binSeq_07(62): Test +TestCasesOverlap.test_binSeq_08(68): Test +TestCasesOverlap.test_binSeq_09(74): Test +TestCasesOverlap.test_binSeq_10(80): Test +TestCasesOverlap.test_binSeq_11(87): Test +TestCasesOverlap.test_binSeq_12(94): Test +TestCasesOverlap.test_binSeq_13(100): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +TestCasesStructuralTranslocations.test02_2_nonFs(532): Test +TestCasesStructuralTranslocations.test01_0_nonFs(286): Test +TestCasesStructuralTranslocations.test01_0(260): Test +TestCasesStructuralTranslocations.test01_1(314): Test +TestCasesStructuralTranslocations.test01_2(341): Test +TestCasesStructuralTranslocations.test01_3(368): Test +TestCasesStructuralTranslocations.test02_0(423): Test +TestCasesStructuralTranslocations.test02_1(450): Test +TestCasesStructuralTranslocations.test02_2(505): Test +TestCasesStructuralTranslocations.test02_3(560): Test +TestCasesStructuralTranslocations.test03_0(587): Test +TestCasesStructuralTranslocations.test03_1(614): Test +TestCasesStructuralTranslocations.test03_2(669): Test +TestCasesStructuralTranslocations.test03_3(724): Test +TestCasesStructuralTranslocations.test04_0(751): Test +TestCasesStructuralTranslocations.test04_1(806): Test +TestCasesStructuralTranslocations.test04_2(833): Test +TestCasesStructuralTranslocations.test04_3(860): Test +TestCasesStructuralTranslocations.test05_2_one_gene(951): Test +TestCasesStructuralTranslocations.test04_3_nonFs(887): Test +TestCasesStructuralTranslocations.test03_1_nonFs(641): Test +TestCasesStructuralTranslocations.test05_1_one_gene(919): Test +TestCasesStructuralTranslocations.test03_2_nonFs(696): Test +TestCasesStructuralTranslocations.test01_3_noFs(395): Test +TestCasesStructuralTranslocations.test04_0_nonFs(778): Test +TestCasesStructuralTranslocations.test02_1_nonFs(477): Test +TestCasesStructuralTranslocations.test06_no_gene(981): Test +[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.784 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +TestCasesIntervals.test_00(140): Test +TestCasesIntervals.test_01(152): Test +TestCasesIntervals.test_02(163): Test +TestCasesIntervals.test_03(175): Test +TestCasesIntervals.test_04(187): Test +TestCasesIntervals.test_05(200): Test +TestCasesIntervals.test_06(231): Test +TestCasesIntervals.test_08(392): Test +TestCasesIntervals.test_10_chrOrder(475): Test +TestCasesIntervals.test_09_chrOrder(460): Test +TestCasesIntervals.test_07_01(271): Test +TestCasesIntervals.test_07_02(292): Test +TestCasesIntervals.test_07_03(313): Test +TestCasesIntervals.test_07_04(337): Test +TestCasesIntervals.test_07_05(362): Test +TestCasesIntervals.test_08_02(413): Test +TestCasesIntervals.test_08_03(438): Test +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.334 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative +TestCasesHgvsDnaDupNegative.test_01(34): Test +TestCasesHgvsDnaDupNegative.test_02(61): Test +TestCasesHgvsDnaDupNegative.test_03(91): Test +TestCasesHgvsDnaDupNegative.test_04(122): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.054 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap TestCasesDnaOverlap.test_10_overlap(332): Test TestCasesDnaOverlap.test_07_overlap(297): Test @@ -5835,153 +6000,12 @@ Max words: 8 ......... Max words: 9 ......... Done. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.556 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -TestCasesHgvsIntron.test_01_intron(23): Test -............................................................... -100 ............................................................ -200 ................................................................ -300 ......................................................... -400 ......................................................................................................................... -600 ......................................................................................................... -800 ....................................................... -900 .................................................................. -1000 ............................................................. -1100 .................................................................. -1200 ......................................................... -1300 ........................................................................................................... -1500 ....................................................... -1600 ............................................................... -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.373 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup -TestCasesHgvsDnaDup.test_01(31): Test -TestCasesHgvsDnaDup.test_02(54): Test -TestCasesHgvsDnaDup.test_03(81): Test -TestCasesHgvsDnaDup.test_04(111): Test -TestCasesHgvsDnaDup.test_05(141): Test -TestCasesHgvsDnaDup.test_06(167): Test -TestCasesHgvsDnaDup.test_07(195): Test -TestCasesHgvsDnaDup.test_08(221): Test -TestCasesHgvsDnaDup.test_09(247): Test -TestCasesHgvsDnaDup.test_10(277): Test -TestCasesHgvsDnaDup.test_11(308): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.471 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -TestCasesIntervals.test_00(140): Test -TestCasesIntervals.test_01(152): Test -TestCasesIntervals.test_02(163): Test -TestCasesIntervals.test_03(175): Test -TestCasesIntervals.test_04(187): Test -TestCasesIntervals.test_05(200): Test -TestCasesIntervals.test_06(231): Test -TestCasesIntervals.test_08(392): Test -TestCasesIntervals.test_10_chrOrder(475): Test -TestCasesIntervals.test_09_chrOrder(460): Test -TestCasesIntervals.test_07_01(271): Test -TestCasesIntervals.test_07_02(292): Test -TestCasesIntervals.test_07_03(313): Test -TestCasesIntervals.test_07_04(337): Test -TestCasesIntervals.test_07_05(362): Test -TestCasesIntervals.test_08_02(413): Test -TestCasesIntervals.test_08_03(438): Test -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.918 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervals -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -TestCasesOverlap.test_binSeq_01(26): Test -TestCasesOverlap.test_binSeq_02(32): Test -TestCasesOverlap.test_binSeq_03(38): Test -TestCasesOverlap.test_binSeq_04(44): Test -TestCasesOverlap.test_binSeq_05(50): Test -TestCasesOverlap.test_binSeq_06(56): Test -TestCasesOverlap.test_binSeq_07(62): Test -TestCasesOverlap.test_binSeq_08(68): Test -TestCasesOverlap.test_binSeq_09(74): Test -TestCasesOverlap.test_binSeq_10(80): Test -TestCasesOverlap.test_binSeq_11(87): Test -TestCasesOverlap.test_binSeq_12(94): Test -TestCasesOverlap.test_binSeq_13(100): Test -[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesOverlap -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic -TestCasesIntergenic.test_01(30): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative -TestCasesHgvsDnaDupNegative.test_01(34): Test -TestCasesHgvsDnaDupNegative.test_02(61): Test -TestCasesHgvsDnaDupNegative.test_03(91): Test -TestCasesHgvsDnaDupNegative.test_04(122): Test -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -TestCasesStructuralDel.test02(249): Test -TestCasesStructuralDel.test03(266): Test -TestCasesStructuralDel.test04(283): Test -TestCasesStructuralDel.test05(302): Test -TestCasesStructuralDel.test06(321): Test -TestCasesStructuralDel.test07(342): Test -TestCasesStructuralDel.test08(360): Test -TestCasesStructuralDel.test09(379): Test -TestCasesStructuralDel.test10(398): Test -TestCasesStructuralDel.test01_delTr(230): Test -TestCasesStructuralDel.test01_delGene(212): Test -[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.277 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels -TestCasesDels.test_01(138): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.822 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIns -TestCasesIns.test_01(38): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.324 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIns -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -TestCasesApplySnp.test_apply_variant_01(21): Test -TestCasesApplySnp.test_apply_variant_02(31): Test -TestCasesApplySnp.test_apply_variant_04(41): Test -TestCasesApplySnp.test_apply_variant_05(59): Test -TestCasesApplySnp.test_apply_variant_06(77): Test -TestCasesApplySnp.test_apply_variant_08(95): Test -TestCasesApplySnp.test_apply_variant_09(106): Test -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.549 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -TestCasesChiSquare.test_1(26): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.039 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDel -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFasta -TestCasesFasta.test_01(23): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFasta -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector -TestCasesGenotypeVector.test_01(23): Test -TestCasesGenotypeVector.test_02(48): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAlign -TestCasesAlign.test_01(23): Test -TestCasesAlign.test_02(113): Test -TestCasesAlign.test_StringDiff_06(106): -Sequence 1 : acgtactgatagtcagtcatgctagtcXgtcgatctagtcgacatcatgctagcgatcatg - diff : | | | - Name2 : XcgtactgatagtcagtcatgctagtcagX - -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAlign -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 14.922 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesBinomial +TestCasesBinomial.test_01(86): Test +TestCasesBinomial.test_02(191): Test +TestCasesBinomial.test_03(299): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.snpeff.snpEffect.testCases.unity.TestCasesBinomial [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence TestCasesDnaSequence.test_02_long_replaceBase(277): Test TestCasesDnaSequence.test_05_fastqReader(320): Test @@ -5995,37 +6019,10 @@ TestCasesDnaSequence.test_01_short_getBase(218): Test TestCasesDnaSequence.test_04_Pe(287): Test TestCasesDnaSequence.test_01_short_replaceBase(238): Test -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.897 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -TestCasesSpliceSite.test_01(34): Test -.................................................................................................... -100 .................................................................................................... -200 .................................................................................................... -300 .................................................................................................... -400 .................................................................................................... -500 .................................................................................................... -600 .................................................................................................... -700 .................................................................................................... -800 .................................................................................................... -900 .................................................................................................... -1000 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric -TestCasesHypergeometric.test_0(77): Test -TestCasesHypergeometric.test_01_hyper(83): Test -TestCasesHypergeometric.test_02_hyper(202): Test -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList -TestCasesGenePvalueList.test_01(28): Test -TestCasesGenePvalueList.test_02(46): Test -TestCasesGenePvalueList.test_03(64): Test -TestCasesGenePvalueList.test_04(82): Test -TestCasesGenePvalueList.test_05(111): Test -TestCasesGenePvalueList.test_06(129): Test -TestCasesGenePvalueList.test_07(155): Test -TestCasesGenePvalueList.test_08(187): Test -TestCasesGenePvalueList.test_09(209): Test -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.805 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.415 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion +TestCasesSpliceRegion.test_01(33): Test +..................[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.278 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesNextProt TestCasesNextProt.test_10_nextprotFactory(205): Test TestCasesNextProt.test_09_nextprotFactory(182): Test @@ -6046,87 +6043,70 @@ TestCasesNextProt.test_05_nextprotFactory(98): Test TestCasesNextProt.test_02_nextprotFactory(42): Test TestCasesNextProt.test_13_nextprotFactory(277): Test -[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -TestCasesSequenceIndexer.test_01(69): Test -TestCasesSequenceIndexer.test_02(100): Test -TestCasesSequenceIndexer.test_03(125): Test -TestCasesSequenceIndexer.test_04(152): Test -TestCasesSequenceIndexer.test_05(182): Test -TestCasesSequenceIndexer.test_06(207): Test -TestCasesSequenceIndexer.test_07(225): Test -TestCasesSequenceIndexer.test_08(247): Test -TestCasesSequenceIndexer.test_09(267): Test -TestCasesSequenceIndexer.test_10(287): Test -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.992 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -TestCasesEffectCollapse2.test_01(40): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.461 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -TestCasesMarkerUtils.test_collapseZeroGap(107): Test -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -TestCasesStructuralTranslocations.test02_2_nonFs(532): Test -TestCasesStructuralTranslocations.test01_0_nonFs(286): Test -TestCasesStructuralTranslocations.test01_0(260): Test -TestCasesStructuralTranslocations.test01_1(314): Test -TestCasesStructuralTranslocations.test01_2(341): Test -TestCasesStructuralTranslocations.test01_3(368): Test -TestCasesStructuralTranslocations.test02_0(423): Test -TestCasesStructuralTranslocations.test02_1(450): Test -TestCasesStructuralTranslocations.test02_2(505): Test -TestCasesStructuralTranslocations.test02_3(560): Test -TestCasesStructuralTranslocations.test03_0(587): Test -TestCasesStructuralTranslocations.test03_1(614): Test -TestCasesStructuralTranslocations.test03_2(669): Test -TestCasesStructuralTranslocations.test03_3(724): Test -TestCasesStructuralTranslocations.test04_0(751): Test -TestCasesStructuralTranslocations.test04_1(806): Test -TestCasesStructuralTranslocations.test04_2(833): Test -TestCasesStructuralTranslocations.test04_3(860): Test -TestCasesStructuralTranslocations.test05_2_one_gene(951): Test -TestCasesStructuralTranslocations.test04_3_nonFs(887): Test -TestCasesStructuralTranslocations.test03_1_nonFs(641): Test -TestCasesStructuralTranslocations.test05_1_one_gene(919): Test -TestCasesStructuralTranslocations.test03_2_nonFs(696): Test -TestCasesStructuralTranslocations.test01_3_noFs(395): Test -TestCasesStructuralTranslocations.test04_0_nonFs(778): Test -TestCasesStructuralTranslocations.test02_1_nonFs(477): Test -TestCasesStructuralTranslocations.test06_no_gene(981): Test -[INFO] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.301 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -TestCasesIntervalTree.test_01(141): Test -. -0 .................................................................................................... -10000 .................................................................................................... -20000 .................................................................................................... -30000 .................................................................................................... -40000 .................................................................................................... -50000 .................................................................................................... -60000 .................................................................................................... -70000 .................................................................................................... -80000 .................................................................................................... -90000 ................................................................................................... -TestCasesIntervalTree.test_02(164): Test -. -0 .................................................................................................... -1000 .................................................................................................... -2000 .................................................................................................... -3000 .................................................................................................... -4000 .................................................................................................... -5000 .................................................................................................... -6000 .................................................................................................... -7000 .................................................................................................... -8000 .................................................................................................... -9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.822 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree -[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest -TestCasesFisherExactTest.test_05_fisher(313): Test -TestCasesFisherExactTest.test_0(97): Test -TestCasesFisherExactTest.test_03_fisher(103): Test -TestCasesFisherExactTest.test_06_fisher_vs_chi2(352): Test -TestCasesFisherExactTest.test_04_fisher(208): Test -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 s - in org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest +[INFO] Tests run: 19, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 s - in org.snpeff.snpEffect.testCases.unity.TestCasesNextProt +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +TestCasesApplyDel.test_apply_variant_01(21): Test +TestCasesApplyDel.test_apply_variant_02(31): Test +TestCasesApplyDel.test_apply_variant_03(42): Test +TestCasesApplyDel.test_apply_variant_04(59): Test +TestCasesApplyDel.test_apply_variant_05(77): Test +TestCasesApplyDel.test_apply_variant_06(95): Test +TestCasesApplyDel.test_apply_variant_07(113): Test +TestCasesApplyDel.test_apply_variant_08(131): Test +TestCasesApplyDel.test_apply_variant_09(142): Test +TestCasesApplyDel.test_apply_variant_10(153): Test +TestCasesApplyDel.test_apply_variant_11(176): Test +TestCasesApplyDel.test_apply_variant_12(199): Test +TestCasesApplyDel.test_apply_variant_13(223): Test +[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.185 s - in org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDels +TestCasesDels.test_01(138): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.706 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDels +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesMnps +TestCasesMnps.test_01(187): Test +.................................................................................................... +100 .................................................................................................... +200 .................................................................................................... +300 .................................................................................................... +400 .................................................................................................... +500 .................................................................................................... +600 .................................................................................................... +700 .................................................................................................... +800 .................................................................................................... +900 .................................................................................................... +1000 +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.623 s - in org.snpeff.snpEffect.testCases.unity.TestCasesMnps +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +TestCasesGenotypeVector.test_01(23): Test +TestCasesGenotypeVector.test_02(48): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +TestCasesCochranArmitage.test_01(18): Test +TestCasesCochranArmitage.test_02(28): Test +TestCasesCochranArmitage.test_03(37): Test +TestCasesCochranArmitage.test_04(46): Test +TestCasesCochranArmitage.test_05(57): Test +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +TestCasesSeekableReader.test_00(60): Test +ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf +TestCasesSeekableReader.test_01(74): Test +ffffffff232744e0 ffffffff232744e0 tests/unity/seekableReader/testLukas.vcf +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.551 s - in org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare +TestCasesChiSquare.test_1(26): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri TestCasesIntervalTree.test_01(141): Test . @@ -6152,11 +6132,67 @@ 7000 .................................................................................................... 8000 .................................................................................................... 9000 ................................................................................................... -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.724 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.846 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse +TestCasesAnnParse.test_EffectType(29): Test +TestCasesAnnParse.test_old_SO(45): Test +TestCasesAnnParse.test_old_SO_vcf(53): Test +TestCasesAnnParse.testCase_tfbs_ablation(71): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.217 s - in org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse [INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesJaspar TestCasesJaspar.test_01(22): Test TestCasesJaspar.test_02(56): Test -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.853 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.105 s - in org.snpeff.snpEffect.testCases.unity.TestCasesJaspar +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +TestCasesEffectCollapse2.test_01(40): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.494 s - in org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2 +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +TestCasesVariantDecompose.test_00_decomposeVariant_01(35): Test +TestCasesVariantDecompose.test_00_decomposeVariant_02(45): Test +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesCircular +TestCasesCircular.test_circular_01(26): Test +TestCasesCircular.test_circular_02(54): Test +TestCasesCircular.test_circular_03(83): Test +TestCasesCircular.test_circular_04(103): Test +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpeff.snpEffect.testCases.unity.TestCasesCircular +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +TestCasesDnaNSequence.test_02_long_replaceBase(243): Test +TestCasesDnaNSequence.test_13_reverseWc(253): Test +TestCasesDnaNSequence.test_02_long_getBases(233): Test +TestCasesDnaNSequence.test_01_short_getBases(194): Test +TestCasesDnaNSequence.test_01_short(175): Test +TestCasesDnaNSequence.test_02_long(214): Test +TestCasesDnaNSequence.test_02_long_getBase(223): Test +TestCasesDnaNSequence.test_01_short_getBase(184): Test +TestCasesDnaNSequence.test_01_short_replaceBase(204): Test +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.381 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +TestCasesHypergeometric.test_0(77): Test +TestCasesHypergeometric.test_01_hyper(83): Test +TestCasesHypergeometric.test_02_hyper(202): Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +TestCasesIntergenic.test_01(30): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.336 s - in org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +TestCasesDnaSequenceByte.test_01(18): Test +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 s - in org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte +[INFO] Running org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel +TestCasesStructuralDel.test02(249): Test +TestCasesStructuralDel.test03(266): Test +TestCasesStructuralDel.test04(283): Test +TestCasesStructuralDel.test05(302): Test +TestCasesStructuralDel.test06(321): Test +TestCasesStructuralDel.test07(342): Test +TestCasesStructuralDel.test08(360): Test +TestCasesStructuralDel.test09(379): Test +TestCasesStructuralDel.test10(398): Test +TestCasesStructuralDel.test01_delTr(230): Test +TestCasesStructuralDel.test01_delGene(212): Test +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.737 s - in org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel [INFO] [INFO] Results: [INFO] @@ -6165,8 +6201,8 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 04:52 min -[INFO] Finished at: 2024-05-25T19:10:05-12:00 +[INFO] Total time: 02:40 min +[INFO] Finished at: 2025-06-29T03:42:40+14:00 [INFO] ------------------------------------------------------------------------ create-stamp debian/debhelper-build-stamp dh_prep @@ -6189,11 +6225,11 @@ [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.968 s -[INFO] Finished at: 2024-05-25T19:10:08-12:00 +[INFO] Total time: 0.411 s +[INFO] Finished at: 2025-06-29T03:42:42+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibsnpeff-java --javadoc --base-directory=/build/reproducible-path/snpeff-5.2.b\+dfsg --non-explore -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -6209,7 +6245,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -6225,7 +6261,7 @@ at org.debian.maven.repo.POMTransformer.usePluginVersionsFromRepository(POMTransformer.java:107) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:907) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -6241,7 +6277,7 @@ at org.debian.maven.packager.DependenciesSolver.solveDependencies(DependenciesSolver.java:237) at org.debian.maven.packager.DependenciesSolver.main(DependenciesSolver.java:922) -Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.1.0/biojava-structure-6.1.0.pom +Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom javax.xml.stream.XMLStreamException: ParseError at [row,col]:[117,21] Message: Element type "debian.org.rcsb." must be followed by either attribute specifications, ">" or "/>". at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) @@ -6265,7 +6301,7 @@ [error] Package libbiojava6-java (6.1.0+dfsg) is already installed and contains a possible match, but I cannot resolve library org.biojava:biojava-structure:jar:6.x in it. [error] Please check manually that the library is up to date, otherwise it may be necessary to package version 6.x in Debian. -May 25, 2024 7:10:20 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Jun 29, 2025 3:42:53 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/snpeff-5.2.b+dfsg/pom.xml: Dependency not found org.biojava:biojava-structure:jar:6.x ERROR: pom.xml: dependency is not packaged in the Maven repository for Debian: org.biojava:biojava-structure:6.x @@ -6399,17 +6435,17 @@ dh_missing dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined -dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:Depends} unused, but is defined -dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: package libsnpeff-java: substitution variable ${maven:DocDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:Depends} unused, but is defined +dpkg-gencontrol: warning: package libsnpeff-java-doc: substitution variable ${maven:DocDepends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-deb: building package 'snpeff' in '../snpeff_5.2.b+dfsg-1_all.deb'. dpkg-deb: building package 'libsnpeff-java' in '../libsnpeff-java_5.2.b+dfsg-1_all.deb'. +dpkg-deb: building package 'libsnpeff-java-doc' in '../libsnpeff-java-doc_5.2.b+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../snpeff_5.2.b+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../snpeff_5.2.b+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6417,12 +6453,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2870149/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2870149/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/2592240 and its subdirectories -I: Current time: Sat May 25 19:13:59 -12 2024 -I: pbuilder-time-stamp: 1716707639 +I: removing directory /srv/workspace/pbuilder/2870149 and its subdirectories +I: Current time: Sun Jun 29 03:46:06 +14 2025 +I: pbuilder-time-stamp: 1751118366