[med-svn] [picard-tools] branch upstream updated (115543b -> 9175c40)
Vincent Danjean
vdanjean at debian.org
Thu Jul 7 10:00:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a change to branch upstream
in repository picard-tools.
from 115543b Imported Upstream version 2.1.1+dfsg
new 9175c40 Imported Upstream version 2.5.0-gradle+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 3 +-
.travis.yml | 14 +-
Picard-public.fbp | 18 -
Picard-public.iml | 54 --
Picard-public.ipr | 351 ----------
README.md | 2 +
build.gradle | 326 +++++++++
build.sbt | 140 ----
build.xml | 631 +----------------
gradle/wrapper/gradle-wrapper.properties | 6 +
gradlew | 164 +++++
.../analysis/directed/TargetedPcrMetrics.java | 148 ----
src/java/picard/sam/RevertSam.java | 414 -----------
src/{ => main}/java/picard/PicardException.java | 0
src/{ => main}/java/picard/Test.java | 0
.../java/picard/analysis/AdapterUtility.java | 4 +-
.../picard/analysis/AlignmentSummaryMetrics.java | 0
.../analysis/AlignmentSummaryMetricsCollector.java | 23 +-
.../analysis/BaseDistributionByCycleMetrics.java | 0
.../java/picard/analysis/ChimeraUtil.java | 0
.../analysis/CollectAlignmentSummaryMetrics.java | 28 +-
.../analysis/CollectBaseDistributionByCycle.java | 33 +-
.../java/picard/analysis/CollectGcBiasMetrics.java | 12 +-
.../picard/analysis/CollectInsertSizeMetrics.java | 16 +-
.../analysis/CollectJumpingLibraryMetrics.java | 62 +-
.../picard/analysis/CollectMultipleMetrics.java | 51 +-
.../java/picard/analysis/CollectOxoGMetrics.java | 10 +-
.../analysis/CollectQualityYieldMetrics.java | 3 +-
.../java/picard/analysis/CollectRawWgsMetrics.java | 14 +-
.../java/picard/analysis/CollectRnaSeqMetrics.java | 47 +-
.../java/picard/analysis/CollectRrbsMetrics.java | 55 +-
.../java/picard/analysis/CollectWgsMetrics.java | 322 +++++----
.../analysis/CollectWgsMetricsFromQuerySorted.java | 3 +
.../CollectWgsMetricsFromSampledSites.java | 8 +-
.../CollectWgsMetricsWithNonZeroCoverage.java | 172 +++++
.../java/picard/analysis/CompareMetrics.java | 0
.../analysis/FingerprintingDetailMetrics.java | 0
.../analysis/FingerprintingSummaryMetrics.java | 0
.../java/picard/analysis/GcBiasDetailMetrics.java | 2 +-
.../picard/analysis/GcBiasMetricsCollector.java | 0
.../java/picard/analysis/GcBiasSummaryMetrics.java | 14 +-
.../java/picard/analysis/GcBiasUtils.java | 0
.../java/picard/analysis/InsertSizeMetrics.java | 0
.../picard/analysis/JumpingLibraryMetrics.java | 10 +-
.../java/picard/analysis/MeanQualityByCycle.java | 3 +-
.../picard/analysis/MetricAccumulationLevel.java | 0
.../picard/analysis/QualityScoreDistribution.java | 16 +-
.../java/picard/analysis/RnaSeqMetrics.java | 44 +-
.../java/picard/analysis/RrbsCpgDetailMetrics.java | 2 +-
.../java/picard/analysis/RrbsMetrics.java | 0
.../java/picard/analysis/RrbsMetricsCollector.java | 0
.../java/picard/analysis/RrbsSummaryMetrics.java | 4 +-
.../java/picard/analysis/SinglePassSamProgram.java | 0
.../picard/analysis/TheoreticalSensitivity.java | 47 +-
.../picard/analysis/artifacts/ArtifactCounter.java | 3 +-
.../CollectSequencingArtifactMetrics.java | 64 +-
.../analysis/artifacts/ContextAccumulator.java | 0
.../artifacts/ConvertSequencingArtifactToOxoG.java | 47 +-
.../artifacts/SequencingArtifactMetrics.java | 0
.../java/picard/analysis/artifacts/Transition.java | 0
.../analysis/directed/CalculateHsMetrics.java | 0
.../picard/analysis/directed/CollectHsMetrics.java | 46 +-
.../analysis/directed/CollectTargetedMetrics.java | 8 +-
.../directed/CollectTargetedPcrMetrics.java | 47 +-
.../analysis/directed/HsMetricCollector.java | 0
.../java/picard/analysis/directed/HsMetrics.java | 63 +-
.../directed/InsertSizeMetricsCollector.java | 8 +-
.../analysis/directed/RnaSeqMetricsCollector.java | 0
.../analysis/directed/TargetMetricsCollector.java | 121 ++--
.../analysis/directed/TargetedPcrMetrics.java | 156 +++++
.../directed/TargetedPcrMetricsCollector.java | 0
.../CollectIndependentReplicateMetrics.java | 529 ++++++++++++++
.../replicates/IndependentReplicateMetric.java | 222 ++++++
.../analysis/replicates/MergeableMetricBase.java | 189 +++++
.../picard/annotation/AnnotationException.java | 0
src/{ => main}/java/picard/annotation/Gene.java | 0
.../picard/annotation/GeneAnnotationReader.java | 0
.../java/picard/annotation/LocusFunction.java | 0
.../java/picard/annotation/RefFlatReader.java | 0
.../java/picard/cmdline/ClassFinder.java | 0
.../java/picard/cmdline/CommandLineDefaults.java | 4 +-
.../picard/cmdline/CommandLineParseException.java | 0
.../java/picard/cmdline/CommandLineParser.java | 17 +-
.../CommandLineParserDefinitionException.java | 0
.../java/picard/cmdline/CommandLineProgram.java | 3 +-
.../picard/cmdline/CommandLineProgramGroup.java | 0
.../cmdline/CommandLineProgramProperties.java | 0
.../picard/cmdline/CreateHtmlDocForProgram.java | 0
.../cmdline/CreateHtmlDocForStandardOptions.java | 0
.../java/picard/cmdline/NestedOptions.java | 0
src/{ => main}/java/picard/cmdline/Option.java | 0
.../java/picard/cmdline/PicardCommandLine.java | 0
.../java/picard/cmdline/PositionalArguments.java | 0
.../picard/cmdline/StandardOptionDefinitions.java | 1 +
.../java/picard/cmdline/programgroups/Alpha.java | 0
.../java/picard/cmdline/programgroups/Fasta.java | 0
.../picard/cmdline/programgroups/Illumina.java | 0
.../picard/cmdline/programgroups/Intervals.java | 0
.../java/picard/cmdline/programgroups/Metrics.java | 0
.../java/picard/cmdline/programgroups/None.java | 0
.../picard/cmdline/programgroups/SamOrBam.java | 0
.../java/picard/cmdline/programgroups/Testing.java | 0
.../picard/cmdline/programgroups/VcfOrBcf.java | 0
src/{ => main}/java/picard/fastq/BamToBfq.java | 0
.../java/picard/fastq/BamToBfqWriter.java | 0
.../java/picard/fastq/Casava18ReadNameEncoder.java | 25 +-
.../java/picard/fastq/IlluminaReadNameEncoder.java | 0
.../java/picard/fastq/ReadNameEncoder.java | 0
.../picard/filter/CountingDuplicateFilter.java | 0
.../java/picard/filter/CountingFilter.java | 0
.../java/picard/filter/CountingMapQFilter.java | 0
.../java/picard/filter/CountingPairedFilter.java | 0
.../java/picard/fingerprint/CheckFingerprint.java | 0
.../CrosscheckReadGroupFingerprints.java | 0
.../java/picard/fingerprint/DiploidGenotype.java | 0
.../java/picard/fingerprint/DiploidHaplotype.java | 0
.../java/picard/fingerprint/Fingerprint.java | 0
.../picard/fingerprint/FingerprintChecker.java | 67 +-
.../picard/fingerprint/FingerprintResults.java | 0
.../java/picard/fingerprint/GenotypeReader.java | 0
.../java/picard/fingerprint/HaplotypeBlock.java | 0
.../java/picard/fingerprint/HaplotypeMap.java | 0
.../picard/fingerprint/HaplotypeProbabilities.java | 0
...otypeProbabilitiesFromContaminatorSequence.java | 0
.../HaplotypeProbabilitiesFromGenotype.java | 28 +-
...lotypeProbabilitiesFromGenotypeLikelihoods.java | 0
.../HaplotypeProbabilitiesFromSequence.java | 0
.../HaplotypeProbabilitiesUsingLogLikelihoods.java | 0
.../HaplotypeProbabilityOfNormalGivenTumor.java | 19 +-
.../java/picard/fingerprint/LocusResult.java | 0
.../java/picard/fingerprint/MatchResults.java | 0
src/{ => main}/java/picard/fingerprint/Snp.java | 0
.../picard/illumina/CheckIlluminaDirectory.java | 38 +-
.../picard/illumina/ClusterDataToSamConverter.java | 93 ++-
.../CollectIlluminaBasecallingMetrics.java | 57 +-
.../illumina/CollectIlluminaLaneMetrics.java | 24 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 62 +-
.../illumina/IlluminaBasecallingMetrics.java | 0
.../illumina/IlluminaBasecallsConverter.java | 6 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 60 +-
.../picard/illumina/IlluminaBasecallsToSam.java | 67 +-
.../java/picard/illumina/IlluminaLaneMetrics.java | 0
.../picard/illumina/IlluminaPhasingMetrics.java | 6 +-
.../illumina/LanePhasingMetricsCollector.java | 0
.../java/picard/illumina/MarkIlluminaAdapters.java | 21 +-
.../java/picard/illumina/parser/BarcodeParser.java | 0
.../java/picard/illumina/parser/BclData.java | 0
.../java/picard/illumina/parser/BclParser.java | 0
.../java/picard/illumina/parser/ClusterData.java | 0
.../parser/ClusterIntensityFileReader.java | 0
.../illumina/parser/CycleIlluminaFileMap.java | 0
.../java/picard/illumina/parser/FilterParser.java | 0
.../illumina/parser/FourChannelIntensityData.java | 0
.../java/picard/illumina/parser/IlluminaData.java | 0
.../illumina/parser/IlluminaDataProvider.java | 0
.../parser/IlluminaDataProviderFactory.java | 7 +-
.../picard/illumina/parser/IlluminaDataType.java | 0
.../picard/illumina/parser/IlluminaFileMap.java | 0
.../parser/IlluminaFileNotFoundException.java | 0
.../picard/illumina/parser/IlluminaFileUtil.java | 10 +-
.../illumina/parser/IlluminaMetricsCode.java | 0
.../picard/illumina/parser/IlluminaParser.java | 0
.../illumina/parser/IlluminaTextIterator.java | 0
.../picard/illumina/parser/IntensityChannel.java | 0
.../illumina/parser/MultiTileBclFileUtil.java | 0
.../picard/illumina/parser/MultiTileBclParser.java | 8 +-
.../picard/illumina/parser/MultiTileFileUtil.java | 0
.../illumina/parser/MultiTileFilterParser.java | 0
.../illumina/parser/MultiTileLocsParser.java | 0
.../picard/illumina/parser/MultiTileParser.java | 0
.../java/picard/illumina/parser/OutputMapping.java | 0
.../illumina/parser/ParameterizedFileUtil.java | 0
.../picard/illumina/parser/PerTileCycleParser.java | 16 +-
.../picard/illumina/parser/PerTileFileUtil.java | 0
.../java/picard/illumina/parser/PerTileParser.java | 0
.../illumina/parser/PerTilePerCycleFileUtil.java | 0
.../java/picard/illumina/parser/PosParser.java | 0
.../java/picard/illumina/parser/Range.java | 0
.../java/picard/illumina/parser/ReadData.java | 0
.../picard/illumina/parser/ReadDescriptor.java | 0
.../java/picard/illumina/parser/ReadStructure.java | 0
.../java/picard/illumina/parser/ReadType.java | 0
.../java/picard/illumina/parser/Tile.java | 5 +-
.../java/picard/illumina/parser/TileIndex.java | 0
.../picard/illumina/parser/TileMetricsUtil.java | 0
.../picard/illumina/parser/TilePhasingValue.java | 0
.../picard/illumina/parser/TileTemplateRead.java | 0
.../illumina/parser/fakers/BarcodeFileFaker.java | 0
.../illumina/parser/fakers/BciFileFaker.java | 0
.../illumina/parser/fakers/BclFileFaker.java | 0
.../illumina/parser/fakers/ClocsFileFaker.java | 0
.../picard/illumina/parser/fakers/FileFaker.java | 0
.../illumina/parser/fakers/FilterFileFaker.java | 0
.../illumina/parser/fakers/LocsFileFaker.java | 0
.../parser/fakers/MultiTileBclFileFaker.java | 0
.../parser/fakers/MultiTileLocsFileFaker.java | 0
.../illumina/parser/fakers/PosFileFaker.java | 0
.../AbstractIlluminaPositionFileReader.java | 0
.../illumina/parser/readers/BarcodeFileReader.java | 0
.../illumina/parser/readers/BclIndexReader.java | 0
.../readers/BclQualityEvaluationStrategy.java | 2 +-
.../picard/illumina/parser/readers/BclReader.java | 0
.../illumina/parser/readers/ClocsFileReader.java | 0
.../illumina/parser/readers/FilterFileReader.java | 0
.../illumina/parser/readers/LocsFileReader.java | 0
.../parser/readers/MMapBackedIteratorFactory.java | 0
.../illumina/parser/readers/PosFileReader.java | 0
.../parser/readers/TileMetricsOutReader.java | 0
.../quality/CollectHiSeqXPfFailMetrics.java | 78 ++-
.../java/picard/metrics/GcBiasMetrics.java | 0
.../java/picard/metrics/MultiLevelCollector.java | 0
.../java/picard/metrics/MultilevelMetrics.java | 0
.../picard/metrics/PerUnitMetricCollector.java | 0
.../java/picard/metrics/SAMRecordAndReference.java | 0
.../SAMRecordAndReferenceMultiLevelCollector.java | 0
.../metrics/SAMRecordMultiLevelCollector.java | 0
src/{ => main}/java/picard/pedigree/PedFile.java | 2 +-
src/{ => main}/java/picard/pedigree/Sex.java | 0
.../java/picard/reference/ExtractSequences.java | 0
.../java/picard/reference/NonNFastaSize.java | 0
.../java/picard/reference/NormalizeFasta.java | 0
.../java/picard/sam/AbstractAlignmentMerger.java | 29 +-
.../java/picard/sam/AddCommentsToBam.java | 0
.../java/picard/sam/AddOrReplaceReadGroups.java | 0
src/{ => main}/java/picard/sam/BamIndexStats.java | 0
.../sam/BestEndMapqPrimaryAlignmentStrategy.java | 0
.../BestMapqPrimaryAlignmentSelectionStrategy.java | 0
src/{ => main}/java/picard/sam/BuildBamIndex.java | 0
.../picard/sam/CalculateReadGroupChecksum.java | 0
.../java/picard/sam/CheckTerminatorBlock.java | 0
src/{ => main}/java/picard/sam/CleanSam.java | 0
src/{ => main}/java/picard/sam/CompareSAMs.java | 31 +-
.../java/picard/sam/CreateSequenceDictionary.java | 0
src/{ => main}/java/picard/sam/DownsampleSam.java | 0
.../java/picard/sam/DuplicationMetrics.java | 11 +-
...tFragmentPrimaryAlignmentSelectionStrategy.java | 0
src/{ => main}/java/picard/sam/FastqToSam.java | 0
src/{ => main}/java/picard/sam/FilterSamReads.java | 0
.../java/picard/sam/FixMateInformation.java | 0
src/{ => main}/java/picard/sam/GatherBamFiles.java | 0
src/{ => main}/java/picard/sam/HitsForInsert.java | 0
.../java/picard/sam/MergeBamAlignment.java | 0
src/{ => main}/java/picard/sam/MergeSamFiles.java | 0
...stDistantPrimaryAlignmentSelectionStrategy.java | 0
.../picard/sam/MultiHitAlignedReadIterator.java | 0
.../picard/sam/PositionBasedDownsampleSam.java | 0
.../sam/PrimaryAlignmentSelectionStrategy.java | 0
src/{ => main}/java/picard/sam/ReorderSam.java | 0
.../java/picard/sam/ReplaceSamHeader.java | 0
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 0
src/main/java/picard/sam/RevertSam.java | 758 +++++++++++++++++++++
.../java/picard/sam/SamAlignmentMerger.java | 3 +
.../java/picard/sam/SamFormatConverter.java | 0
src/{ => main}/java/picard/sam/SamToFastq.java | 11 +-
.../java/picard/sam/SetNmAndUqTags.java} | 68 +-
src/{ => main}/java/picard/sam/SortSam.java | 14 +-
.../java/picard/sam/SplitSamByLibrary.java | 0
.../java/picard/sam/ValidateSamFile.java | 29 +-
src/{ => main}/java/picard/sam/ViewSam.java | 0
.../markduplicates/EstimateLibraryComplexity.java | 59 +-
.../picard/sam/markduplicates/MarkDuplicates.java | 217 ++++--
.../MarkDuplicatesWithMateCigar.java | 11 +-
.../MarkDuplicatesWithMateCigarIterator.java | 14 +-
.../AbstractMarkDuplicatesCommandLineProgram.java | 48 +-
...ctOpticalDuplicateFinderCommandLineProgram.java | 0
.../DiskBasedReadEndsForMarkDuplicatesMap.java | 0
.../markduplicates/util/LibraryIdGenerator.java | 12 +-
.../picard/sam/markduplicates/util/MarkQueue.java | 0
.../MemoryBasedReadEndsForMarkDuplicatesMap.java | 0
.../util/OpticalDuplicateFinder.java | 58 +-
.../util/PhysicalLocationForMateCigar.java | 0
.../util/PhysicalLocationForMateCigarSet.java | 0
.../picard/sam/markduplicates/util/ReadEnds.java | 0
.../util/ReadEndsForMarkDuplicates.java | 7 +-
.../util/ReadEndsForMarkDuplicatesCodec.java | 2 +-
.../util/ReadEndsForMarkDuplicatesMap.java | 0
.../ReadEndsForMarkDuplicatesWithBarcodes.java | 12 +
...ReadEndsForMarkDuplicatesWithBarcodesCodec.java | 0
.../markduplicates/util/ReadEndsForMateCigar.java | 0
...amRecordWithOrdinalAndSetDuplicateReadFlag.java | 0
.../java/picard/sam/util/PhysicalLocation.java | 0
.../java/picard/sam/util/PhysicalLocationInt.java | 0
.../picard/sam/util/PhysicalLocationShort.java | 0
.../java/picard/sam/util/ReadNameParser.java | 0
.../java/picard/util/AbstractInputParser.java | 0
src/{ => main}/java/picard/util/AdapterMarker.java | 0
src/{ => main}/java/picard/util/AdapterPair.java | 0
src/{ => main}/java/picard/util/AsyncIterator.java | 0
.../java/picard/util/AtomicIterator.java | 0
src/{ => main}/java/picard/util/BaitDesigner.java | 31 +-
.../java/picard/util/BasicInputParser.java | 0
.../java/picard/util/BedToIntervalList.java | 0
.../java/picard/util/CircularByteBuffer.java | 0
.../java/picard/util/ClippingUtility.java | 6 +-
.../java/picard/util/CsvInputParser.java | 0
.../java/picard/util/DbSnpBitSetUtil.java | 0
.../util/DelimitedTextFileWithHeaderIterator.java | 0
src/{ => main}/java/picard/util/FifoBuffer.java | 0
.../picard/util/FileChannelJDKBugWorkAround.java | 0
src/{ => main}/java/picard/util/IlluminaUtil.java | 0
.../java/picard/util/IntervalListScatterer.java | 0
.../java/picard/util/IntervalListToBed.java | 0
.../java/picard/util/IntervalListTools.java | 8 +-
src/{ => main}/java/picard/util/Iterators.java | 0
.../java/picard/util/LiftOverIntervalList.java | 0
src/{ => main}/java/picard/util/MathUtil.java | 0
src/{ => main}/java/picard/util/MetricsDoclet.java | 39 +-
.../util/QuerySortedReadPairIteratorUtil.java | 0
src/{ => main}/java/picard/util/RExecutor.java | 0
.../java/picard/util/ScatterIntervalsByNs.java | 45 +-
.../java/picard/util/TabbedInputParser.java | 0
.../util/TabbedTextFileWithHeaderParser.java | 9 +
.../java/picard/util/UnsignedTypeUtil.java | 0
src/{ => main}/java/picard/util/VariantType.java | 0
.../vcf/ByIntervalListVariantContextIterator.java | 0
.../java/picard/vcf/CallingMetricAccumulator.java | 0
.../picard/vcf/CollectVariantCallingMetrics.java | 4 +-
src/{ => main}/java/picard/vcf/GA4GHScheme.java | 0
.../picard/vcf/GA4GHSchemeWithMissingAsHomRef.java | 0
src/{ => main}/java/picard/vcf/GatherVcfs.java | 10 +-
.../java/picard/vcf/GenotypeConcordance.java | 238 +++----
.../vcf/GenotypeConcordanceContingencyMetrics.java | 2 +-
.../java/picard/vcf/GenotypeConcordanceCounts.java | 5 +-
.../vcf/GenotypeConcordanceDetailMetrics.java | 0
.../java/picard/vcf/GenotypeConcordanceScheme.java | 0
.../vcf/GenotypeConcordanceSchemeFactory.java | 0
.../picard/vcf/GenotypeConcordanceStateCodes.java | 0
.../java/picard/vcf/GenotypeConcordanceStates.java | 6 +-
.../vcf/GenotypeConcordanceSummaryMetrics.java | 2 +-
.../java/picard/vcf/GvcfMetricAccumulator.java | 0
src/{ => main}/java/picard/vcf/LiftoverVcf.java | 48 +-
.../java/picard/vcf/MakeSitesOnlyVcf.java | 0
src/{ => main}/java/picard/vcf/MergeVcfs.java | 3 +-
.../vcf/PairedVariantSubContextIterator.java | 119 ++++
.../java/picard/vcf/RenameSampleInVcf.java | 0
src/{ => main}/java/picard/vcf/SortVcf.java | 0
src/{ => main}/java/picard/vcf/SplitVcfs.java | 0
.../picard/vcf/UpdateVcfSequenceDictionary.java | 0
.../java/picard/vcf/VcfFormatConverter.java | 0
.../java/picard/vcf/VcfToIntervalList.java | 0
.../picard/vcf/filter/AlleleBalanceFilter.java | 0
.../java/picard/vcf/filter/DepthFilter.java | 0
.../vcf/filter/FilterApplyingVariantIterator.java | 0
.../java/picard/vcf/filter/FilterVcf.java | 0
.../java/picard/vcf/filter/FisherStrandFilter.java | 0
.../java/picard/vcf/filter/GenotypeFilter.java | 0
.../picard/vcf/filter/GenotypeQualityFilter.java | 0
.../java/picard/vcf/filter/QdFilter.java | 0
.../java/picard/vcf/filter/VariantFilter.java | 0
.../vcf/processor/VariantAccumulatorExecutor.java | 0
.../vcf/processor/VariantIteratorProducer.java | 0
.../picard/vcf/processor/VariantProcessor.java | 0
.../java/picard/vcf/processor/VcfFileSegment.java | 0
.../vcf/processor/VcfFileSegmentGenerator.java | 0
.../PredicateFilterDecoratingClosableIterator.java | 0
.../picard/analysis/baseDistributionByCycle.R | 0
.../resources}/picard/analysis/gcBias.R | 0
.../picard/analysis/insertSizeHistogram.R | 0
.../picard/analysis/meanQualityByCycle.R | 0
.../picard/analysis/qualityScoreDistribution.R | 0
.../resources}/picard/analysis/rnaSeqCoverage.R | 0
.../resources}/picard/analysis/rrbsQc.R | 0
src/main/resources/picard/analysis/wgsHistogram.R | 121 ++++
.../resources}/picard/docker_helper.sh | 0
src/main/resources/release_picard.sh | 290 ++++++++
src/scripts/release_picard.sh | 285 --------
.../CollectAlignmentSummaryMetricsTest.java | 0
.../picard/analysis/CollectGcBiasMetricsTest.java | 0
.../analysis/CollectInsertSizeMetricsTest.java | 0
.../analysis/CollectMultipleMetricsTest.java | 0
.../analysis/CollectQualityYieldMetricsTest.java | 0
.../picard/analysis/CollectRnaSeqMetricsTest.java | 0
.../CollectWgsMetricsFromQuerySortedTest.java | 2 +-
.../CollectWgsMetricsFromSampledSitesTest.java | 62 +-
.../picard/analysis/CollectWgsMetricsTest.java | 116 ++++
.../picard/analysis/MultiLevelCollectorTest.java | 0
.../analysis/TheoreticalSensitivityTest.java | 4 +-
.../CollectSequencingArtifactMetricsTest.java | 0
.../analysis/directed/CollectHsMetricsTest.java | 0
.../directed/CollectTargetedMetricsTest.java | 0
.../CollectIndependentReplicatesMetricTest.java | 222 ++++++
.../replicates/MergeableMetricBaseTest.java | 161 +++++
.../java/picard/cmdline/CommandLineParserTest.java | 25 +
.../picard/cmdline/CommandLineProgramTest.java | 0
.../java/picard/cmdline/PicardCommandLineTest.java | 0
.../picard/fingerprint/FingerprintCheckerTest.java | 78 +++
.../java/picard/fingerprint/HaplotypeMapTest.java | 0
.../fingerprint/HaplotypeProbabilitiesTest.java | 0
...HaplotypeProbabilityOfNormalGivenTumorTest.java | 55 ++
.../illumina/CheckIlluminaDirectoryTest.java | 0
.../CollectIlluminaBasecallingMetricsTest.java | 0
.../illumina/ExtractIlluminaBarcodesTest.java | 0
.../illumina/IlluminaBasecallsToFastqTest.java | 0
.../IlluminaBasecallsToSamAdapterClippingTest.java | 0
.../illumina/IlluminaBasecallsToSamTest.java | 126 +++-
.../illumina/IlluminaLaneMetricsCollectorTest.java | 0
.../java/picard/illumina/ReadStructureTest.java | 0
.../java/picard/illumina/parser/BclParserTest.java | 0
.../java/picard/illumina/parser/BinTdUtil.java | 0
.../illumina/parser/CycleIlluminaFileMapTest.java | 0
.../picard/illumina/parser/FilterParserTest.java | 0
.../parser/IlluminaDataProviderFactoryTest.java | 0
.../illumina/parser/IlluminaDataProviderTest.java | 0
.../illumina/parser/IlluminaFileUtilTest.java | 0
.../picard/illumina/parser/PerTileParserTest.java | 0
.../illumina/parser/PerTilePerCycleParserTest.java | 0
.../java/picard/illumina/parser/PosParserTest.java | 0
.../illumina/parser/fakers/BclFileFakerTest.java | 0
.../AbstractIlluminaPositionFileReaderTest.java | 0
.../illumina/parser/readers/BclReaderTest.java | 0
.../parser/readers/ClocsFileReaderTest.java | 0
.../parser/readers/FilterFileReaderTest.java | 0
.../parser/readers/IlluminaFileUtilTest.java | 0
.../parser/readers/LocsFileReaderTest.java | 0
.../readers/MMapBackedIteratorFactoryTest.java | 0
.../illumina/parser/readers/PosFileReaderTest.java | 0
.../picard/metrics/CollectRrbsMetricsTest.java | 0
.../java/picard/pedigree/PedFileTest.java | 0
.../java/picard/reference/NonNFastaSizeTest.java | 0
.../java/picard/sam/AddCommentsToBamTest.java | 0
.../java/picard/sam/CleanSamTest.java | 0
.../java/picard/sam/CompareSAMsTest.java | 4 +
.../picard/sam/CreateSequenceDictionaryTest.java | 0
.../java/picard/sam/FastqToSamTest.java | 0
.../java/picard/sam/FilterSamReadsTest.java | 0
.../java/picard/sam/FixMateInformationTest.java | 0
.../java/picard/sam/GatherBamFilesTest.java | 0
.../java/picard/sam/MergeBamAlignmentTest.java | 0
.../java/picard/sam/MergeSamFilesTest.java | 0
.../picard/sam/PositionBasedDownsampleSamTest.java | 0
src/test/java/picard/sam/RevertSamTest.java | 449 ++++++++++++
.../java/picard/sam/SamFileConverterTest.java | 0
.../java/picard/sam/SamToFastqTest.java | 0
src/test/java/picard/sam/SetNmAndUqTagsTest.java | 70 ++
.../java/picard/sam/SplitSamByLibraryTest.java | 0
.../java/picard/sam/ViewSamTest.java | 0
...stractMarkDuplicatesCommandLineProgramTest.java | 67 +-
...ractMarkDuplicatesCommandLineProgramTester.java | 28 +-
.../markduplicates/AsIsMarkDuplicatesTester.java | 68 ++
.../BySumOfBaseQAndInOriginalOrderMDTester.java} | 19 +-
.../EstimateLibraryComplexityTest.java | 24 +-
.../MarkDuplicateWithMissingBarcodeTest.java | 0
...MarkDuplicateWithMissingReadOneBarcodeTest.java | 0
...MarkDuplicateWithMissingReadTwoBarcodeTest.java | 0
.../MarkDuplicateWithMissingSampleBarcodeTest.java | 0
.../sam/markduplicates/MarkDuplicatesTest.java | 0
.../sam/markduplicates/MarkDuplicatesTester.java | 0
.../MarkDuplicatesWithMateCigarTest.java | 0
.../MarkDuplicatesWithMateCigarTester.java | 0
.../QuerySortedMarkDuplicatesTester.java} | 9 +-
.../SimpleMarkDuplicatesWithMateCigar.java | 35 +-
.../SimpleMarkDuplicatesWithMateCigarTest.java | 0
.../SimpleMarkDuplicatesWithMateCigarTester.java | 0
.../util/OpticalDuplicateFinderTest.java | 3 -
.../java/picard/sam/testers/CleanSamTester.java | 0
.../java/picard/sam/testers/SamFileTester.java | 116 ++--
.../java/picard/sam/testers/ValidateSamTester.java | 0
.../java/picard/sam/util/ReadNameParserTests.java | 0
.../java/picard/util/BedToIntervalListTest.java | 0
.../java/picard/util/ClippingUtilityTest.java | 0
.../DelimitedTextFileWithHeaderIteratorTest.java | 0
.../java/picard/util/FifoBufferTest.java | 0
.../util/FileChannelJDKBugWorkAroundTest.java | 0
.../java/picard/util/IlluminaUtilTest.java | 0
.../picard/util/IntervalListScattererTest.java | 0
.../java/picard/util/IntervalListToBedTest.java | 0
.../java/picard/util/MathUtilTest.java | 0
.../java/picard/util/MergingIteratorTest.java | 0
.../util/QuerySortedReadPairIteratorUtilTest.java | 0
.../java/picard/util/RExecutorTest.java | 0
.../java/picard/util/ScatterIntervalsByNsTest.java | 2 -
.../util/TabbedTextFileWithHeaderParserTest.java | 0
src/{ => test}/java/picard/util/TestNGUtil.java | 0
.../java/picard/util/TextFileParsersTest.java | 0
.../java/picard/util/UnsignedTypeUtilTest.java | 0
.../picard/vcf/AbstractVcfMergingClpTester.java | 0
.../picard/vcf/CallingMetricAccumulatorTest.java | 0
.../vcf/CollectVariantCallingMetricsTest.java | 0
.../vcf/GenotypeConcordanceGA4GHSchemeTest.java | 0
...otypeConcordanceGA4GHSchemeWithMissingTest.java | 0
.../java/picard/vcf/GenotypeConcordanceTest.java | 6 +-
.../java/picard/vcf/LiftoverVcfTest.java | 45 +-
.../java/picard/vcf/MergeVcfsTest.java | 0
.../java/picard/vcf/SortVcfsTest.java | 0
.../java/picard/vcf/SplitVcfsTest.java | 0
.../vcf/UpdateVcfSequenceDictionaryTest.java | 0
.../picard/vcf/VariantContextComparatorTest.java | 0
.../java/picard/vcf/VcfFormatConverterTest.java | 0
.../java/picard/vcf/filter/TestFilterVcf.java | 0
.../vcf/processor/AccumulatorExecutorTest.java | 0
.../picard/vcf/processor/ByWholeContigTest.java | 0
.../java/picard/vcf/processor/ThreadsafeTest.java | 0
.../vcf/processor/VcfFileSegmentGeneratorTest.java | 0
.../vcf/processor/WidthLimitingDecoratorTest.java | 0
src/{tests/scripts => test/resources}/failing.R | 0
src/{tests/scripts => test/resources}/passing.R | 0
src/{tests => test}/resources/testng.xml | 0
.../picard/fingerprint/FingerprintCheckerTest.java | 29 -
...HaplotypeProbabilityOfNormalGivenTumorTest.java | 56 --
src/tests/java/picard/sam/RevertSamTest.java | 180 -----
...nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam | 182 +++++
.../nonBarcodedWithTagPerMolecularIndex4M4M.sam | 182 +++++
testdata/picard/independent_replicates/aTriple.sam | 22 +
.../independent_replicates/aTripleWithUMIs.sam | 22 +
testdata/picard/independent_replicates/hets.vcf | 14 +
.../picard/independent_replicates/hets_pos20.vcf | 11 +
.../independent_replicates/hets_pos21_HOMREF_G.vcf | 11 +
.../hets_pos22_IncorrectAlleles.vcf | 12 +
.../independent_replicates/multipleContigs.sam | 42 ++
.../independent_replicates/multipleContigs.vcf | 15 +
.../independent_replicates/twoSamplesHet.vcf | 12 +
.../picard/independent_replicates/twopairs.sam | 21 +
.../independent_replicates/twopairsWithBadUMIs.sam | 18 +
.../independent_replicates/twopairsWithUMIs.sam | 18 +
.../twopairsWithUMIsMultipleOrientations.sam | 30 +
.../CompareSAMs/genomic_sorted_same_position.sam | 5 +
.../picard/sam/CompareSAMs/unmapped_second.sam | 2 +-
.../EstimateLibraryComplexity/dupes_with_sos.sam | 20 +
.../sameUnclipped5primeEndCoordinateSortedv1.sam | 28 +
.../sameUnclipped5primeEndCoordinateSortedv2.sam | 28 +
.../sameUnclipped5primeEndCoordinateSortedv3.sam | 28 +
.../sameUnclipped5primeEndCoordinateSortedv4.sam | 28 +
.../MarkDuplicates/sameUnclipped5primeEndv1.sam | 28 +
.../MarkDuplicates/sameUnclipped5primeEndv2.sam | 28 +
testdata/picard/sam/largeIntervals.interval_list | 10 +
.../sam/revert_sam_bad_header_output_map.txt | 3 +
.../sam/revert_sam_positive_test_output_map.txt | 4 +
....sam => revert_sam_sample_library_override.sam} | 0
testdata/picard/sam/revert_sam_single_end.sam | 5 +
.../picard/sam/revert_sam_valid_output_map.txt | 3 +
.../sam/summary_alignment_stats_test_chimeras.sam | 24 +-
testdata/picard/vcf/vcfFormatTest.bad_dict.vcf | 2 +-
532 files changed, 7561 insertions(+), 3528 deletions(-)
delete mode 100644 Picard-public.fbp
delete mode 100644 Picard-public.iml
delete mode 100644 Picard-public.ipr
create mode 100644 build.gradle
delete mode 100644 build.sbt
mode change 100755 => 100644 build.xml
create mode 100644 gradle/wrapper/gradle-wrapper.properties
create mode 100755 gradlew
delete mode 100644 src/java/picard/analysis/directed/TargetedPcrMetrics.java
delete mode 100644 src/java/picard/sam/RevertSam.java
rename src/{ => main}/java/picard/PicardException.java (100%)
rename src/{ => main}/java/picard/Test.java (100%)
rename src/{ => main}/java/picard/analysis/AdapterUtility.java (97%)
rename src/{ => main}/java/picard/analysis/AlignmentSummaryMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/AlignmentSummaryMetricsCollector.java (95%)
rename src/{ => main}/java/picard/analysis/BaseDistributionByCycleMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/ChimeraUtil.java (100%)
rename src/{ => main}/java/picard/analysis/CollectAlignmentSummaryMetrics.java (84%)
rename src/{ => main}/java/picard/analysis/CollectBaseDistributionByCycle.java (95%)
rename src/{ => main}/java/picard/analysis/CollectGcBiasMetrics.java (95%)
rename src/{ => main}/java/picard/analysis/CollectInsertSizeMetrics.java (93%)
rename src/{ => main}/java/picard/analysis/CollectJumpingLibraryMetrics.java (80%)
rename src/{ => main}/java/picard/analysis/CollectMultipleMetrics.java (89%)
rename src/{ => main}/java/picard/analysis/CollectOxoGMetrics.java (98%)
rename src/{ => main}/java/picard/analysis/CollectQualityYieldMetrics.java (98%)
rename src/{ => main}/java/picard/analysis/CollectRawWgsMetrics.java (89%)
rename src/{ => main}/java/picard/analysis/CollectRnaSeqMetrics.java (68%)
rename src/{ => main}/java/picard/analysis/CollectRrbsMetrics.java (78%)
rename src/{ => main}/java/picard/analysis/CollectWgsMetrics.java (53%)
rename src/{ => main}/java/picard/analysis/CollectWgsMetricsFromQuerySorted.java (99%)
rename src/{ => main}/java/picard/analysis/CollectWgsMetricsFromSampledSites.java (91%)
create mode 100644 src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
rename src/{ => main}/java/picard/analysis/CompareMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/FingerprintingDetailMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/FingerprintingSummaryMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/GcBiasDetailMetrics.java (96%)
rename src/{ => main}/java/picard/analysis/GcBiasMetricsCollector.java (100%)
rename src/{ => main}/java/picard/analysis/GcBiasSummaryMetrics.java (83%)
rename src/{ => main}/java/picard/analysis/GcBiasUtils.java (100%)
rename src/{ => main}/java/picard/analysis/InsertSizeMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/JumpingLibraryMetrics.java (85%)
rename src/{ => main}/java/picard/analysis/MeanQualityByCycle.java (97%)
rename src/{ => main}/java/picard/analysis/MetricAccumulationLevel.java (100%)
rename src/{ => main}/java/picard/analysis/QualityScoreDistribution.java (92%)
rename src/{ => main}/java/picard/analysis/RnaSeqMetrics.java (53%)
rename src/{ => main}/java/picard/analysis/RrbsCpgDetailMetrics.java (96%)
rename src/{ => main}/java/picard/analysis/RrbsMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/RrbsMetricsCollector.java (100%)
rename src/{ => main}/java/picard/analysis/RrbsSummaryMetrics.java (95%)
rename src/{ => main}/java/picard/analysis/SinglePassSamProgram.java (100%)
rename src/{ => main}/java/picard/analysis/TheoreticalSensitivity.java (80%)
rename src/{ => main}/java/picard/analysis/artifacts/ArtifactCounter.java (99%)
rename src/{ => main}/java/picard/analysis/artifacts/CollectSequencingArtifactMetrics.java (82%)
rename src/{ => main}/java/picard/analysis/artifacts/ContextAccumulator.java (100%)
rename src/{ => main}/java/picard/analysis/artifacts/ConvertSequencingArtifactToOxoG.java (81%)
rename src/{ => main}/java/picard/analysis/artifacts/SequencingArtifactMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/artifacts/Transition.java (100%)
rename src/{ => main}/java/picard/analysis/directed/CalculateHsMetrics.java (100%)
rename src/{ => main}/java/picard/analysis/directed/CollectHsMetrics.java (64%)
rename src/{ => main}/java/picard/analysis/directed/CollectTargetedMetrics.java (96%)
rename src/{ => main}/java/picard/analysis/directed/CollectTargetedPcrMetrics.java (61%)
rename src/{ => main}/java/picard/analysis/directed/HsMetricCollector.java (100%)
rename src/{ => main}/java/picard/analysis/directed/HsMetrics.java (76%)
rename src/{ => main}/java/picard/analysis/directed/InsertSizeMetricsCollector.java (97%)
rename src/{ => main}/java/picard/analysis/directed/RnaSeqMetricsCollector.java (100%)
rename src/{ => main}/java/picard/analysis/directed/TargetMetricsCollector.java (92%)
create mode 100644 src/main/java/picard/analysis/directed/TargetedPcrMetrics.java
rename src/{ => main}/java/picard/analysis/directed/TargetedPcrMetricsCollector.java (100%)
create mode 100644 src/main/java/picard/analysis/replicates/CollectIndependentReplicateMetrics.java
create mode 100644 src/main/java/picard/analysis/replicates/IndependentReplicateMetric.java
create mode 100644 src/main/java/picard/analysis/replicates/MergeableMetricBase.java
rename src/{ => main}/java/picard/annotation/AnnotationException.java (100%)
rename src/{ => main}/java/picard/annotation/Gene.java (100%)
rename src/{ => main}/java/picard/annotation/GeneAnnotationReader.java (100%)
rename src/{ => main}/java/picard/annotation/LocusFunction.java (100%)
rename src/{ => main}/java/picard/annotation/RefFlatReader.java (100%)
rename src/{ => main}/java/picard/cmdline/ClassFinder.java (100%)
rename src/{ => main}/java/picard/cmdline/CommandLineDefaults.java (91%)
rename src/{ => main}/java/picard/cmdline/CommandLineParseException.java (100%)
rename src/{ => main}/java/picard/cmdline/CommandLineParser.java (99%)
rename src/{ => main}/java/picard/cmdline/CommandLineParserDefinitionException.java (100%)
rename src/{ => main}/java/picard/cmdline/CommandLineProgram.java (99%)
rename src/{ => main}/java/picard/cmdline/CommandLineProgramGroup.java (100%)
rename src/{ => main}/java/picard/cmdline/CommandLineProgramProperties.java (100%)
rename src/{ => main}/java/picard/cmdline/CreateHtmlDocForProgram.java (100%)
rename src/{ => main}/java/picard/cmdline/CreateHtmlDocForStandardOptions.java (100%)
rename src/{ => main}/java/picard/cmdline/NestedOptions.java (100%)
rename src/{ => main}/java/picard/cmdline/Option.java (100%)
rename src/{ => main}/java/picard/cmdline/PicardCommandLine.java (100%)
rename src/{ => main}/java/picard/cmdline/PositionalArguments.java (100%)
rename src/{ => main}/java/picard/cmdline/StandardOptionDefinitions.java (97%)
rename src/{ => main}/java/picard/cmdline/programgroups/Alpha.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/Fasta.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/Illumina.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/Intervals.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/Metrics.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/None.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/SamOrBam.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/Testing.java (100%)
rename src/{ => main}/java/picard/cmdline/programgroups/VcfOrBcf.java (100%)
rename src/{ => main}/java/picard/fastq/BamToBfq.java (100%)
rename src/{ => main}/java/picard/fastq/BamToBfqWriter.java (100%)
rename src/{ => main}/java/picard/fastq/Casava18ReadNameEncoder.java (59%)
rename src/{ => main}/java/picard/fastq/IlluminaReadNameEncoder.java (100%)
rename src/{ => main}/java/picard/fastq/ReadNameEncoder.java (100%)
rename src/{ => main}/java/picard/filter/CountingDuplicateFilter.java (100%)
rename src/{ => main}/java/picard/filter/CountingFilter.java (100%)
rename src/{ => main}/java/picard/filter/CountingMapQFilter.java (100%)
rename src/{ => main}/java/picard/filter/CountingPairedFilter.java (100%)
rename src/{ => main}/java/picard/fingerprint/CheckFingerprint.java (100%)
rename src/{ => main}/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java (100%)
rename src/{ => main}/java/picard/fingerprint/DiploidGenotype.java (100%)
rename src/{ => main}/java/picard/fingerprint/DiploidHaplotype.java (100%)
rename src/{ => main}/java/picard/fingerprint/Fingerprint.java (100%)
rename src/{ => main}/java/picard/fingerprint/FingerprintChecker.java (93%)
rename src/{ => main}/java/picard/fingerprint/FingerprintResults.java (100%)
rename src/{ => main}/java/picard/fingerprint/GenotypeReader.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeBlock.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeMap.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilities.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilitiesFromContaminatorSequence.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilitiesFromGenotype.java (75%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilitiesFromGenotypeLikelihoods.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilitiesFromSequence.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilitiesUsingLogLikelihoods.java (100%)
rename src/{ => main}/java/picard/fingerprint/HaplotypeProbabilityOfNormalGivenTumor.java (83%)
rename src/{ => main}/java/picard/fingerprint/LocusResult.java (100%)
rename src/{ => main}/java/picard/fingerprint/MatchResults.java (100%)
rename src/{ => main}/java/picard/fingerprint/Snp.java (100%)
rename src/{ => main}/java/picard/illumina/CheckIlluminaDirectory.java (84%)
rename src/{ => main}/java/picard/illumina/ClusterDataToSamConverter.java (65%)
rename src/{ => main}/java/picard/illumina/CollectIlluminaBasecallingMetrics.java (82%)
rename src/{ => main}/java/picard/illumina/CollectIlluminaLaneMetrics.java (83%)
rename src/{ => main}/java/picard/illumina/ExtractIlluminaBarcodes.java (90%)
rename src/{ => main}/java/picard/illumina/IlluminaBasecallingMetrics.java (100%)
rename src/{ => main}/java/picard/illumina/IlluminaBasecallsConverter.java (99%)
rename src/{ => main}/java/picard/illumina/IlluminaBasecallsToFastq.java (87%)
rename src/{ => main}/java/picard/illumina/IlluminaBasecallsToSam.java (87%)
rename src/{ => main}/java/picard/illumina/IlluminaLaneMetrics.java (100%)
rename src/{ => main}/java/picard/illumina/IlluminaPhasingMetrics.java (88%)
rename src/{ => main}/java/picard/illumina/LanePhasingMetricsCollector.java (100%)
rename src/{ => main}/java/picard/illumina/MarkIlluminaAdapters.java (93%)
rename src/{ => main}/java/picard/illumina/parser/BarcodeParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/BclData.java (100%)
rename src/{ => main}/java/picard/illumina/parser/BclParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ClusterData.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ClusterIntensityFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/CycleIlluminaFileMap.java (100%)
rename src/{ => main}/java/picard/illumina/parser/FilterParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/FourChannelIntensityData.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaData.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaDataProvider.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaDataProviderFactory.java (98%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaDataType.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaFileMap.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaFileNotFoundException.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaFileUtil.java (97%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaMetricsCode.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IlluminaTextIterator.java (100%)
rename src/{ => main}/java/picard/illumina/parser/IntensityChannel.java (100%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileBclFileUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileBclParser.java (94%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileFileUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileFilterParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileLocsParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/MultiTileParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/OutputMapping.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ParameterizedFileUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/PerTileCycleParser.java (92%)
rename src/{ => main}/java/picard/illumina/parser/PerTileFileUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/PerTileParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/PerTilePerCycleFileUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/PosParser.java (100%)
rename src/{ => main}/java/picard/illumina/parser/Range.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ReadData.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ReadDescriptor.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ReadStructure.java (100%)
rename src/{ => main}/java/picard/illumina/parser/ReadType.java (100%)
rename src/{ => main}/java/picard/illumina/parser/Tile.java (94%)
rename src/{ => main}/java/picard/illumina/parser/TileIndex.java (100%)
rename src/{ => main}/java/picard/illumina/parser/TileMetricsUtil.java (100%)
rename src/{ => main}/java/picard/illumina/parser/TilePhasingValue.java (100%)
rename src/{ => main}/java/picard/illumina/parser/TileTemplateRead.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/BarcodeFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/BciFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/BclFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/ClocsFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/FileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/FilterFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/LocsFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/MultiTileBclFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/MultiTileLocsFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/fakers/PosFileFaker.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/BarcodeFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/BclIndexReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java (98%)
rename src/{ => main}/java/picard/illumina/parser/readers/BclReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/ClocsFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/FilterFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/LocsFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/MMapBackedIteratorFactory.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/PosFileReader.java (100%)
rename src/{ => main}/java/picard/illumina/parser/readers/TileMetricsOutReader.java (100%)
rename src/{ => main}/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java (82%)
rename src/{ => main}/java/picard/metrics/GcBiasMetrics.java (100%)
rename src/{ => main}/java/picard/metrics/MultiLevelCollector.java (100%)
rename src/{ => main}/java/picard/metrics/MultilevelMetrics.java (100%)
rename src/{ => main}/java/picard/metrics/PerUnitMetricCollector.java (100%)
rename src/{ => main}/java/picard/metrics/SAMRecordAndReference.java (100%)
rename src/{ => main}/java/picard/metrics/SAMRecordAndReferenceMultiLevelCollector.java (100%)
rename src/{ => main}/java/picard/metrics/SAMRecordMultiLevelCollector.java (100%)
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copy src/{java/picard/sam/SortSam.java => main/java/picard/sam/SetNmAndUqTags.java} (51%)
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rename src/{tests => test}/java/picard/sam/AddCommentsToBamTest.java (100%)
rename src/{tests => test}/java/picard/sam/CleanSamTest.java (100%)
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rename src/{tests => test}/java/picard/sam/PositionBasedDownsampleSamTest.java (100%)
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create mode 100644 src/test/java/picard/sam/markduplicates/AsIsMarkDuplicatesTester.java
copy src/{tests/java/picard/sam/markduplicates/SimpleMarkDuplicatesWithMateCigarTester.java => test/java/picard/sam/markduplicates/BySumOfBaseQAndInOriginalOrderMDTester.java} (70%)
rename src/{tests => test}/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java (84%)
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delete mode 100644 src/tests/java/picard/fingerprint/FingerprintCheckerTest.java
delete mode 100644 src/tests/java/picard/fingerprint/HaplotypeProbabilityOfNormalGivenTumorTest.java
delete mode 100755 src/tests/java/picard/sam/RevertSamTest.java
create mode 100644 testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithTagPerMolecularIndex4M4M.sam
create mode 100644 testdata/picard/independent_replicates/aTriple.sam
create mode 100644 testdata/picard/independent_replicates/aTripleWithUMIs.sam
create mode 100755 testdata/picard/independent_replicates/hets.vcf
create mode 100755 testdata/picard/independent_replicates/hets_pos20.vcf
create mode 100755 testdata/picard/independent_replicates/hets_pos21_HOMREF_G.vcf
create mode 100755 testdata/picard/independent_replicates/hets_pos22_IncorrectAlleles.vcf
create mode 100644 testdata/picard/independent_replicates/multipleContigs.sam
create mode 100755 testdata/picard/independent_replicates/multipleContigs.vcf
create mode 100755 testdata/picard/independent_replicates/twoSamplesHet.vcf
create mode 100644 testdata/picard/independent_replicates/twopairs.sam
create mode 100644 testdata/picard/independent_replicates/twopairsWithBadUMIs.sam
create mode 100644 testdata/picard/independent_replicates/twopairsWithUMIs.sam
create mode 100644 testdata/picard/independent_replicates/twopairsWithUMIsMultipleOrientations.sam
create mode 100755 testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam
create mode 100644 testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam
create mode 100644 testdata/picard/sam/largeIntervals.interval_list
create mode 100644 testdata/picard/sam/revert_sam_bad_header_output_map.txt
create mode 100644 testdata/picard/sam/revert_sam_positive_test_output_map.txt
rename testdata/picard/sam/{revert_sam_negative.sam => revert_sam_sample_library_override.sam} (100%)
create mode 100755 testdata/picard/sam/revert_sam_single_end.sam
create mode 100644 testdata/picard/sam/revert_sam_valid_output_map.txt
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