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commit a63bb64b4a515c38fc73c395b4513dca1c03e4dd Merge: 8a24eb4 9175c40 Author: Vincent Danjean <[email protected]> Date: Thu Jul 7 09:18:10 2016 +0200 Merge tag 'upstream/2.5.0-gradle+dfsg' into sid Upstream version 2.5.0-gradle+dfsg .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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
