[Debian-med-packaging] Bug#1002155: libgoby-java: FTBFS: [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist
Lucas Nussbaum
lucas at debian.org
Tue Dec 21 16:02:40 GMT 2021
Source: libgoby-java
Version: 3.3.1+dfsg2-5
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20211220 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with javahelper
> dh_update_autotools_config
> dh_autoreconf
> dh_auto_configure
> mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo
> jh_linkjars
> dh_auto_build
> /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=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
> [INFO] Scanning for projects...
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
> [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 226, column 16
> [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 292, column 16
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 294, column 15
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
> [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
> [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
> [WARNING]
> [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
> [WARNING]
> [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
> [WARNING]
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Build Order:
> [INFO]
> [INFO] Goby Framework [pom]
> [INFO] Goby I/O [jar]
> [INFO] Goby Full Distribution [jar]
> [INFO]
> [INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
> [INFO] Building Goby Framework 3.3.1 [1/3]
> [INFO] --------------------------------[ pom ]---------------------------------
> [INFO]
> [INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
> [INFO] Building Goby I/O 3.3.1 [2/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-classes) @ goby-io ---
> [INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-java-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [mkdir] Created dir: /<<PKGBUILDDIR>>/goby-io/target/generated-sources
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-cpp-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ goby-io ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 2 resources
> [INFO] Copying 1 resource
> [INFO] Copying 1 resource
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ goby-io ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 260 source files to /<<PKGBUILDDIR>>/goby-io/target/classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (default) @ goby-io ---
> [WARNING] Parameter tasks is deprecated, use target instead
> [INFO] Executing tasks
>
> main:
> [copy] Copying 1 file to /<<PKGBUILDDIR>>
> [copy] Copying 1 file to /<<PKGBUILDDIR>>/goby-io/target/classes
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ goby-io ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-io/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ goby-io ---
> [INFO] No sources to compile
> [INFO]
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
> [INFO] Tests are skipped.
> [INFO]
> [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ goby-io ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1.jar
> [INFO]
> [INFO] >>> maven-source-plugin:3.0.1:jar (attach-sources) > generate-sources @ goby-io >>>
> [INFO]
> [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-classes) @ goby-io ---
> [INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-java-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-cpp-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] <<< maven-source-plugin:3.0.1:jar (attach-sources) < generate-sources @ goby-io <<<
> [INFO]
> [INFO]
> [INFO] --- maven-source-plugin:3.0.1:jar (attach-sources) @ goby-io ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1-sources.jar
> [INFO]
> [INFO] --- maven-javadoc-plugin:3.0.1:jar (attach-javadocs) @ goby-io ---
> [INFO] Adding the --ignore-source-errors option
> [INFO]
> Loading source files for package samples...
> Loading source files for package org.campagnelab.goby.modes...
> Loading source files for package org.campagnelab.goby.modes.formats...
> Loading source files for package org.campagnelab.goby.modes.core...
> Loading source files for package org.campagnelab.goby.modes.dsv...
> Loading source files for package org.campagnelab.goby.readers.vcf...
> Loading source files for package org.campagnelab.goby.readers...
> Loading source files for package org.campagnelab.goby.readers.sam...
> Loading source files for package org.campagnelab.goby.methylation...
> Loading source files for package org.campagnelab.goby.algorithmic.algorithm...
> Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr...
> Loading source files for package org.campagnelab.goby.algorithmic.compression...
> Loading source files for package org.campagnelab.goby.algorithmic.indels...
> Loading source files for package org.campagnelab.goby.algorithmic.data...
> Loading source files for package org.campagnelab.goby.algorithmic.data.ranges...
> Loading source files for package org.campagnelab.goby.algorithmic.data.xml...
> Loading source files for package org.campagnelab.goby.algorithmic.dsv...
> Loading source files for package org.campagnelab.goby.compression...
> Loading source files for package org.campagnelab.goby.xml...
> Loading source files for package org.campagnelab.goby.util...
> Loading source files for package org.campagnelab.goby.util.pool...
> Loading source files for package org.campagnelab.goby.util.commits...
> Loading source files for package org.campagnelab.goby.util.dynoptions...
> Loading source files for package org.campagnelab.goby.util.motifs...
> Loading source files for package org.campagnelab.goby.util.barcode...
> Loading source files for package org.campagnelab.goby.reads...
> Loading source files for package org.campagnelab.goby.config...
> Loading source files for package org.campagnelab.goby.R...
> Loading source files for package org.campagnelab.goby.parsers...
> Loading source files for package org.campagnelab.goby...
> Loading source files for package org.campagnelab.goby.stats...
> Loading source files for package org.campagnelab.goby.cli...
> Loading source files for package org.campagnelab.goby.baseinfo...
> Loading source files for package org.campagnelab.goby.predictions...
> Loading source files for package org.campagnelab.goby.counts...
> Loading source files for package org.campagnelab.goby.counts.compound...
> Loading source files for package org.campagnelab.goby.exception...
> Loading source files for package org.campagnelab.goby.alignments...
> Loading source files for package org.campagnelab.goby.alignments.perms...
> Loading source files for package org.campagnelab.goby.alignments.processors...
> Loading source files for package org.campagnelab.goby.alignments.filters...
> Loading source files for package org.campagnelab.goby.alignments.htsjdk...
> Loading source files for package org.campagnelab.dl.varanalysis.protobuf...
> Constructing Javadoc information...
> Standard Doclet version 11.0.13
> Building tree for all the packages and classes...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequencyOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutputOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.BaseOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePositionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SampleOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/GobyVersion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeaderOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndexOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHitsOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMappingOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/LastParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Merge.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/Peak.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SortMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/StatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TrimMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VersionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/Predictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/GobyRengine.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/MultiReads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaDataOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DataProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SamplePair.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FromToFreq.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/GrepReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/IOUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/IsDone.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/NamedCounters.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/SamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/StreamSignal.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Timer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/WarningCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/MethylStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/IterateAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ModifyAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseReadsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/constant-values.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/serialized-form.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaDataOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndexOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHitsOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMappingOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeaderOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntry.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntryOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutputOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequencyOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfoOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-use.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-use.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-use.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-use.html...
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> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-use.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-use.html...
> Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-use.html...
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> Building index for all the packages and classes...
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> Building index for all classes...
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> Building index for all classes...
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> 100 warnings
> [WARNING] Javadoc Warnings
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.PJProperties;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist
> [WARNING] import org.apache.commons.exec.CommandLine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist
> [WARNING] import org.apache.commons.exec.DefaultExecutor;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist
> [WARNING] import org.apache.commons.exec.PumpStreamHandler;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBContext;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBException;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.Marshaller;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlRootElement;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol
> [WARNING] @XmlRootElement
> [WARNING] ^
> [WARNING] symbol: class XmlRootElement
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol
> [WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException {
> [WARNING] ^
> [WARNING] symbol: class JAXBException
> [WARNING] location: class MethylStatsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.IntegerForLoop;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.ParallelRegion;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.ParallelTeam;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBContext;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBException;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.Marshaller;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol
> [WARNING] private ParallelTeam team;
> [WARNING] ^
> [WARNING] symbol: class ParallelTeam
> [WARNING] location: class CompactAlignmentToAnnotationCountsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol
> [WARNING] protected synchronized ParallelTeam getParallelTeam() {
> [WARNING] ^
> [WARNING] symbol: class ParallelTeam
> [WARNING] location: class CompactAlignmentToAnnotationCountsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlElement;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlElementWrapper;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlRootElement;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol
> [WARNING] @XmlRootElement(name = "info-output")
> [WARNING] ^
> [WARNING] symbol: class XmlRootElement
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol
> [WARNING] private void writeInfoOutput() throws JAXBException, IOException {
> [WARNING] ^
> [WARNING] symbol: class JAXBException
> [WARNING] location: class CompactAlignmentToAnnotationCountsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlAccessType;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlAccessorType;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
> [WARNING] @XmlAccessorType(XmlAccessType.FIELD)
> [WARNING] ^
> [WARNING] symbol: class XmlAccessorType
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlAccessType;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist
> [WARNING] import javax.xml.bind.annotation.XmlAccessorType;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
> [WARNING] @XmlAccessorType(XmlAccessType.FIELD)
> [WARNING] ^
> [WARNING] symbol: class XmlAccessorType
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol
> [WARNING] class BasenameParallelRegion extends ParallelRegion {
> [WARNING] ^
> [WARNING] symbol: class ParallelRegion
> [WARNING] location: class CompactAlignmentToAnnotationCountsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.ParallelTeam;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBContext;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.JAXBException;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist
> [WARNING] import javax.xml.bind.Unmarshaller;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol
> [WARNING] private ParallelTeam team;
> [WARNING] ^
> [WARNING] symbol: class ParallelTeam
> [WARNING] location: class StatsMode
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.REXP;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.RVector;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol
> [WARNING] private static Result evaluateFisherExpression(final Rengine rengine,
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class FisherExact
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol
> [WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks {
> [WARNING] ^
> [WARNING] symbol: class RMainLoopCallbacks
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol
> [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol
> [WARNING] public void rBusy(final Rengine rengine, final int which) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol
> [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol
> [WARNING] public void rShowMessage(final Rengine rengine, final String message) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol
> [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol
> [WARNING] public void rFlushConsole(final Rengine rengine) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol
> [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol
> [WARNING] public void rLoadHistory(final Rengine re, final String filename) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RLoggerMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol
> [WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks {
> [WARNING] ^
> [WARNING] symbol: class RMainLoopCallbacks
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol
> [WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol
> [WARNING] public void rBusy(final Rengine rengine, final int which) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol
> [WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol
> [WARNING] public void rShowMessage(final Rengine rengine, final String message) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol
> [WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol
> [WARNING] public void rFlushConsole(final Rengine rengine) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol
> [WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol
> [WARNING] public void rLoadHistory(final Rengine re, final String filename) {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class RConsoleMainLoopCallback
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol
> [WARNING] private Rengine rengine;
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class GobyRengine
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol
> [WARNING] public Rengine getRengine() {
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class GobyRengine
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol
> [WARNING] Rengine rEngine;
> [WARNING] ^
> [WARNING] symbol: class Rengine
> [WARNING] location: class FisherExactRCalculator
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist
> [WARNING] import DistLib.hypergeometric;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist
> [WARNING] import org.rosuda.JRI.Rengine;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.ParallelTeam;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol
> [WARNING] private ParallelTeam team;
> [WARNING] ^
> [WARNING] symbol: class ParallelTeam
> [WARNING] location: class DoInParallel
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol
> [WARNING] protected synchronized ParallelTeam getParallelTeam() {
> [WARNING] ^
> [WARNING] symbol: class ParallelTeam
> [WARNING] location: class DoInParallel
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.IntegerForLoop;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist
> [WARNING] import edu.rit.pj.ParallelRegion;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol
> [WARNING] class BasenameParallelRegion extends ParallelRegion {
> [WARNING] ^
> [WARNING] symbol: class ParallelRegion
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist
> [WARNING] import org.apache.commons.cli.*;
> [WARNING] ^
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
> [WARNING] @XmlAccessorType(XmlAccessType.FIELD)
> [WARNING] ^
> [WARNING] symbol: variable XmlAccessType
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol
> [WARNING] @XmlElement(name = "al")
> [WARNING] ^
> [WARNING] symbol: class XmlElement
> [WARNING] location: class InfoOutput
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol
> [WARNING] @XmlElementWrapper(name = "annotation-lengths")
> [WARNING] ^
> [WARNING] symbol: class XmlElementWrapper
> [WARNING] location: class InfoOutput
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
> [WARNING] @XmlAccessorType(XmlAccessType.FIELD)
> [WARNING] ^
> [WARNING] symbol: variable XmlAccessType
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol
> [WARNING] @XmlElement(name = "tc")
> [WARNING] ^
> [WARNING] symbol: class XmlElement
> [WARNING] location: class InfoOutput
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol
> [WARNING] @XmlElementWrapper(name = "total-counts")
> [WARNING] ^
> [WARNING] symbol: class XmlElementWrapper
> [WARNING] location: class InfoOutput
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.java:286: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.java:299: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.java:312: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &rct
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &q
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &esrc
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &source
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &cd
> [WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning - invalid usage of tag &cts
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1-javadoc.jar
> [INFO]
> [INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
> [INFO] Building Goby Full Distribution 3.3.1 [3/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ goby-distribution ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 3 resources
> [INFO] Copying 72 resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ goby-distribution ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 525 source files to /<<PKGBUILDDIR>>/goby-distribution/target/classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ goby-distribution ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-distribution/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ goby-distribution ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 120 source files to /<<PKGBUILDDIR>>/goby-distribution/target/test-classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/counts/TestCountAdaptiveBinningAdaptor.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/counts/TestCountAdaptiveBinningAdaptor.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSamHelper.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSamHelper.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
> [INFO] Tests are skipped.
> [INFO]
> [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ goby-distribution ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1.jar
> [INFO]
> [INFO] >>> maven-source-plugin:3.0.1:jar (attach-sources) > generate-sources @ goby-distribution >>>
> [INFO]
> [INFO] <<< maven-source-plugin:3.0.1:jar (attach-sources) < generate-sources @ goby-distribution <<<
> [INFO]
> [INFO]
> [INFO] --- maven-source-plugin:3.0.1:jar (attach-sources) @ goby-distribution ---
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1-sources.jar
> [INFO]
> [INFO] --- maven-javadoc-plugin:3.0.1:jar (attach-javadocs) @ goby-distribution ---
> [INFO] Adding the --ignore-source-errors option
> [ERROR] Error fetching link: /<<PKGBUILDDIR>>/goby-io/target/apidocs/package-list. Ignored it.
> [INFO]
> Loading source files for package samples...
> Loading source files for package org.campagnelab.goby.modes...
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> Loading source files for package org.campagnelab.goby.alignments.filters...
> Loading source files for package org.campagnelab.goby.alignments.htsjdk...
> Constructing Javadoc information...
> Standard Doclet version 11.0.13
> Building tree for all the packages and classes...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/GobyVersion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/Peak.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VersionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/Predictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/GobyRengine.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/MultiReads.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DataProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FromToFreq.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/GrepReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/WarningCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseReadsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/package-summary.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/package-tree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/constant-values.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/serialized-form.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html...
> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html...
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> Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html...
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.java:286: warning - invalid usage of tag >
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:27: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:29: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning - Tag @see: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder(MG4J)
> [WARNING] Date: 1/15/12
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning - @return tag cannot be used in method with void return type.
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning - Tag @link: reference not found: #BITS
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning - invalid usage of tag <
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning - Tag @see: reference not found: org.campagnelab.goby.aligners.LastagAligner
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning - invalid usage of tag <
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> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning - @return tag cannot be used in method with void return type.
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:219: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:219: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:144: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:234: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:234: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:234: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:234: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:264: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:264: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:264: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:264: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning - invalid usage of tag <
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF.java:16: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF.java:18: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF.java:20: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF2.java:13: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF2.java:15: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF2.java:17: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF3.java:16: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF3.java:18: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/FormatIndelVCF3.java:20: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/MergeIndelFrom.java:16: warning - invalid usage of tag >
> [WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/predictions/MergeIndelFrom.java:17: warning - invalid usage of tag >
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1-javadoc.jar
> [INFO]
> [INFO] --- maven-assembly-plugin:3.1.0:single (make-assembly) @ goby-distribution ---
> [INFO] Reading assembly descriptor: assembly/assembly.xml
> [INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-bin.jar
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Summary for Goby Framework 3.3.1:
> [INFO]
> [INFO] Goby Framework ..................................... SUCCESS [ 0.026 s]
> [INFO] Goby I/O ........................................... SUCCESS [ 15.936 s]
> [INFO] Goby Full Distribution ............................. SUCCESS [ 17.117 s]
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD SUCCESS
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 33.173 s
> [INFO] Finished at: 2021-12-20T18:34:41Z
> [INFO] ------------------------------------------------------------------------
> debian/rules override_dh_auto_test
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # Create a symlink to the directory with test data for tests run from the
> # goby-distribution directory.
> ln -s ../test-data goby-distribution/test-data
> # Putting the JRI location in the path, as indicated in GobyRengine.java.
> # Also indicating R_HOME, as found in http://rforge.net/JRI/.
> export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \
> export R_HOME="/usr/lib/R" && \
> 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=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test
> [INFO] Scanning for projects...
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
> [WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 226, column 16
> [WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 292, column 16
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 294, column 15
> [WARNING]
> [WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
> [WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
> [WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
> [WARNING]
> [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
> [WARNING]
> [WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
> [WARNING]
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Build Order:
> [INFO]
> [INFO] Goby Framework [pom]
> [INFO] Goby I/O [jar]
> [INFO] Goby Full Distribution [jar]
> [INFO]
> [INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
> [INFO] Building Goby Framework 3.3.1 [1/3]
> [INFO] --------------------------------[ pom ]---------------------------------
> [INFO]
> [INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
> [INFO] Building Goby I/O 3.3.1 [2/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-classes) @ goby-io ---
> [INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-java-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (exec-python-cpp-protoc) @ goby-io ---
> [INFO] Executing tasks
>
> main:
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ goby-io ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 2 resources
> [INFO] Copying 1 resource
> [INFO] Copying 1 resource
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ goby-io ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 260 source files to /<<PKGBUILDDIR>>/goby-io/target/classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-antrun-plugin:1.8:run (default) @ goby-io ---
> [WARNING] Parameter tasks is deprecated, use target instead
> [INFO] Executing tasks
>
> main:
> [copy] Copying 1 file to /<<PKGBUILDDIR>>
> [copy] Copying 1 file to /<<PKGBUILDDIR>>/goby-io/target/classes
> [INFO] Executed tasks
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ goby-io ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-io/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ goby-io ---
> [INFO] No sources to compile
> [INFO]
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
> [INFO] No tests to run.
> [INFO]
> [INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
> [INFO] Building Goby Full Distribution 3.3.1 [3/3]
> [INFO] --------------------------------[ jar ]---------------------------------
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ goby-distribution ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 3 resources
> [INFO] Copying 72 resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ goby-distribution ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 525 source files to /<<PKGBUILDDIR>>/goby-distribution/target/classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ goby-distribution ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-distribution/src/test/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:3.8.1:testCompile (default-testCompile) @ goby-distribution ---
> [INFO] Changes detected - recompiling the module!
> [INFO] Compiling 120 source files to /<<PKGBUILDDIR>>/goby-distribution/target/test-classes
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/counts/TestCountAdaptiveBinningAdaptor.java: Some input files use or override a deprecated API.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/counts/TestCountAdaptiveBinningAdaptor.java: Recompile with -Xlint:deprecation for details.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSamHelper.java: Some input files use unchecked or unsafe operations.
> [INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSamHelper.java: Recompile with -Xlint:unchecked for details.
> [INFO]
> [INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
> [INFO]
> [INFO] -------------------------------------------------------
> [INFO] T E S T S
> [INFO] -------------------------------------------------------
> [INFO] Running TestSuite
> SLF4J: Class path contains multiple SLF4J bindings.
> SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> SLF4J: Found binding in [jar:file:/<<PKGBUILDDIR>>/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class]
> SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
> SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
> Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short_1_per_chunk.compact-reads to test-results/reformat-test-subset.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-exclude-read-lengths-at-extrreme.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short_1_per_chunk.compact-reads to test-results/reformat-test-exclude-read-lengths.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-start-end.compact-reads
> Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short_1_per_chunk.compact-reads to test-results/reformat-test-start.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-exclude-read-lengths-at-extrreme.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test.compact-reads
> Converting [1/1] test-data/compact-reads/small-paired.compact-reads to test-results/reformat-test-trim-paired.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-chunk-size.compact-reads
> Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to test-results/with-meta-data-output-same.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-extremes.compact-reads
> Converting [1/1] test-data/compact-reads/s_1_sequence_short.compact-reads to test-results/reformat-test-zero-zero.compact-reads
> Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
> [Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback -
>
> [Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - R version 4.1.2 (2021-11-01) -- "Bird Hippie"
> Copyright (C) 2021 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
>
> [Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>
> [Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
>
> [Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=10000
> Loading test-data/fdr-mode/file1.vcf
> Loading test-data/fdr-mode/file2.vcf
> Loading test-data/fdr-mode/file3.vcf
> adjusting column: PCHI2
> Combining test-data/fdr-mode/file1.vcf
> Combining test-data/fdr-mode/file2.vcf
> Combining test-data/fdr-mode/file3.vcf
> Loading test-data/fdr-mode/file-B-1.vcf
> Loading test-data/fdr-mode/file-B-2.vcf
> adjusting column: PCHI2
> Combining test-data/fdr-mode/file-B-1.vcf
> Combining test-data/fdr-mode/file-B-2.vcf
> Loading test-data/fdr-mode/file-B-1.vcf
> Loading test-data/fdr-mode/file-B-2.vcf
> adjusting column: PCHI2
> Combining test-data/fdr-mode/file-B-1.vcf
> Combining test-data/fdr-mode/file-B-2.vcf
> Loading test-data/fdr-mode/file1.vcf
> Loading test-data/fdr-mode/file2.vcf
> Loading test-data/fdr-mode/file3.vcf
> Combining test-data/fdr-mode/file1.vcf
> Combining test-data/fdr-mode/file2.vcf
> Combining test-data/fdr-mode/file3.vcf
> Scanning target file..
> Target file had 1 entries.
> Wrote 1 target ids to alignment header.
> Setting quality threshold to 0.05
> Total logical entries written: 2
> Total bytes written: 0
> Average bytes/logical entry: 0.0
> Min query index: 0
> Max query index: 0
> Number of queries: 3
> Number of targets: 3
> Removed by quality filter: 0
> Not best score: 1
> Number of alignments written: 2
> [main] WARN org.campagnelab.goby.GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent.
> query_index: 0
> target_index: 0
> position: 14977972
> score: 780.0
> matching_reverse_strand: false
> multiplicity: 1
> number_of_mismatches: 1
> number_of_indels: 0
> query_length: 142
> query_aligned_length: 134
> target_aligned_length: 134
> sequence_variations {
> to: "T"
> from: "A"
> position: 6
> to_quality: "/"
> read_index: 14
> }
> fragment_index: 0
> query_index_occurrences: 2
> ambiguity: 1
>
> Processing test-data/sample-qual-scores/30reads.fa
> Processed 0 read entries.
> Min quality score: 2147483647
> Max quality score: -2147483648
> Avg quality score: 0
> Probable quality encoding scheme: fasta
> Processing test-data/sample-qual-scores/30reads.fq
> Processed 30 read entries.
> Min quality score: 69
> Max quality score: 98
> Avg quality score: 94
> Probable quality encoding scheme: Illumina/Solexa
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> 1/1 ..T
>
> TTC[27]->CGT[27] / qual=1:2:3
> A[15]->G[20] / qual=20
> A[15]->G[20] / qual=20
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> Comparing A/B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Filtering reads that have these criteria:
> q<30
> #count(allele) < (2 *#filtered)
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> Associating basename: basen0 to group: A
> Associating basename: basen1 to group: A
> Associating basename: basen2 to group: A
> Associating basename: basen3 to group: A
> Associating basename: basen4 to group: A
> Associating basename: basen5 to group: B
> Associating basename: basen6 to group: B
> Associating basename: basen7 to group: B
> Associating basename: basen8 to group: B
> Associating basename: basen9 to group: B
> sample: basen0 group A
> sample: basen2 group A
> sample: basen4 group A
> sample: basen3 group A
> sample: basen1 group A
> sample: basen9 group B
> sample: basen6 group B
> sample: basen5 group B
> sample: basen7 group B
> sample: basen8 group B
> Using processor NONE
> Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support.
> Filtering reads that have these criteria:
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci
> [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
> [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
> info: + ref: A s=0
> info: + ref: A s=0
> info: + ref: A s=0
> info: + ref: A s=0
> info: + ref: A s=0
> info: + /T q=40 s=0
> info: - /T q=40 s=0
> info: + /C q=10 s=0
> info: + /C q=20 s=0
> info: + /C q=30 s=0
> info: + /C q=40 s=0
> info: + /C q=40 s=0
> info: + /C q=40 s=0
> info: + /C q=40 s=0
> info: + /C q=10 s=0
> info: + /C q=20 s=0
> info: + /N q=30 s=0
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + ref: A s=1
> info: + /T q=40 s=1
> info: + /T q=10 s=1
> info: + /T q=20 s=1
> info: + /T q=30 s=1
> info: + /N q=40 s=1
> info: + /N q=40 s=1
> list: pos=-1 #bases: 33 #indels: 0
> filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1}
> field CHROM value: 0
> field POS value: 145497099
> field ID value: .
> field REF value: A
> field ALT value: G
> field QUAL value: 17.1
> field FILTER value: .
> field INFO[DP] value: 2
> field INFO[DP4] value: 0,0,2,0
> field INFO[MQ] value: 25
> field INFO[FQ] value: -30.8
> field INFO[AF1] value: 0.9999
> field INFO[CI95] value: 0.5,1
> field INFO[PV4] value:
> field INFO[INDEL] value: INDEL
> field INFO[PC2] value: 3,3
> field INFO[PCHI2] value: 0.752
> field INFO[QCHI2] value: 1
> field INFO[RP] value:
> field FORMAT[GT] value:
> field FORMAT[GQ] value:
> field FORMAT[GL] value:
> field FORMAT[DP] value:
> field FORMAT[SP] value:
> field FORMAT[PL] value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1
> field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42
> field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0
> field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1
> field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42
> field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0
> field CHROM gfi:0 value: 0
> field POS gfi:1 value: 145497099
> field ID gfi:2 value: .
> field REF gfi:3 value: A
> field ALT gfi:4 value: G
> field QUAL gfi:5 value: 17.1
> field FILTER gfi:6 value: .
> field FORMAT[GT] gfi:7 value:
> field FORMAT[GQ] gfi:8 value:
> field FORMAT[GL] gfi:9 value:
> field FORMAT[DP] gfi:10 value:
> field FORMAT[SP] gfi:11 value:
> field FORMAT[PL] gfi:12 value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1
> field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11
> field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value:
> field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0
> field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1
> field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42
> field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value:
> field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0
> Total logical entries written: 1
> Total bytes written: 0
> Average bytes/logical entry: 0.0
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 45
> Total logical entries written: 4
> Total bytes written: 0
> Average bytes/logical entry: 0.0
> Min query index: 1
> Max query index: 1
> Number of queries: 1
> Number of targets: 2
> Total logical entries written: 4
> Total bytes written: 62
> Average bytes/logical entry: 15.5
> Min query index: 1
> Max query index: 1
> Number of queries: 1
> Number of targets: 2
> Annotations loaded
> Annotations loaded
> Annotations loaded
> Annotations loaded
> Annotations loaded
> [main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2
> count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3}
> count keys [0, 3, 5, 11, 13]
> -1 0.0
> 0 0.0
> 1 0.0
> 2 0.0
> 3 0.0
> 4 0.0
> 5 0.0
> 6 0.0
> 7 0.0
> 8 0.0
> 9 0.0
> 10 0.0
> 11 0.0
> 12 0.0
> 13 0.0
> 14 0.0
> 15 0.0
> 16 0.0
> 17 0.0
> 18 0.0
> 19 0.0
> 20 0.0
> 21 0.0
> 22 0.0
> 23 0.0
> 24 0.0
> 25 0.0
> 26 0.0
> 27 0.0
> 28 0.0
> 29 0.0
> 30 0.0
> overlapping count 3, 4 0.0
> overlapping count 15, 17 0.0
> overlapping count 9, 18 2.0
> overlapping count 3, 8 2.0
> overlapping count 11, 12 0.0
> overlapping count 9, 10 1.0
> overlapping count 8, 9 0.0
> overlapping count 8, 8 0.0
> overlapping count 5, 6 0.0
> overlapping count 3, 3 0.0
> overlapping count 3, 12 5.0
> overlapping count -1, 2 0.0
> overlapping count 0, 45 6.0
> overlapping count 13, 15 0.0
> -1 0.0
> 0 0.0
> 1 0.0
> 2 0.0
> 3 2.0
> 4 2.0
> 5 3.0
> 6 3.0
> 7 3.0
> 8 3.0
> 9 3.0
> 10 3.0
> 11 2.0
> 12 2.0
> 13 0.0
> 14 0.0
> 15 1.0
> 16 1.0
> 17 1.0
> 18 1.0
> 19 0.0
> 20 0.0
> 21 0.0
> 22 0.0
> 23 0.0
> 24 0.0
> 25 0.0
> 26 0.0
> 27 0.0
> 28 0.0
> 29 0.0
> 30 0.0
> overlapping count 3, 4 2.0
> overlapping count 2, 3 2.0
> overlapping count 3, 8 4.0
> overlapping count 11, 12 2.0
> overlapping count 9, 10 3.0
> overlapping count 8, 9 4.0
> overlapping count 8, 8 3.0
> overlapping count 5, 6 3.0
> overlapping count 3, 3 2.0
> overlapping count 3, 12 5.0
> overlapping count -1, 2 0.0
> overlapping count 0, 45 6.0
> overlapping count 13, 15 1.0
> [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits
> [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 1
> decoding: 2
> decoding: 3
> decoding: 4
> decoding: 3
> decoding: 1
> decoding: 2
> decoding: 1
> decoding: 2
> decoding: 3
> decoding: 1
> decoding: 2
> decoding: 1
> decoding: 2
> decoding: 1
> [ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits
> [ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0
> {1} {0}decoding: 4
> {0} {0}decoding: 4
> {0} {0}decoding: 4
> {0}decoding: 4
> {0}decoding: 4
> {0}decoding: 4
> decoding: 4
> {0}decoding: 4
> {0}decoding: 4
> decoding: 4
> {0}decoding: 4
> decoding: 4
> {0}decoding: 4
> decoding: 4
> {0} {0} {0} {0} {0}decoding: 1
> {0} {0} {0} {0}decoding: 2
> {0} {0} {0} {0} {0}decoding: 3
> decoding: 4
> {0} {0} {0} {0}decoding: 3
> {0} {0} {0}decoding: 1
> {0} {0} {0} {0}decoding: 2
> {0} {0} {0}decoding: 1
> {0} {0} {0}decoding: 2
> {0} {0} {0} {0}decoding: 3
> {0} {0} {0}decoding: 1
> {0} {0} {0}decoding: 2
> {0} {0}decoding: 1
> {0} {0} {0}decoding: 2
> {0} {0}decoding: 1
> [ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits
> [ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 4
> decoding: 1
> decoding: 2
> decoding: 3
> decoding: 4
> decoding: 3
> decoding: 1
> decoding: 2
> decoding: 1
> decoding: 2
> decoding: 3
> decoding: 1
> decoding: 2
> decoding: 1
> decoding: 2
> decoding: 1
> [main] INFO org.campagnelab.goby.util.barcode.TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0
> [main] INFO org.campagnelab.goby.util.barcode.TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds
> qPhred=1
> qPhred=2
> qPhred=3
> qPhred=4
> qPhred=5
> qPhred=6
> qPhred=7
> qPhred=8
> qPhred=9
> qPhred=10
> qPhred=11
> qPhred=12
> qPhred=13
> qPhred=14
> qPhred=15
> qPhred=16
> qPhred=17
> qPhred=18
> qPhred=19
> qPhred=20
> qPhred=21
> qPhred=22
> qPhred=23
> qPhred=24
> qPhred=25
> qPhred=26
> qPhred=27
> qPhred=28
> qPhred=29
> qPhred=30
> qPhred=31
> qPhred=32
> qPhred=33
> qPhred=34
> qPhred=35
> qPhred=36
> qPhred=37
> qPhred=38
> qPhred=39
> qPhred=40
> qPhred=41
> qPhred=42
> qPhred=43
> qPhred=44
> qPhred=45
> qPhred=46
> qPhred=47
> qPhred=48
> qPhred=49
> qPhred=50
> qPhred=51
> qPhred=52
> qPhred=53
> qPhred=54
> qPhred=55
> qPhred=56
> qPhred=57
> qPhred=58
> qPhred=59
> qPhred=60
> qPhred=61
> 0
> AAC 3
> ACC 6
> ATC 9
> AGC 12
> AAC 15
> ACC 18
> ATC 21
> AGC 24
> AAC 27
> ACC 30
> ATC 33
> AGC 36
> AAC 39
> ACC 42
> ATC 45
> AGC 48
> AAC 51
> ACC 54
> ATC 57
> AGC 60
> AAC 63
> ACC 66
> ATC 69
> AGC 72
> AAC 75
> ACC 78
> ATC 81
> AGC[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=9
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=9
> Total logical entries written: 39
> Total bytes written: 660
> Average bytes/logical entry: 16.923077
> Number of bits/base 3.6590436
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=9
> Total logical entries written: 39
> Total bytes written: 685
> Average bytes/logical entry: 17.564102
> Number of bits/base 3.797644
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=9
> Total logical entries written: 39
> Total bytes written: 660
> Average bytes/logical entry: 16.923077
> Number of bits/base 3.6590436
> >1
> NNTGAATGAGACCTA
>
> Creating base test directory: test-results/stats
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
> [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
> [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52884.1 for sample B-7
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52814.1 for sample B-3
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 101641 for sample A-3
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 105698 for sample A-12
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51485.0 for sample B-15
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52534.3 for sample B-14
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 54003.3 for sample B-11
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104229 for sample A-17
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51135.3 for sample B-2
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51694.9 for sample B-10
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102830 for sample A-16
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52814.1 for sample B-8
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 53303.8 for sample B-4
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102690 for sample A-2
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 105209 for sample A-0
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51764.8 for sample B-6
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104929 for sample A-9
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102970 for sample A-8
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100732 for sample A-5
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 105488 for sample A-4
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104719 for sample A-6
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 105908 for sample A-7
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 54213.2 for sample B-5
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104789 for sample A-10
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102201 for sample A-14
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 53933.4 for sample B-9
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 101431 for sample A-1
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52954.0 for sample B-0
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50645.6 for sample B-12
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52114.6 for sample B-13
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104509 for sample A-19
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102271 for sample A-18
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104229 for sample A-15
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52604.3 for sample B-1
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 104439 for sample A-13
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 105698 for sample A-11
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52324.4 for sample B-16
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51485.0 for sample B-17
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 51694.9 for sample B-19
> [main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52884.1 for sample B-18
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed.
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
> [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed.
> list3:element-id p-value p-value-BH-FDR-q-value
> [ 0 [2.354054E-7, 1.177027E-5] ]
> [ 1 [2.10159E-5, 4.294736666666667E-4] ]
> [ 2 [2.576842E-5, 4.294736666666667E-4] ]
> [ 3 [9.814783E-5, 9.471342857142858E-4] ]
> [ 4 [1.05261E-4, 9.471342857142858E-4] ]
> [ 5 [1.241481E-4, 9.471342857142858E-4] ]
> [ 6 [1.325988E-4, 9.471342857142858E-4] ]
> [ 7 [1.568503E-4, 9.803143750000002E-4] ]
> [ 8 [2.254557E-4, 0.0012525316666666666] ]
> [ 9 [3.79538E-4, 0.00189769] ]
> [ 10 [6.114943E-4, 0.0027795195454545455] ]
> [ 11 [0.001613954, 0.006724808333333334] ]
> [ 12 [0.00330243, 0.012636935714285714] ]
> [ 13 [0.003538342, 0.012636935714285714] ]
> [ 14 [0.005236997, 0.017456656666666667] ]
> [ 15 [0.006831909, 0.020762429411764708] ]
> [ 16 [0.007059226, 0.020762429411764708] ]
> [ 17 [0.008805129, 0.024458691666666667] ]
> [ 18 [0.00940104, 0.02473957894736842] ]
> [ 19 [0.01129798, 0.028244949999999998] ]
> [ 20 [0.02115017, 0.050357547619047614] ]
> [ 21 [0.04922736, 0.11188036363636364] ]
> [ 22 [0.06053298, 0.1304633125] ]
> [ 23 [0.06262239, 0.1304633125] ]
> [ 24 [0.07395153, 0.14790306] ]
> [ 25 [0.08281103, 0.15925198076923075] ]
> [ 26 [0.08633331, 0.1598765] ]
> [ 27 [0.1190654, 0.21261678571428572] ]
> [ 28 [0.1890796, 0.32599931034482754] ]
> [ 29 [0.2058494, 0.3430823333333333] ]
> [ 30 [0.2209214, 0.3563248387096774] ]
> [ 31 [0.2856, 0.44625000000000004] ]
> [ 32 [0.3048895, 0.4619537878787878] ]
> [ 33 [0.4660682, 0.6835770833333333] ]
> [ 34 [0.4830809, 0.6835770833333333] ]
> [ 35 [0.4921755, 0.6835770833333333] ]
> [ 36 [0.5319453, 0.718845] ]
> [ 37 [0.575155, 0.7414352564102564] ]
> [ 38 [0.5783195, 0.7414352564102564] ]
> [ 39 [0.6185894, 0.7626062790697675] ]
> [ 40 [0.636362, 0.7626062790697675] ]
> [ 41 [0.6448587, 0.7626062790697675] ]
> [ 42 [0.6558414, 0.7626062790697675] ]
> [ 43 [0.6885884, 0.7824868181818182] ]
> [ 44 [0.7189864, 0.7988737777777778] ]
> [ 45 [0.8179539, 0.8802645744680851] ]
> [ 46 [0.8274487, 0.8802645744680851] ]
> [ 47 [0.89713, 0.9304775510204082] ]
> [ 48 [0.911868, 0.9304775510204082] ]
> [ 49 [0.943789, 0.943789] ]
>
> element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B
> [ id-1 [1.0026817729032942, 0.5002384783094364, 0.003863801861380308, -0.9993120610967015, 0.0, 0.0] ]
>
> truncated fdr=3.53108e-05 original=3.53108e-05
> truncated fdr=0.00128842 original=0.00128842
> truncated fdr=0.00128842 original=0.00128842
> truncated fdr=0.00284140 original=0.00284140
> truncated fdr=0.00284140 original=0.00284140
> truncated fdr=0.00284140 original=0.00284140
> truncated fdr=0.00284140 original=0.00284140
> truncated fdr=0.00294094 original=0.00294094
> truncated fdr=0.00375760 original=0.00375760
> truncated fdr=0.00569307 original=0.00569307
> truncated fdr=0.00833856 original=0.00833856
> truncated fdr=0.0201744 original=0.0201744
> truncated fdr=0.0379108 original=0.0379108
> truncated fdr=0.0379108 original=0.0379108
> truncated fdr=0.0523700 original=0.0523700
> truncated fdr=0.0622873 original=0.0622873
> truncated fdr=0.0622873 original=0.0622873
> truncated fdr=0.0733761 original=0.0733761
> truncated fdr=0.0742187 original=0.0742187
> truncated fdr=0.0847349 original=0.0847349
> truncated fdr=0.151073 original=0.151073
> truncated fdr=0.335641 original=0.335641
> truncated fdr=0.391390 original=0.391390
> truncated fdr=0.391390 original=0.391390
> truncated fdr=0.443709 original=0.443709
> truncated fdr=0.477756 original=0.477756
> truncated fdr=0.479630 original=0.479630
> truncated fdr=0.637850 original=0.637850
> truncated fdr=0.977998 original=0.977998
> truncated fdr=1.00000 original=1.00000
> truncated fdr=1.00000 original=1.00000
> truncated fdr=1.00000 original=1.00000
> truncated fdr=1.00000 original=1.00000
> [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
> [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
> [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
> [main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
> ##fileformat=VCFv4.1
> ##Goby=UNKNOWN
> ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data,
> ##INFO=<ID=p-value1,Number=1,Type=Float,Description="A P-value">
> ##INFO=<ID=p-value2,Number=1,Type=Float,Description="A P-value">
> ##INFO=<ID=#Cm_Group[Group_1],Number=1,Type=Float,Description="Some count">
> ##FORMAT=<ID=Zygosity,Number=1,Type=String,Description="Zygosity">
> ##FORMAT=<ID=Another,Number=1,Type=String,Description="Another">
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB
>
> Creating base test directory: test-results/stats-writer
> allele: A ref: [CC] alt: [T]original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT
> original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G
> original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT
> original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT
> appending (count=0,length=1)
> appending (count=4,length=3)
> appending (count=1,length=3)
> appending (count=0,length=2)
> appending (count=3,length=1)
> appending (count=1,length=1)
> appending (count=0,length=1)
> appending (count=4,length=3)
> appending (count=0,length=5)
> appending (count=3,length=1)
> appending (count=0,length=2)
> appending (count=2,length=1)
> appending (count=0,length=2)
> appending (count=3,length=1)
> appending (count=2,length=1)
> appending (count=0,length=1)
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=6 count=1
> (0,1)
> loading transition for reader[0] position=1 length=3 count=3
> (0,1)(1,4)
> loading transition for reader[0] position=4 length=2 count=0
> (0,1)(1,4)(4,1)
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=4 count=0
> (0,0)
> loading transition for reader[0] position=1 length=1 count=1
> (0,0)(1,1)
> loading transition for reader[0] position=2 length=4 count=0
> (0,0)(1,1)(2,0)
> loading transition for reader[1] position=4 length=10 count=1
> (0,0)(1,1)(2,0)(4,1)
> loading transition for reader[0] position=6 length=2 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)
> loading transition for reader[0] position=8 length=1 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
> loading transition for reader[0] position=9 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
> loading transition for reader[0] position=10 length=2 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
> loading transition for reader[0] position=12 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
> loading transition for reader[0] position=13 length=3 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
> loading transition for reader[0] position=16 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=4 count=0
> loading transition for reader[0] position=1 length=1 count=1
> loading transition for reader[0] position=2 length=4 count=0
> loading transition for reader[1] position=4 length=10 count=1
> loading transition for reader[0] position=6 length=2 count=1
> loading transition for reader[0] position=8 length=1 count=0
> loading transition for reader[0] position=9 length=1 count=1
> loading transition for reader[0] position=10 length=2 count=0
> loading transition for reader[0] position=12 length=1 count=1
> loading transition for reader[0] position=13 length=3 count=0
> loading transition for reader[0] position=16 length=1 count=1
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=6 count=1
> (0,1)
> loading transition for reader[0] position=1 length=3 count=3
> (0,1)(1,4)
> loading transition for reader[0] position=4 length=2 count=0
> (0,1)(1,4)(4,1)
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=4 count=0
> (0,0)
> loading transition for reader[0] position=1 length=1 count=1
> (0,0)(1,1)
> loading transition for reader[0] position=2 length=4 count=0
> (0,0)(1,1)(2,0)
> loading transition for reader[1] position=4 length=10 count=1
> (0,0)(1,1)(2,0)(4,1)
> loading transition for reader[0] position=6 length=2 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)
> loading transition for reader[0] position=8 length=1 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
> loading transition for reader[0] position=9 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
> loading transition for reader[0] position=10 length=2 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
> loading transition for reader[0] position=12 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
> loading transition for reader[0] position=13 length=3 count=0
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
> loading transition for reader[0] position=16 length=1 count=1
> (0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
> loading transition for reader[0] position=0 length=1 count=0
> loading transition for reader[1] position=0 length=4 count=0
> loading transition for reader[0] position=1 length=1 count=1
> loading transition for reader[0] position=2 length=4 count=0
> loading transition for reader[1] position=4 length=10 count=1
> loading transition for reader[0] position=6 length=2 count=1
> loading transition for reader[0] position=8 length=1 count=0
> loading transition for reader[0] position=9 length=1 count=1
> loading transition for reader[0] position=10 length=2 count=0
> loading transition for reader[0] position=12 length=1 count=1
> loading transition for reader[0] position=13 length=3 count=0
> loading transition for reader[0] position=16 length=1 count=1
> loading transition for reader[0] position=0 length=1 count=0
> (0,0)
> loading transition for reader[0] position=1 length=3 count=1
> (0,0)(1,1)
> appending (count=10,length=4)
> appending (count=1,length=0)
> appending (count=2,length=8)
> Hello
> appending (count=10,length=4)
> Appending count: 33107 length: 2
> Appending count: 39151 length: 3
> Appending count: 27061 length: 9
> Appending count: 34872 length: 6
> Appending count: 14150 length: 6
> Appending count: 29832 length: 4
> Appending count: 28472 length: 5
> Appending count: 133 length: 6
> Appending count: 12763 length: 3
> Appending count: 46597 length: 6
> Appending count: 39556 length: 3
> Appending count: 37138 length: 9
> Appending count: 26326 length: 5
> Appending count: 26218 length: 6
> Appending count: 25039 length: 6
> Appending count: 48976 length: 5
> Appending count: 39649 length: 10
> Appending count: 20691 length: 9
> Appending count: 12924 length: 7
> Appending count: 25304 length: 2
> Appending count: 4085 length: 4
> Appending count: 30518 length: 4
> Appending count: 35045 length: 6
> Appending count: 44046 length: 4
> Appending count: 30161 length: 7
> Appending count: 38357 length: 8
> Appending count: 41937 length: 10
> Appending count: 47696 length: 3
> Appending count: 22398 length: 7
> Appending count: 3291 length: 1
> position= 0 count= 33107
> position= 1 count= 33107
> position= 2 count= 39151
> position= 3 count= 39151
> position= 4 count= 39151
> position= 5 count= 27061
> position= 6 count= 27061
> position= 7 count= 27061
> position= 8 count= 27061
> position= 9 count= 27061
> position= 10 count= 27061
> position= 11 count= 27061
> position= 12 count= 27061
> position= 13 count= 27061
> position= 14 count= 34872
> position= 15 count= 34872
> position= 16 count= 34872
> position= 17 count= 34872
> position= 18 count= 34872
> position= 19 count= 34872
> position= 20 count= 14150
> position= 21 count= 14150
> position= 22 count= 14150
> position= 23 count= 14150
> position= 24 count= 14150
> position= 25 count= 14150
> position= 26 count= 29832
> position= 27 count= 29832
> position= 28 count= 29832
> position= 29 count= 29832
> position= 30 count= 28472
> position= 31 count= 28472
> position= 32 count= 28472
> position= 33 count= 28472
> position= 34 count= 28472
> position= 35 count= 133
> position= 36 count= 133
> position= 37 count= 133
> position= 38 count= 133
> position= 39 count= 133
> position= 40 count= 133
> position= 41 count= 12763
> position= 42 count= 12763
> position= 43 count= 12763
> position= 44 count= 46597
> position= 45 count= 46597
> position= 46 count= 46597
> position= 47 count= 46597
> position= 48 count= 46597
> position= 49 count= 46597
> position= 50 count= 39556
> position= 51 count= 39556
> position= 52 count= 39556
> position= 53 count= 37138
> position= 54 count= 37138
> position= 55 count= 37138
> position= 56 count= 37138
> position= 57 count= 37138
> position= 58 count= 37138
> position= 59 count= 37138
> position= 60 count= 37138
> position= 61 count= 37138
> position= 62 count= 26326
> position= 63 count= 26326
> position= 64 count= 26326
> position= 65 count= 26326
> position= 66 count= 26326
> position= 67 count= 26218
> position= 68 count= 26218
> position= 69 count= 26218
> position= 70 count= 26218
> position= 71 count= 26218
> position= 72 count= 26218
> position= 73 count= 25039
> position= 74 count= 25039
> position= 75 count= 25039
> position= 76 count= 25039
> position= 77 count= 25039
> position= 78 count= 25039
> position= 79 count= 48976
> position= 80 count= 48976
> position= 81 count= 48976
> position= 82 count= 48976
> position= 83 count= 48976
> position= 84 count= 39649
> position= 85 count= 39649
> position= 86 count= 39649
> position= 87 count= 39649
> position= 88 count= 39649
> position= 89 count= 39649
> position= 90 count= 39649
> position= 91 count= 39649
> position= 92 count= 39649
> position= 93 count= 39649
> position= 94 count= 20691
> position= 95 count= 20691
> position= 96 count= 20691
> position= 97 count= 20691
> position= 98 count= 20691
> position= 99 count= 20691
> position= 100 count= 20691
> position= 101 count= 20691
> position= 102 count= 20691
> position= 103 count= 12924
> position= 104 count= 12924
> position= 105 count= 12924
> position= 106 count= 12924
> position= 107 count= 12924
> position= 108 count= 12924
> position= 109 count= 12924
> position= 110 count= 25304
> position= 111 count= 25304
> position= 112 count= 4085
> position= 113 count= 4085
> position= 114 count= 4085
> position= 115 count= 4085
> position= 116 count= 30518
> position= 117 count= 30518
> position= 118 count= 30518
> position= 119 count= 30518
> position= 120 count= 35045
> position= 121 count= 35045
> position= 122 count= 35045
> position= 123 count= 35045
> position= 124 count= 35045
> position= 125 count= 35045
> position= 126 count= 44046
> position= 127 count= 44046
> position= 128 count= 44046
> position= 129 count= 44046
> position= 130 count= 30161
> position= 131 count= 30161
> position= 132 count= 30161
> position= 133 count= 30161
> position= 134 count= 30161
> position= 135 count= 30161
> position= 136 count= 30161
> position= 137 count= 38357
> position= 138 count= 38357
> position= 139 count= 38357
> position= 140 count= 38357
> position= 141 count= 38357
> position= 142 count= 38357
> position= 143 count= 38357
> position= 144 count= 38357
> position= 145 count= 41937
> position= 146 count= 41937
> position= 147 count= 41937
> position= 148 count= 41937
> position= 149 count= 41937
> position= 150 count= 41937
> position= 151 count= 41937
> position= 152 count= 41937
> position= 153 count= 41937
> position= 154 count= 41937
> position= 155 count= 47696
> position= 156 count= 47696
> position= 157 count= 47696
> position= 158 count= 22398
> position= 159 count= 22398
> position= 160 count= 22398
> position= 161 count= 22398
> position= 162 count= 22398
> position= 163 count= 22398
> position= 164 count= 22398
> position= 165 count= 3291
> peak : start :5 count :13 length :100010
> peak : start :100020 count :10 length :1
> [main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 101 7
> [main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 111 7
> [main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 131 8
> [main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 141 8
> [main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 151 8
> Processing queryIndex=8 with description '8 perfect start of ref'
> Processing queryIndex=9 with description '9 perfect start of ref reverse strand'
> Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1'
> Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1'
> Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1'
> Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2'
> Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2'
> Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2'
> Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20'
> Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20'
> Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2'
> Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2'
> Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20'
> Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)'
> Processing queryIndex=0 with description '0 perfect match'
> Processing queryIndex=1 with description '1 perfect match on reverse strand'
> Processing queryIndex=2 with description '2 mutation'
> Processing queryIndex=3 with description '3 mutation on reverse strand'
> Processing queryIndex=4 with description '4 insertion'
> Processing queryIndex=6 with description '6 deletion'
> Processing queryIndex=7 with description '7 deletion on reverse strand'
> Processing queryIndex=27 with description '27 padding left & right, deletion then mutation'
> Processing queryIndex=24 with description '24 padding left & right, mutation, deletion'
> Processing queryIndex=5 with description '5 insertion on reverse strand'
> Processing queryIndex=10 with description '10 perfect end of ref'
> Processing queryIndex=11 with description '11 perfect end of ref reverse strand'
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> Total logical entries written: 20000
> Total bytes written: 77210
> Average bytes/logical entry: 3.8605
> Min query index: 0
> Max query index: 1999
> Number of queries: 2000
> Number of targets: 10
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
> entry:query_index: 0
> target_index: 0
> position: 5
> score: 5.0
> matching_reverse_strand: false
> query_length: 20
> query_aligned_length: 20
> target_aligned_length: 20
> sequence_variations {
> to: "CTAG"
> from: "----"
> position: 10
> read_index: 10
> }
>
> entry:query_index: 1
> target_index: 0
> position: 5
> matching_reverse_strand: false
> query_length: 20
> query_aligned_length: 20
> target_aligned_length: 20
> sequence_variations {
> to: "CTAG"
> from: "----"
> position: 10
> to_quality: "(((("
> read_index: 10
> }
>
> entry: query_index: 0
> target_index: 0
> position: 0
> matching_reverse_strand: false
> query_length: 10
> query_aligned_length: 10
> sequence_variations {
> to: "AAA"
> from: "---"
> position: 3
> read_index: 3
> }
>
> processing entry on target 0 at position 0
> processing entry on target 0 at position 5
> processing entry on target 1 at position 0
> processing entry on target 1 at position 5
> processing entry on target 4 at position 0
> processing entry on target 4 at position 5
> entry:query_index: 0
> target_index: 0
> position: 10
> matching_reverse_strand: false
> query_length: 50
> query_aligned_length: 50
> sequence_variations {
> to: "AAA"
> from: "---"
> position: 20
> read_index: 20
> }
>
> entry:query_index: 1
> target_index: 0
> position: 1
> matching_reverse_strand: false
> query_length: 50
> query_aligned_length: 50
> sequence_variations {
> to: "T"
> from: "A"
> position: 20
> read_index: 20
> }
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> 0
> 23
> query_index: 0
> target_index: 0
> position: 0
> query_position: 0
> matching_reverse_strand: false
> query_length: 75
> query_aligned_length: 75
> target_aligned_length: 75
> mapping_quality: 255
> pair_flags: 0
> fragment_index: 0
> ambiguity: 1
>
> query_index: 1
> target_index: 0
> position: 1
> query_position: 0
> matching_reverse_strand: false
> query_length: 75
> query_aligned_length: 75
> target_aligned_length: 75
> mapping_quality: 255
> pair_flags: 0
> fragment_index: 0
> ambiguity: 1
>
> read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT
> expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
> recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
> read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG
> expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG
> expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> read =TAAAACCTAAAAAAAAAAAAAAACCCC
> expected =TAAAA--TAAAAAAAAAAAAAAACCCC
> recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC
> read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA
> expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
> recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
> read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG
> expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
> read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT
> expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
> recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 0
> Total bytes written: 31
> Average bytes/logical entry: Infinity
> Min query index: 2147483647
> Max query index: -2147483648
> Number of queries: 2
> Number of targets: 0
> 97
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 6
> Total bytes written: 162
> Average bytes/logical entry: 27.0
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 6
> Total bytes written: 162
> Average bytes/logical entry: 27.0
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 6
> Total bytes written: 162
> Average bytes/logical entry: 27.0
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 6
> Total bytes written: 162
> Average bytes/logical entry: 27.0
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
> Total logical entries written: 7
> Total bytes written: 219
> Average bytes/logical entry: 31.285715
> Min query index: 0
> Max query index: 0
> Number of queries: 1
> Number of targets: 3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 424.57M/3.70G/937.53M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> found entry: query_index: 0
> target_index: 1999
> position: 19991
> score: 20020.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 1
> target_index: 1999
> position: 19992
> score: 20021.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 1999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 1999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 1999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 1999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 1999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 1999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 1999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 1999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 467.56M/3.66G/894.54M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 µs/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]; used/avail/free/total/max mem: 548.31M/3.58G/813.80M/1.36G/4.13G
> found entry: query_index: 2
> target_index: 1999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 1999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 1999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 1999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 1999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 1999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 1999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 1999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 3999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 3999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 3999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 3999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 3999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 3999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 3999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 3999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 602.83M/3.52G/759.27M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
> notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 %
> found entry: query_index: 0
> target_index: 1
> position: 2
> score: 31.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 0
> target_index: 2
> position: 3
> score: 31.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 4
> position: 6
> score: 30.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 630.09M/3.50G/732.01M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> Finding max number of reads...
> Found input file with 2 target(s)
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> Found input file with 2 target(s)
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> ... max number of reads was 10
> First pass: determine which reads should be kept in the merged alignment.
> Scanning align-105
> Scanning align-106
> Found 40 logical alignment entries.
> Prepare merged too many hits information.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 657.37M/3.47G/704.73M/1.36G/4.13G
> Second pass: writing the merged alignment.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
> Wrote 20 skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000%
> Total logical entries written: 20
> Total bytes written: 0
> Average bytes/logical entry: 0.0
> Min query index: 0
> Max query index: 9
> Number of queries: 10
> Number of targets: 4
> Percent aligned: 100.0
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 684.09M/3.44G/678.01M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
> found entry: query_index: 0
> target_index: 1
> position: 11
> score: 40.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 1
> target_index: 1
> position: 12
> score: 41.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 1
> position: 13
> score: 42.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 1
> position: 14
> score: 43.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 1
> position: 15
> score: 44.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 1
> position: 16
> score: 45.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 1
> position: 17
> score: 46.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 1
> position: 18
> score: 47.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 1
> position: 19
> score: 48.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 1
> position: 20
> score: 49.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]; used/avail/free/total/max mem: 737.57M/3.39G/624.53M/1.36G/4.13G
> found entry: query_index: 2
> target_index: 1999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 1999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 1999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 1999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 1999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 1999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 1999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 1999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 3999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 3999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 3999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 3999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 3999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 3999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 3999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 3999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> preparing 105
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
> [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
> Warning: could not find depth/max-length-of-match in too many hits information.
> [main] INFO org.campagnelab.goby.alignments.Merge - Completed.
> [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 818.31M/3.31G/543.79M/1.36G/4.13G
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
> found entry: query_index: 0
> target_index: 1999
> position: 19991
> score: 20020.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 1
> target_index: 1999
> position: 19992
> score: 20021.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 1999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 1999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 1999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 1999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 1999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 1999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 1999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 1999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 0
> target_index: 3999
> position: 19991
> score: 20020.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 1
> target_index: 3999
> position: 19992
> score: 20021.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 2
> target_index: 3999
> position: 19993
> score: 20022.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 3
> target_index: 3999
> position: 19994
> score: 20023.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 4
> target_index: 3999
> position: 19995
> score: 20024.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 5
> target_index: 3999
> position: 19996
> score: 20025.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 6
> target_index: 3999
> position: 19997
> score: 20026.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 7
> target_index: 3999
> position: 19998
> score: 20027.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 8
> target_index: 3999
> position: 19999
> score: 20028.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> found entry: query_index: 9
> target_index: 3999
> position: 20000
> score: 20029.0
> matching_reverse_strand: false
> multiplicity: 1
> query_length: 35
>
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
>
> [main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression.
> Setting quality threshold to 0.02
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> entry.position(): 1
> entry.position(): 2
> entry.position(): 3
> entry.position(): 5
> entry.position(): 6
> entry.position(): 7
> entry.position(): 8
> entry.position(): 9
> entry.position(): 10
> entry.position(): 10
> entry.position(): 12
> entry.position(): 99
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2
> [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits.
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> entry: score=30.0000 readOriginIndex=0
> entry: score=30.0000 readOriginIndex=0
> entry: score=50.0000 readOriginIndex=3
> entry: score=50.0000 readOriginIndex=3
> entry: score=50.0000 readOriginIndex=3
> Scanned 5 entries
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> entry: score=30.0000 readOriginIndex=0
> entry: score=30.0000 readOriginIndex=0
> Scanned 2 entries
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> 0
> 2
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102
> [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
> entry: score=50.0000 readOriginIndex=3
> entry: score=50.0000 readOriginIndex=3
> entry: score=50.0000 readOriginIndex=3
> entry: score=30.0000 readOriginIndex=0
> entry: score=30.0000 readOriginIndex=0
> Scanned 5 entries
> [ERROR] Tests run: 512, Failures: 14, Errors: 0, Skipped: 32, Time elapsed: 65.863 s <<< FAILURE! - in TestSuite
> [ERROR] testHasStatsWithSampling on testHasStatsWithSampling(org.campagnelab.goby.modes.TestReadQualityStatsMode)(org.campagnelab.goby.modes.TestReadQualityStatsMode) Time elapsed: 0.027 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/five-with-quality.compact-reads.read-qual-stats.tsv (No such file or directory)
> at org.campagnelab.goby.modes.TestReadQualityStatsMode.testHasStatsWithSampling(TestReadQualityStatsMode.java:56)
>
> [ERROR] testHasStats on testHasStats(org.campagnelab.goby.modes.TestReadQualityStatsMode)(org.campagnelab.goby.modes.TestReadQualityStatsMode) Time elapsed: 0 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/five-with-quality.compact-reads.read-qual-stats.tsv (No such file or directory)
> at org.campagnelab.goby.modes.TestReadQualityStatsMode.testHasStats(TestReadQualityStatsMode.java:42)
>
> [ERROR] reformatSubsetOfCompactFile on reformatSubsetOfCompactFile(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-subset.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.reformatSubsetOfCompactFile(TestReformatCompactReadsMode.java:216)
>
> [ERROR] excludeReadLengthsAt35 on excludeReadLengthsAt35(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-exclude-read-lengths-at-extrreme.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.excludeReadLengthsAt35(TestReformatCompactReadsMode.java:318)
>
> [ERROR] excludeReadLengthsOf23 on excludeReadLengthsOf23(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-exclude-read-lengths.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.excludeReadLengthsOf23(TestReformatCompactReadsMode.java:255)
>
> [ERROR] startAndEndAtExactLength on startAndEndAtExactLength(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.002 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-start-end.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.startAndEndAtExactLength(TestReformatCompactReadsMode.java:97)
>
> [ERROR] reformatStartOfCompactFile on reformatStartOfCompactFile(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-start.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.reformatStartOfCompactFile(TestReformatCompactReadsMode.java:184)
>
> [ERROR] trimReadLengthsAt35 on trimReadLengthsAt35(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-exclude-read-lengths-at-extrreme.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.trimReadLengthsAt35(TestReformatCompactReadsMode.java:340)
>
> [ERROR] noChange on noChange(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.noChange(TestReformatCompactReadsMode.java:55)
>
> [ERROR] trimPairedReadsAt10 on trimPairedReadsAt10(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-trim-paired.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.trimPairedReadsAt10(TestReformatCompactReadsMode.java:285)
>
> [ERROR] reformatChunkSize on reformatChunkSize(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.004 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-chunk-size.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.reformatChunkSize(TestReformatCompactReadsMode.java:142)
>
> [ERROR] reformatQualityScoreLength on reformatQualityScoreLength(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.002 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/with-meta-data-output-same.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.reformatQualityScoreLength(TestReformatCompactReadsMode.java:446)
>
> [ERROR] startAndEndAtExtremes on startAndEndAtExtremes(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-extremes.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.startAndEndAtExtremes(TestReformatCompactReadsMode.java:76)
>
> [ERROR] zeroEntries on zeroEntries(org.campagnelab.goby.modes.TestReformatCompactReadsMode)(org.campagnelab.goby.modes.TestReformatCompactReadsMode) Time elapsed: 0.001 s <<< FAILURE!
> java.io.FileNotFoundException: test-results/reformat-test-zero-zero.compact-reads (No such file or directory)
> at org.campagnelab.goby.modes.TestReformatCompactReadsMode.zeroEntries(TestReformatCompactReadsMode.java:117)
>
> [GobyRengine-ShutdownHook] INFO org.campagnelab.goby.R.GobyRengine - Shutdown hook is terminating R
> [INFO]
> [INFO] Results:
> [INFO]
> [ERROR] Failures:
> [ERROR] TestReadQualityStatsMode.testHasStats:42 » FileNotFound test-results/five-with...
> [ERROR] TestReadQualityStatsMode.testHasStatsWithSampling:56 » FileNotFound test-resul...
> [ERROR] TestReformatCompactReadsMode.excludeReadLengthsAt35:318 » FileNotFound test-re...
> [ERROR] TestReformatCompactReadsMode.excludeReadLengthsOf23:255 » FileNotFound test-re...
> [ERROR] TestReformatCompactReadsMode.noChange:55 » FileNotFound test-results/reformat-...
> [ERROR] TestReformatCompactReadsMode.reformatChunkSize:142 » FileNotFound test-results...
> [ERROR] TestReformatCompactReadsMode.reformatQualityScoreLength:446 » FileNotFound tes...
> [ERROR] TestReformatCompactReadsMode.reformatStartOfCompactFile:184 » FileNotFound tes...
> [ERROR] TestReformatCompactReadsMode.reformatSubsetOfCompactFile:216 » FileNotFound te...
> [ERROR] TestReformatCompactReadsMode.startAndEndAtExactLength:97 » FileNotFound test-r...
> [ERROR] TestReformatCompactReadsMode.startAndEndAtExtremes:76 » FileNotFound test-resu...
> [ERROR] TestReformatCompactReadsMode.trimPairedReadsAt10:285 » FileNotFound test-resul...
> [ERROR] TestReformatCompactReadsMode.trimReadLengthsAt35:340 » FileNotFound test-resul...
> [ERROR] TestReformatCompactReadsMode.zeroEntries:117 » FileNotFound test-results/refor...
> [INFO]
> [ERROR] Tests run: 512, Failures: 14, Errors: 0, Skipped: 32
> [INFO]
> [INFO] ------------------------------------------------------------------------
> [INFO] Reactor Summary for Goby Framework 3.3.1:
> [INFO]
> [INFO] Goby Framework ..................................... SUCCESS [ 0.029 s]
> [INFO] Goby I/O ........................................... SUCCESS [ 5.881 s]
> [INFO] Goby Full Distribution ............................. FAILURE [01:15 min]
> [INFO] ------------------------------------------------------------------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------------------
> [INFO] Total time: 01:21 min
> [INFO] Finished at: 2021-12-20T18:36:03Z
> [INFO] ------------------------------------------------------------------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.3:test (default-test) on project goby-distribution: There are test failures.
> [ERROR]
> [ERROR] Please refer to /<<PKGBUILDDIR>>/goby-distribution/target/surefire-reports for the individual test results.
> [ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
> [ERROR] -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the command
> [ERROR] mvn <args> -rf :goby-distribution
> dh_auto_test: error: /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=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test returned exit code 1
> make[1]: *** [debian/rules:19: override_dh_auto_test] Error 25
The full build log is available from:
http://qa-logs.debian.net/2021/12/20/libgoby-java_3.3.1+dfsg2-5_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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