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Project: gatk (GitHub Link)
  • gatk-master
    • jitpack.yml
    • .github
      • ISSUE_TEMPLATE.md
    • resources_for_CI
      • servicekey.json.enc
      • github_deploy_key.enc
      • README.md
    • src
      • main
        • resources
          • log4j.properties
          • log4j2.xml
          • large
            • cnn_score_variants
              • 2d_cnn_mix_train.hd5
              • 2d_cnn_mix_train.json
              • 1d_cnn_mix_train_full_bn.json
              • small_2d.hd5
              • 1d_cnn_mix_train_full_bn.hd5
              • small_2d.json
            • sv_evidence_classifier.bin
            • testResourceFile.txt
          • org
            • broadinstitute
              • hellbender
                • utils
                  • recalibration
                    • BQSR.R
                  • helpTemplates
                    • gatkDoc.css
                    • common.html
                    • generic.index.template.html
                    • generic.template.html
                  • config
                    • GATKConfig.properties
                  • wdlTemplates
                    • wdlToolTemplate.wdl.ftl
                    • wdlJSONTemplateAllArgsTest.json.ftl
                    • common.html
                    • wdlToolTemplateAllArgsTest.wdl.ftl
                    • wdlIndexTemplate.html.ftl
                    • wdlJSONTemplateAllArgs.json.ftl
                    • wdlToolTemplateAllArgs.wdl.ftl
                    • wdlJSONTemplate.json.ftl
                  • R
                    • gsalib.tar.gz
                • tools
                  • copynumber
                    • cohort_determine_ploidy_and_depth.py
                    • utils
                      • annotatedinterval
                        • annotated_region_default.config
                    • segment_gcnv_calls.py
                    • case_determine_ploidy_and_depth.py
                    • case_denoising_calling.py
                    • cohort_denoising_calling.py
                    • plotting
                      • PlotModeledSegments.R
                      • CNVPlottingLibrary.R
                      • PlotDenoisedCopyRatios.R
                  • examples
                    • copyInputFileToOutputFile.py
                  • walkers
                    • varianteval
                      • plotAlleleFrequencyQC.R
                    • vqsr
                      • training.py
                      • plot_Tranches.R
                  • spark
                    • pipelines
                      • metrics
                        • meanQualityByCycle.R
                        • baseDistributionByCycle.R
                        • qualityScoreDistribution.R
                  • funcotator
                    • simple_funcotator_seg_file.config
                    • gene_list_output.config
                    • Homo_sapiens_assembly19.dict
                • metrics
                  • insertSizeHistogram.R
        • python
          • org
            • broadinstitute
              • hellbender
                • vqsr_cnn
                  • vqsr_cnn
                    • models.py
                    • __init__.py
                    • inference.py
                    • tensor_maps.py
                    • arguments.py
                    • plots.py
                    • defines.py
                  • __init__.py
                  • _version.py
                • gcnvkernel
                  • utils
                    • cli_commons.py
                    • rls.py
                    • __init__.py
                    • math.py
                  • postprocess
                    • viterbi_segmentation.py
                    • segment_quality_utils.py
                    • __init__.py
                  • config.py
                  • models
                    • theano_hmm.py
                    • commons.py
                    • dists.py
                    • model_ploidy.py
                    • fancy_model.py
                    • __init__.py
                    • model_denoising_calling.py
                  • structs
                    • segment.py
                    • metadata.py
                    • __init__.py
                    • interval.py
                  • README.txt
                  • io
                    • io_commons.py
                    • io_adamax.py
                    • io_intervals_and_counts.py
                    • io_consts.py
                    • io_metadata.py
                    • io_denoising_calling.py
                    • __init__.py
                    • io_ploidy.py
                  • tasks
                    • task_case_denoising_calling.py
                    • task_cohort_ploidy_determination.py
                    • task_case_ploidy_determination.py
                    • __init__.py
                    • inference_task_base.py
                    • task_cohort_denoising_calling.py
                  • __init__.py
                  • _version.py
                  • inference
                    • param_tracker.py
                    • deterministic_annealing.py
                    • __init__.py
                    • fancy_optimizers.py
                    • convergence_tracker.py
                  • types.py
                  • LICENSE.txt
                  • MANIFEST.in
                  • preprocess
                    • interval_list_mask.py
                    • __init__.py
                • setup.py
                • README.md
                • setup_vqsr_cnn.py
                • gatktool
                  • toolconstants.py
                  • __init__.py
                  • _version.py
                  • tool.py
                • setup_gcnvkernel.py
        • java
          • htsjdk
            • samtools
              • SAMRecordSparkCodec.java
          • org
            • broadinstitute
              • hellbender
                • testutils
                  • TestingReadThreadingGraph.java
                • transformers
                  • MappingQualityReadTransformer.java
                  • ReadTransformer.java
                  • BaseQualityClipReadTransformer.java
                  • VariantTransformer.java
                  • NDNCigarReadTransformer.java
                  • PalindromeArtifactClipReadTransformer.java
                  • MisencodedBaseQualityReadTransformer.java
                  • DUSTReadTransformer.java
                  • StripMateNumberTransformer.java
                  • BaseQualityReadTransformer.java
                  • SimpleRepeatMaskTransformer.java
                  • AdapterTrimTransformer.java
                  • BQSRReadTransformer.java
                • utils
                  • MatrixSummaryUtils.java
                  • pileup
                    • ReadPileup.java
                    • PileupElement.java
                  • solver
                    • SynchronizedUnivariateSolver.java
                    • RobustBrentSolver.java
                    • UnivariateSolverSpecifications.java
                    • UnivariateSolverJobDescription.java
                  • Nucleotide.java
                  • activityprofile
                    • BandPassActivityProfile.java
                    • ActivityProfileStateRange.java
                    • ActivityProfileState.java
                    • ActivityProfile.java
                  • recalibration
                    • RecalUtils.java
                    • RecalibrationTables.java
                    • EventType.java
                    • covariates
                      • CovariateKeyCache.java
                      • StandardCovariateList.java
                      • ContextCovariate.java
                      • Covariate.java
                      • ReadGroupCovariate.java
                      • ReadCovariates.java
                      • CycleCovariate.java
                      • QualityScoreCovariate.java
                    • RecalibrationArgumentCollection.java
                    • RecalDatum.java
                    • QualQuantizer.java
                    • BaseRecalibrationEngine.java
                    • RecalibrationReport.java
                    • QuantizationInfo.java
                    • ReadRecalibrationInfo.java
                  • LRUCache.java
                  • NaturalLogUtils.java
                  • help
                    • HelpConstants.java
                    • GATKHelpDoclet.java
                    • GATKWDLWorkUnitHandler.java
                    • GATKWDLDoclet.java
                    • GATKGSONWorkUnit.java
                    • GATKDocWorkUnit.java
                    • GATKHelpDocWorkUnitHandler.java
                  • samples
                    • PedigreeValidationType.java
                    • SampleDB.java
                    • Affection.java
                    • MendelianViolation.java
                    • Trio.java
                    • Sex.java
                    • SampleDBBuilder.java
                    • PedReader.java
                    • Sample.java
                  • downsampling
                    • ReservoirDownsampler.java
                    • Downsampler.java
                    • PassThroughDownsampler.java
                    • PositionalDownsampler.java
                    • MutectDownsampler.java
                    • AlleleBiasedDownsamplingUtils.java
                    • FractionalDownsampler.java
                    • DownsamplingMethod.java
                    • ReadsDownsampler.java
                    • LevelingDownsampler.java
                    • DownsampleType.java
                    • ReadsDownsamplingIterator.java
                  • FisherExactTest.java
                  • HttpUtils.java
                  • haplotype
                    • HaplotypeBAMWriter.java
                    • HaplotypeBAMDestination.java
                    • EventMap.java
                    • SAMFileDestination.java
                    • Haplotype.java
                  • IntegrationUtils.java
                  • SimpleInterval.java
                  • IndexUtils.java
                  • functional
                    • IntToDoubleBiFunction.java
                    • IntBiConsumer.java
                  • iterators
                    • ShardedIntervalIterator.java
                    • ReadTransformingIterator.java
                    • ReadFilteringIterator.java
                    • ByteArrayIterator.java
                    • IntervalOverlappingIterator.java
                    • CloseAtEndIterator.java
                    • PushPullTransformer.java
                    • IntervalLocusIterator.java
                    • SAMRecordToReadIterator.java
                    • PushToPullIterator.java
                    • ReadCachingIterator.java
                    • AllLocusIterator.java
                    • SamReaderQueryingIterator.java
                  • report
                    • GATKReportColumnFormat.java
                    • GATKReportTable.java
                    • GATKReportVersion.java
                    • GATKReportColumn.java
                    • GATKReport.java
                    • GATKReportDataType.java
                  • IntervalMergingRule.java
                  • GenotypeUtils.java
                  • CompressedDataList.java
                  • MannWhitneyU.java
                  • Utils.java
                  • clipping
                    • ClippingOp.java
                    • ReadClipper.java
                    • ClippingRepresentation.java
                  • GenomeLoc.java
                  • DigammaCache.java
                  • bwa
                    • BwaMemAlignmentUtils.java
                    • BwaMemIndexCache.java
                  • variant
                    • GATKVCFIndexType.java
                    • VariantContextVariantAdapter.java
                    • GATKVCFConstants.java
                    • DbSnpVariantType.java
                    • HomoSapiensConstants.java
                    • VcfUtils.java
                    • DbSnpBitSetUtil.java
                    • MinimalVariant.java
                    • writers
                      • GVCFWriter.java
                      • GVCFBlockCombiner.java
                      • GVCFBlockCombiningIterator.java
                      • HomRefBlock.java
                      • GVCFBlock.java
                      • TLODBlock.java
                      • SomaticGVCFWriter.java
                      • SomaticGVCFBlockCombiner.java
                    • GATKVariant.java
                    • GATKVCFHeaderLines.java
                    • VariantContextGetters.java
                    • GATKVariantContextUtils.java
                  • illumina
                    • IlluminaAdapterPair.java
                    • AdapterPair.java
                  • NativeUtils.java
                  • Trilean.java
                  • QualityUtils.java
                  • GenotypeCounts.java
                  • ClassUtils.java
                  • GenomeLocParser.java
                  • mcmc
                    • Decile.java
                    • PosteriorSummaryUtils.java
                    • PosteriorSummary.java
                    • ParameterizedModel.java
                    • ParameterizedState.java
                    • DecileCollection.java
                    • Parameter.java
                    • ParameterTableColumn.java
                    • ParameterEnum.java
                    • SliceSampler.java
                    • DataCollection.java
                    • ParameterSampler.java
                    • AdaptiveMetropolisSampler.java
                    • AbstractSliceSampler.java
                    • GibbsSampler.java
                    • MinibatchSliceSampler.java
                  • Log10Cache.java
                  • tsv
                    • TableUtils.java
                    • SimpleXSVWriter.java
                    • TableColumnCollection.java
                    • TableWriter.java
                    • package-info.java
                    • TableReader.java
                    • DataLine.java
                  • UniqueIDWrapper.java
                  • BaseUtils.java
                  • IntToDoubleFunctionCache.java
                  • runtime
                    • ProcessControllerAckResult.java
                    • ProgressLogger.java
                    • StreamOutput.java
                    • InputStreamSettings.java
                    • StreamLocation.java
                    • ScriptExecutor.java
                    • CapturedStreamOutputSnapshot.java
                    • ProcessControllerBase.java
                    • ScriptExecutorException.java
                    • StreamingToolConstants.java
                    • RuntimeUtils.java
                    • ProcessOutput.java
                    • StreamingProcessController.java
                    • ProcessSettings.java
                    • OutputStreamSettings.java
                    • CapturedStreamOutput.java
                    • ProcessController.java
                    • AsynchronousStreamWriter.java
                  • Log10FactorialCache.java
                  • config
                    • SystemProperty.java
                    • ConfigFactory.java
                    • GATKConfig.java
                    • CustomBooleanConverter.java
                  • spark
                    • SparkConverter.java
                    • JoinReadsWithVariants.java
                    • SparkUtils.java
                  • SerializableFunction.java
                  • Histogram.java
                  • IndexRange.java
                  • IntervalSetRule.java
                  • codecs
                    • copynumber
                      • SimpleCountCodec.java
                    • AnnotatedIntervalCodec.java
                    • sampileup
                      • SAMPileupElement.java
                      • SAMPileupCodec.java
                      • SAMPileupFeature.java
                    • LineIteratorReader.java
                    • ProgressReportingDelegatingCodec.java
                    • table
                      • TableCodec.java
                      • TableFeature.java
                    • refseq
                      • RefSeqFeature.java
                      • RefSeqTranscript.java
                      • RefSeqCodec.java
                    • xsvLocatableTable
                      • XsvLocatableTableCodec.java
                      • XsvTableFeature.java
                    • gtf
                      • GencodeGtfStartCodonFeature.java
                      • GencodeGtfFeatureBaseData.java
                      • GencodeGtfExonFeature.java
                      • GencodeGtfGeneFeature.java
                      • AbstractGtfCodec.java
                      • GencodeGtfStopCodonFeature.java
                      • GencodeGtfSelenocysteineFeature.java
                      • EnsemblGtfCodec.java
                      • GencodeGtfTranscriptFeature.java
                      • GencodeGtfCDSFeature.java
                      • GencodeGtfCodec.java
                      • GencodeGtfUTRFeature.java
                      • GencodeGtfFeature.java
                  • locusiterator
                    • LIBSDownsamplingInfo.java
                    • AlignmentStateMachine.java
                    • SamplePartitioner.java
                    • PerSampleReadStateManager.java
                    • LocusIteratorByState.java
                    • ReadStateManager.java
                    • IntervalAlignmentContextIterator.java
                    • AlignmentContextIteratorBuilder.java
                  • pairhmm
                    • VectorLoglessPairHMM.java
                    • N2MemoryPairHMM.java
                    • LoglessPairHMM.java
                    • PairHMM.java
                    • Log10PairHMM.java
                    • PairHMMModel.java
                  • LoggingUtils.java
                  • baq
                    • BAQ.java
                  • MathUtils.java
                  • python
                    • PythonExecutorBase.java
                    • StreamingPythonScriptExecutor.java
                    • PythonScriptExecutorException.java
                    • PythonScriptExecutor.java
                  • IntervalUtils.java
                  • SequenceDictionaryUtils.java
                  • HasGenomeLocation.java
                  • fragments
                    • FragmentUtils.java
                    • FragmentCollection.java
                  • io
                    • Resource.java
                    • HardThresholdingOutputStream.java
                    • IOUtils.java
                    • DeleteRecursivelyOnExitPathHook.java
                  • collections
                    • IndexedSet.java
                    • Permutation.java
                    • AutoCloseableCollection.java
                    • NestedIntegerArray.java
                  • reference
                    • ReferenceBases.java
                    • ReferenceUtils.java
                  • genotyper
                    • AlleleList.java
                    • IndexedSampleList.java
                    • SampleList.java
                    • AlleleListPermutation.java
                    • IndexedAlleleList.java
                    • AlleleLikelihoods.java
                    • LikelihoodMatrix.java
                  • param
                    • ParamUtils.java
                  • gcs
                    • BucketUtils.java
                  • text
                    • TextFormattingUtils.java
                    • XReadLines.java
                  • NGSPlatform.java
                  • IGVUtils.java
                  • fasta
                    • CachingIndexedFastaSequenceFile.java
                  • MRUCachingSAMSequenceDictionary.java
                  • R
                    • RScriptExecutorException.java
                    • RScriptLibrary.java
                    • RScriptExecutor.java
                  • SATagBuilder.java
                  • KV.java
                  • OptimizationUtils.java
                  • svd
                    • ApacheSingularValueDecomposer.java
                    • SimpleSVD.java
                    • SparkSingularValueDecomposer.java
                    • SVD.java
                    • OjAlgoSingularValueDecomposer.java
                    • SingularValueDecomposer.java
                    • SVDFactory.java
                  • read
                    • ArtificialReadQueryIterator.java
                    • SAMFileGATKReadWriter.java
                    • markduplicates
                      • LibraryIdGenerator.java
                      • MarkDuplicatesScoringStrategy.java
                      • GATKDuplicationMetrics.java
                      • sparkrecords
                        • PairedEnds.java
                        • EmptyFragment.java
                        • Fragment.java
                        • Passthrough.java
                        • TransientFieldPhysicalLocation.java
                        • MarkDuplicatesSparkRecord.java
                        • Pair.java
                      • ReadsKey.java
                    • PrimaryAlignmentKey.java
                    • ReadsWriteFormat.java
                    • GATKReadWriter.java
                    • ArtificialReadIterator.java
                    • ReadConstants.java
                    • ArtificialReadUtils.java
                    • ReadUtils.java
                    • CigarUtils.java
                    • GATKReadToBDGAlignmentRecordConverter.java
                    • SAMRecordToGATKReadAdapter.java
                    • ReadCoordinateComparator.java
                    • GATKRead.java
                    • Fragment.java
                    • CigarBuilder.java
                    • ReadQueryNameComparator.java
                    • AlignmentUtils.java
                    • ArtificialBAMBuilder.java
                    • ClippingTail.java
                    • HeaderlessSAMRecordCoordinateComparator.java
                    • mergealignment
                      • MultiHitAlignedReadIterator.java
                      • BestEndMapqPrimaryAlignmentStrategy.java
                      • BestMapqPrimaryAlignmentSelectionStrategy.java
                      • EarliestFragmentPrimaryAlignmentSelectionStrategy.java
                      • PrimaryAlignmentSelectionStrategy.java
                      • SamAlignmentMerger.java
                      • HitsForInsert.java
                      • MostDistantPrimaryAlignmentSelectionStrategy.java
                      • AbstractAlignmentMerger.java
                    • BDGAlignmentRecordToGATKReadAdapter.java
                  • nio
                    • NioFileCopierWithProgressMeter.java
                    • PathLineIterator.java
                    • NioFileCopierWithProgressMeterResults.java
                  • UnsignedTypeUtil.java
                  • logging
                    • BunnyLog.java
                    • OneShotLogger.java
                  • SequencerFlowClass.java
                  • smithwaterman
                    • SWNativeAlignerWrapper.java
                    • SmithWatermanAlignment.java
                    • SmithWatermanIntelAligner.java
                    • SmithWatermanAligner.java
                    • SmithWatermanJavaAligner.java
                  • Dirichlet.java
                  • GenomeLocSortedSet.java
                • cmdline
                  • CommandLineArgumentValidator.java
                  • PicardCommandLineProgramExecutor.java
                  • StandardArgumentDefinitions.java
                  • ExomeStandardArgumentDefinitions.java
                  • CommandLineProgram.java
                  • argumentcollections
                    • OptionalVariantInputArgumentCollection.java
                    • RequiredIntervalArgumentCollection.java
                    • OptionalIntervalArgumentCollection.java
                    • MultiVariantInputArgumentCollection.java
                    • MetricAccumulationLevelArgumentCollection.java
                    • IntervalArgumentCollection.java
                    • OptionalReadInputArgumentCollection.java
                    • OptionalFeatureInputArgumentCollection.java
                    • RequiredVariantInputArgumentCollection.java
                    • OpticalDuplicatesArgumentCollection.java
                    • MarkDuplicatesSparkArgumentCollection.java
                    • RequiredReferenceInputArgumentCollection.java
                    • RequiredFeatureInputArgumentCollection.java
                    • OptionalReferenceInputArgumentCollection.java
                    • ReferenceInputArgumentCollection.java
                    • RequiredReadInputArgumentCollection.java
                    • ReadInputArgumentCollection.java
                    • DbsnpArgumentCollection.java
                    • SequenceDictionaryValidationArgumentCollection.java
                  • TestProgramGroup.java
                  • ReadFilterArgumentDefinitions.java
                  • PicardCommandLineProgram.java
                  • DeprecatedToolsRegistry.java
                  • GATKPlugin
                    • GATKReadFilterPluginDescriptor.java
                    • GATKAnnotationPluginDescriptor.java
                    • GATKReadFilterArgumentCollection.java
                    • DefaultGATKReadFilterArgumentCollection.java
                    • DefaultGATKVariantAnnotationArgumentCollection.java
                    • GATKAnnotationArgumentCollection.java
                  • programgroups
                    • StructuralVariantDiscoveryProgramGroup.java
                    • ShortVariantDiscoveryProgramGroup.java
                    • MethylationProgramGroup.java
                    • CoverageAnalysisProgramGroup.java
                    • CopyNumberProgramGroup.java
                    • ExampleProgramGroup.java
                    • MetagenomicsProgramGroup.java
                • Main.java
                • engine
                  • ReferenceMemorySource.java
                  • MultiIntervalShard.java
                  • LocusWalker.java
                  • ShardBoundaryShard.java
                  • ReadsPathDataSource.java
                  • MultiVariantWalkerGroupedOnStart.java
                  • FeatureInput.java
                  • VariantLocusWalker.java
                  • FeatureIntervalIterator.java
                  • FeatureManager.java
                  • AssemblyRegionIterator.java
                  • ReferenceDataSource.java
                  • TraversalParameters.java
                  • WalkerBase.java
                  • FeatureDataSource.java
                  • MultiVariantDataSource.java
                  • ReadsDataSource.java
                  • AssemblyRegionFromActivityProfileStateIterator.java
                  • AbstractConcordanceWalker.java
                  • ReadContextData.java
                  • MultiplePassVariantWalker.java
                  • MultiIntervalLocalReadShard.java
                  • GATKTool.java
                  • ReferenceWalker.java
                  • AssemblyRegionEvaluator.java
                  • ReferenceContext.java
                  • LocusWalkerByInterval.java
                  • ReferenceShard.java
                  • ReadsContext.java
                  • VariantShard.java
                  • FeatureWalker.java
                  • ShardBoundary.java
                  • IntervalWalker.java
                  • ReadWalker.java
                  • DuplicateSetWalker.java
                  • spark
                    • AddContextDataToReadSparkOptimized.java
                    • GATKRegistrator.java
                    • AddContextDataToReadSpark.java
                    • LocusWalkerContext.java
                    • ReadWalkerSpark.java
                    • SAMRecordToGATKReadAdapterSerializer.java
                    • AssemblyRegionArgumentCollection.java
                    • SparkContextFactory.java
                    • SparkCommandLineProgram.java
                    • IntervalWalkerSpark.java
                    • AssemblyRegionReadShardArgumentCollection.java
                    • FindAssemblyRegionsSpark.java
                    • ReadWalkerContext.java
                    • VariantWalkerSpark.java
                    • datasources
                      • ReferenceMultiSparkSource.java
                      • DirectFullByteArrayByteAccess.java
                      • ReferenceTwoBitSparkSource.java
                      • ReferenceHadoopSparkSource.java
                      • VariantsSparkSource.java
                      • ReferenceFileSparkSource.java
                      • VariantsSparkSink.java
                      • ReferenceWindowFunctions.java
                      • ReadsSparkSink.java
                      • ReferenceSparkSource.java
                      • ReadsSparkSource.java
                    • AssemblyRegionWalkerContext.java
                    • GATKSparkTool.java
                    • SparkCommandLineArgumentCollection.java
                    • LocusWalkerSpark.java
                    • IntervalWalkerContext.java
                    • SAMRecordSerializer.java
                    • NonChecksumLocalFileSystem.java
                    • RangePartitionCoalescer.java
                    • VariantWalkerContext.java
                    • SparkSharder.java
                    • AssemblyRegionWalkerSpark.java
                  • ProgressMeter.java
                  • PathURI.java
                  • VariantWalkerBase.java
                  • AssemblyRegionWalker.java
                  • filters
                    • AmbiguousBaseReadFilter.java
                    • MateDistantReadFilter.java
                    • ReadFilter.java
                    • CountingReadFilter.java
                    • VariantTypesVariantFilter.java
                    • OverclippedReadFilter.java
                    • ReadGroupBlackListReadFilter.java
                    • ReadStrandFilter.java
                    • CountingVariantFilter.java
                    • IntervalOverlapReadFilter.java
                    • FragmentLengthReadFilter.java
                    • ReadFilterLibrary.java
                    • MetricsReadFilter.java
                    • WellformedReadFilter.java
                    • PlatformReadFilter.java
                    • ReadLengthReadFilter.java
                    • VariantFilterLibrary.java
                    • SoftClippedReadFilter.java
                    • VariantIDsVariantFilter.java
                    • NotOpticalDuplicateReadFilter.java
                    • ReadGroupReadFilter.java
                    • LibraryReadFilter.java
                    • AlignmentAgreesWithHeaderReadFilter.java
                    • ReadNameReadFilter.java
                    • MappingQualityReadFilter.java
                    • SampleReadFilter.java
                    • PlatformUnitReadFilter.java
                    • VariantFilter.java
                  • MultiplePassReadWalker.java
                  • TwoPassVariantWalker.java
                  • GATKPath.java
                  • DoNotSubclass.java
                  • GATKDataSource.java
                  • ShardToMultiIntervalShardAdapter.java
                  • AlignmentContext.java
                  • VariantWalker.java
                  • AssemblyRegion.java
                  • PathSpecifier.java
                  • MultiVariantWalker.java
                  • Shard.java
                  • FeatureCache.java
                  • ReadlessAssemblyRegion.java
                  • FeatureContext.java
                  • ReferenceFileSource.java
                  • ActivityProfileStateIterator.java
                • exceptions
                  • UserException.java
                  • PicardNonZeroExitException.java
                  • GATKException.java
                • tools
                  • copynumber
                    • DenoiseReadCounts.java
                    • CollectReadCounts.java
                    • utils
                      • TagGermlineEvents.java
                      • annotatedinterval
                        • AnnotatedInterval.java
                        • AnnotatedIntervalHeader.java
                        • AnnotatedIntervalCollection.java
                        • SimpleAnnotatedIntervalWriter.java
                        • AnnotatedIntervalUtils.java
                        • AnnotatedIntervalWriter.java
                      • MergeAnnotatedRegions.java
                      • optimization
                        • PersistenceOptimizer.java
                      • germlinetagging
                        • SimpleGermlineTagger.java
                      • CombineSegmentBreakpoints.java
                      • segmentation
                        • KernelSegmenter.java
                      • MergeAnnotatedRegionsByAnnotation.java
                      • HDF5Utils.java
                    • PostprocessGermlineCNVCalls.java
                    • GermlineCNVCaller.java
                    • segmentation
                      • MultidimensionalKernelSegmenter.java
                      • CopyRatioKernelSegmenter.java
                      • AlleleFractionKernelSegmenter.java
                    • arguments
                      • CopyNumberStandardArgument.java
                      • CopyNumberArgumentValidationUtils.java
                      • GermlineCallingArgumentCollection.java
                      • GermlineContigPloidyModelArgumentCollection.java
                      • GermlineContigPloidyHybridADVIArgumentCollection.java
                      • GermlineCNVHybridADVIArgumentCollection.java
                      • GermlineDenoisingModelArgumentCollection.java
                      • HybridADVIArgumentCollection.java
                    • CollectAllelicCountsSpark.java
                    • models
                      • AlleleFractionInitializer.java
                      • CopyRatioSamplers.java
                      • FunctionCache.java
                      • CopyRatioModeller.java
                      • AlleleFractionPrior.java
                      • CopyRatioSegmentedData.java
                      • AlleleFractionModeller.java
                      • AlleleFractionState.java
                      • AlleleFractionGlobalParameters.java
                      • CopyRatioState.java
                      • AlleleFractionParameter.java
                      • MultidimensionalModeller.java
                      • CopyRatioParameter.java
                      • AlleleFractionSegmentedData.java
                      • AlleleFractionSamplers.java
                      • AlleleFractionLikelihoods.java
                    • DetermineGermlineContigPloidy.java
                    • CallCopyRatioSegments.java
                    • gcnv
                      • GermlineCNVNamingConstants.java
                      • GermlineCNVIntervalVariantComposer.java
                      • GermlineCNVVariantComposer.java
                      • GermlineCNVSegmentVariantComposer.java
                      • IntegerCopyNumberState.java
                    • CollectAllelicCounts.java
                    • caller
                      • SimpleCopyRatioCaller.java
                    • ModelSegments.java
                    • AnnotateIntervals.java
                    • denoising
                      • GCBiasCorrector.java
                      • HDF5SVDReadCountPanelOfNormals.java
                      • SVDDenoisingUtils.java
                      • SVDDenoisedCopyRatioResult.java
                      • SVDReadCountPanelOfNormals.java
                    • CreateReadCountPanelOfNormals.java
                    • PreprocessIntervals.java
                    • FilterIntervals.java
                    • plotting
                      • PlotDenoisedCopyRatios.java
                      • PlottingUtils.java
                      • PlotModeledSegments.java
                    • datacollection
                      • AllelicCountCollector.java
                    • formats
                      • CopyNumberFormatsUtils.java
                      • metadata
                        • SimpleSampleMetadata.java
                        • SimpleSampleLocatableMetadata.java
                        • SampleMetadata.java
                        • SimpleLocatableMetadata.java
                        • Metadata.java
                        • LocatableMetadata.java
                        • SampleLocatableMetadata.java
                        • MetadataUtils.java
                      • collections
                        • AbstractRecordCollection.java
                        • ParameterDecileCollection.java
                        • IntegerCopyNumberSegmentCollection.java
                        • SimpleCountCollection.java
                        • CopyNumberPosteriorDistributionCollection.java
                        • LegacySegmentCollection.java
                        • SimpleIntervalCollection.java
                        • LinearCopyRatioCollection.java
                        • AbstractSampleRecordCollection.java
                        • AnnotatedIntervalCollection.java
                        • CalledCopyRatioSegmentCollection.java
                        • AlleleFractionSegmentCollection.java
                        • AbstractLocatableCollection.java
                        • BaselineCopyNumberCollection.java
                        • HDF5SimpleCountCollection.java
                        • AllelicCountCollection.java
                        • AbstractSampleLocatableCollection.java
                        • CoveragePerContigCollection.java
                        • CalledLegacySegmentCollection.java
                        • CopyRatioCollection.java
                        • ModeledSegmentCollection.java
                        • CopyRatioSegmentCollection.java
                        • NonLocatableDoubleCollection.java
                        • MultidimensionalSegmentCollection.java
                      • records
                        • AllelicCount.java
                        • CopyRatio.java
                        • AnnotatedInterval.java
                        • LinearCopyRatio.java
                        • AlleleFractionSegment.java
                        • CopyNumberPosteriorDistribution.java
                        • LegacySegment.java
                        • CalledLegacySegment.java
                        • CoveragePerContig.java
                        • MultidimensionalSegment.java
                        • IntegerCopyNumberSegment.java
                        • SimpleCount.java
                        • annotation
                          • AnnotationKey.java
                          • AnnotationMap.java
                          • CopyNumberAnnotations.java
                        • IntervalCopyNumberGenotypingData.java
                        • CalledCopyRatioSegment.java
                        • ModeledSegment.java
                        • CopyRatioSegment.java
                  • IndexFeatureFile.java
                  • AddOriginalAlignmentTags.java
                  • PrintReadsHeader.java
                  • examples
                    • ExamplePostTraversalPythonExecutor.java
                    • ExampleFeatureWalker.java
                    • ExampleReadWalkerWithVariantsSpark.java
                    • ExampleTwoPassVariantWalker.java
                    • ExampleIntervalWalker.java
                    • ExampleLocusWalkerSpark.java
                    • ExampleReadWalkerWithReferenceSpark.java
                    • ExampleReferenceWalker.java
                    • ExampleVariantWalkerSpark.java
                    • ExampleReadWalkerWithVariants.java
                    • ExampleStreamingPythonExecutor.java
                    • ExampleLocusWalker.java
                    • ExampleAssemblyRegionWalker.java
                    • ExampleVariantWalker.java
                    • ExampleIntervalWalkerSpark.java
                    • metrics
                      • single
                        • ExampleSingleMetricsCollectorSpark.java
                        • ExampleCollectSingleMetricsSpark.java
                        • ExampleSingleMetricsArgumentCollection.java
                        • ExampleSingleMetrics.java
                      • multi
                        • ExampleMultiMetricsCollectorSpark.java
                        • ExampleMultiMetrics.java
                        • PerUnitExampleMultiMetricsCollectorArgs.java
                        • ExampleMultiMetricsArgumentCollection.java
                        • PerUnitExampleMultiMetricsCollector.java
                        • ExampleMultiMetricsCollector.java
                        • ExampleCollectMultiMetricsSpark.java
                    • ExampleAssemblyRegionWalkerSpark.java
                    • ExampleReadWalkerWithReference.java
                  • genomicsdb
                    • GenomicsDBConstants.java
                    • GenomicsDBImport.java
                    • GenomicsDBOptions.java
                    • GenomicsDBUtils.java
                    • GenomicsDBArgumentCollection.java
                  • ConvertHeaderlessHadoopBamShardToBam.java
                  • ApplyBQSRUniqueArgumentCollection.java
                  • LeftAlignIndels.java
                  • FixCallSetSampleOrdering.java
                  • walkers
                    • contamination
                      • ContaminationRecord.java
                      • ContaminationModel.java
                      • PileupSummary.java
                      • GetPileupSummaries.java
                      • ContaminationSegmenter.java
                      • MinorAlleleFractionRecord.java
                      • GatherPileupSummaries.java
                      • CalculateContamination.java
                    • mutect
                      • SomaticRefVsAnyResult.java
                      • PerAlleleCollection.java
                      • SubsettedLikelihoodMatrix.java
                      • SomaticLikelihoodsEngine.java
                      • filtering
                        • StrandArtifactFilter.java
                        • NuMTFilterTool.java
                        • Mutect2VariantFilter.java
                        • PanelOfNormalsFilter.java
                        • ContaminationFilter.java
                        • ErrorProbabilities.java
                        • FilteringOutputStats.java
                        • ThresholdCalculator.java
                        • Mutect2AlleleFilter.java
                        • ReadPositionFilter.java
                        • BaseQualityFilter.java
                        • NRatioFilter.java
                        • MultiallelicFilter.java
                        • AlleleFilterUtils.java
                        • HardFilter.java
                        • M2FiltersArgumentCollection.java
                        • DuplicatedAltReadFilter.java
                        • GermlineFilter.java
                        • FilterMutectCalls.java
                        • Mutect2Filter.java
                        • FragmentLengthFilter.java
                        • MappingQualityFilter.java
                        • StrictStrandBiasFilter.java
                        • FilterStats.java
                        • MinAlleleFractionFilter.java
                        • Mutect2FilteringEngine.java
                        • FilteredHaplotypeFilter.java
                        • ClusteredEventsFilter.java
                        • TumorEvidenceFilter.java
                        • HardAlleleFilter.java
                        • MTLowHeteroplasmyFilterTool.java
                        • NormalArtifactFilter.java
                        • ErrorType.java
                        • ReadOrientationFilter.java
                        • PolymeraseSlippageFilter.java
                      • Mutect2.java
                      • clustering
                        • SomaticClusteringModel.java
                        • BinomialCluster.java
                        • AlleleFractionCluster.java
                        • BetaBinomialCluster.java
                        • Datum.java
                      • SomaticReferenceConfidenceModel.java
                      • MergeMutectStats.java
                      • Mutect2Engine.java
                      • SomaticGenotypingEngine.java
                      • MutectStats.java
                      • M2ArgumentCollection.java
                      • CreateSomaticPanelOfNormals.java
                    • ReferenceConfidenceVariantContextMerger.java
                    • consensus
                      • ReadsWithSameUMI.java
                      • DownsampleByDuplicateSet.java
                      • MoleculeID.java
                    • ReadAnonymizer.java
                    • haplotypecaller
                      • CalledHaplotypes.java
                      • PairHMMNativeArgumentCollection.java
                      • graphs
                        • GraphBasedKBestHaplotypeFinder.java
                        • SharedSequenceMerger.java
                        • MultiSampleEdge.java
                        • LowWeightChainPruner.java
                        • SeqGraph.java
                        • SplitCommonSuffices.java
                        • AdaptiveChainPruner.java
                        • GraphUtils.java
                        • MergeTails.java
                        • BaseGraph.java
                        • BaseEdge.java
                        • VertexBasedTransformer.java
                        • JunctionTreeKBestHaplotypeFinder.java
                        • ChainPruner.java
                        • MergeDiamonds.java
                        • CommonSuffixSplitter.java
                        • KBestHaplotype.java
                        • MergeCommonSuffices.java
                        • SharedVertexSequenceSplitter.java
                        • KBestHaplotypeFinder.java
                        • KmerSearchableGraph.java
                        • JTBestHaplotype.java
                        • SeqVertex.java
                        • BaseVertex.java
                        • Path.java
                      • HaplotypeCallerEngine.java
                      • ReferenceConfidenceResult.java
                      • HaplotypeCaller.java
                      • AssemblyRegionTrimmer.java
                      • AssemblyBasedCallerUtils.java
                      • KMerCounter.java
                      • HaplotypeCallerArgumentCollection.java
                      • RefVsAnyResult.java
                      • ReadErrorCorrector.java
                      • Kmer.java
                      • ReadLikelihoodCalculationEngine.java
                      • readthreading
                        • ReadThreadingGraph.java
                        • JunctionTreeLinkedDeBruijnGraph.java
                        • MultiDeBruijnVertex.java
                        • ReadThreadingAssembler.java
                        • AbstractReadThreadingGraph.java
                      • AssemblyResult.java
                      • ReferenceConfidenceMode.java
                      • HaplotypeCallerGenotypingEngine.java
                      • AssemblyBasedCallerArgumentCollection.java
                      • ReferenceConfidenceUtils.java
                      • LocationAndAlleles.java
                      • MutectReadThreadingAssemblerArgumentCollection.java
                      • LikelihoodEngineArgumentCollection.java
                      • AssemblyResultSet.java
                      • NearbyKmerErrorCorrector.java
                      • ReferenceConfidenceModel.java
                      • HaplotypeCallerReadThreadingAssemblerArgumentCollection.java
                      • PairHMMLikelihoodCalculationEngine.java
                      • PileupReadErrorCorrector.java
                      • ReadThreadingAssemblerArgumentCollection.java
                    • readorientation
                      • ReadOrientation.java
                      • BetaDistributionShape.java
                      • F1R2CountsCollector.java
                      • ArtifactPriorCollection.java
                      • CollectF1R2CountsArgumentCollection.java
                      • F1R2FilterConstants.java
                      • ArtifactState.java
                      • LearnReadOrientationModelEngine.java
                      • ArtifactPrior.java
                      • F1R2FilterUtils.java
                      • CollectF1R2Counts.java
                      • LearnReadOrientationModel.java
                      • AltSiteRecord.java
                      • DepthOneHistograms.java
                    • bqsr
                      • BaseRecalibrator.java
                      • GatherBQSRReports.java
                      • ApplyBQSR.java
                      • AnalyzeCovariates.java
                    • UnmarkDuplicates.java
                    • variantutils
                      • VariantsToTable.java
                      • ReblockGVCF.java
                      • CalculateGenotypePosteriors.java
                      • ValidateVariants.java
                      • FamilyLikelihoods.java
                      • SelectVariants.java
                      • UpdateVCFSequenceDictionary.java
                      • PosteriorProbabilitiesUtils.java
                      • LeftAlignAndTrimVariants.java
                    • qc
                      • CheckPileup.java
                      • Pileup.java
                    • CountVariants.java
                    • annotator
                      • OriginalAlignment.java
                      • HeterozygosityCalculator.java
                      • allelespecific
                        • ReducibleAnnotation.java
                        • AS_StrandOddsRatio.java
                        • AS_RMSMappingQuality.java
                        • ReducibleAnnotationData.java
                        • AlleleSpecificAnnotationData.java
                        • StrandBiasUtils.java
                        • AS_StrandBiasTest.java
                        • AS_ReadPosRankSumTest.java
                        • AS_MappingQualityRankSumTest.java
                        • AS_StandardAnnotation.java
                        • AS_InbreedingCoeff.java
                        • AlleleSpecificAnnotation.java
                        • AS_QualByDepth.java
                        • AS_BaseQualityRankSumTest.java
                        • AS_RankSumTest.java
                        • AS_FisherStrand.java
                      • DepthPerAlleleBySample.java
                      • StandardMutectAnnotation.java
                      • RMSMappingQuality.java
                      • Coverage.java
                      • StrandBiasBySample.java
                      • PedigreeAnnotation.java
                      • AS_StrandBiasMutectAnnotation.java
                      • BaseQuality.java
                      • PossibleDeNovo.java
                      • StandardHCAnnotation.java
                      • UniqueAltReadCount.java
                      • ReferenceBases.java
                      • RankSumTest.java
                      • FisherStrand.java
                      • ChromosomeCounts.java
                      • MappingQuality.java
                      • BaseQualityRankSumTest.java
                      • VariantAnnotation.java
                      • VariantOverlapAnnotator.java
                      • LikelihoodRankSumTest.java
                      • GenotypeSummaries.java
                      • MappingQualityRankSumTest.java
                      • StandardAnnotation.java
                      • StrandBiasTest.java
                      • AnnotationUtils.java
                      • Annotation.java
                      • SampleList.java
                      • PerAlleleAnnotation.java
                      • OrientationBiasReadCounts.java
                      • CountNs.java
                      • MappingQualityZero.java
                      • ClippingRankSumTest.java
                      • ReadPosRankSumTest.java
                      • StrandOddsRatio.java
                      • TandemRepeat.java
                      • DepthPerSampleHC.java
                      • VariantAnnotatorEngine.java
                      • BaseQualityHistogram.java
                      • AlleleFraction.java
                      • QualByDepth.java
                      • InbreedingCoeff.java
                      • InfoFieldAnnotation.java
                      • FragmentLength.java
                      • ExcessHet.java
                      • ReadPosition.java
                      • VariantAnnotator.java
                      • GenotypeAnnotation.java
                    • varianteval
                      • stratifications
                        • FunctionalClass.java
                        • RequiredStratification.java
                        • StandardStratification.java
                        • VariantType.java
                        • Filter.java
                        • CpG.java
                        • Degeneracy.java
                        • SnpEffPositionModifier.java
                        • FilterType.java
                        • EvalFeatureInput.java
                        • Contig.java
                        • IntervalStratification.java
                        • Novelty.java
                        • JexlExpression.java
                        • VariantStratifier.java
                        • Family.java
                        • TandemRepeat.java
                        • OneBPIndel.java
                        • AlleleCount.java
                        • AlleleFrequency.java
                        • manager
                          • Stratifier.java
                          • StratificationManager.java
                          • StratNodeIterator.java
                          • StratNode.java
                        • IndelSize.java
                        • Sample.java
                        • CompFeatureInput.java
                      • AlleleFrequencyQC.java
                      • VariantEvalReportWriter.java
                      • VariantEval.java
                      • evaluators
                        • VariantEvaluator.java
                        • MendelianViolationEvaluator.java
                        • VariantAFEvaluator.java
                        • TiTvVariantEvaluator.java
                        • MultiallelicSummary.java
                        • CountVariants.java
                        • CompOverlap.java
                        • ThetaVariantEvaluator.java
                        • IndelSummary.java
                        • PrintMissingComp.java
                        • StandardEval.java
                        • ValidationReport.java
                        • MetricsCollection.java
                        • GenotypeFilterSummary.java
                        • VariantSummary.java
                        • IndelLengthHistogram.java
                      • util
                        • SortableJexlVCMatchExp.java
                        • Analysis.java
                        • DataPoint.java
                        • EvaluationContext.java
                        • AnalysisModuleScanner.java
                        • SnpEffUtil.java
                        • VariantEvalUtils.java
                        • Molten.java
                    • rnaseq
                      • ASEReadCounter.java
                      • OverhangFixingManager.java
                      • SplitNCigarReads.java
                    • RevertBaseQualityScores.java
                    • sv
                      • PairedEndAndSplitReadEvidenceCollection.java
                    • GenotypeGVCFs.java
                    • filters
                      • VariantFiltration.java
                    • gnarlyGenotyper
                      • GnarlyGenotyper.java
                      • GnarlyGenotyperEngine.java
                    • GenotypeGVCFsEngine.java
                    • genotyper
                      • AlleleLikelihoodMatrixMapper.java
                      • IndependentSampleGenotypesModel.java
                      • GenotypeCalculationArgumentCollection.java
                      • HeterogeneousPloidyModel.java
                      • GenotypingEngine.java
                      • AlleleSubsettingUtils.java
                      • GenotypingLikelihoods.java
                      • UnifiedArgumentCollection.java
                      • StandardCallerArgumentCollection.java
                      • afcalc
                        • AlleleFrequencyCalculator.java
                        • AFCalculationResult.java
                      • HomogeneousPloidyModel.java
                      • MinimalGenotypingEngine.java
                      • GenotypingData.java
                      • OutputMode.java
                      • PloidyModel.java
                      • GenotypeLikelihoodCalculators.java
                      • GenotypeAlleleCounts.java
                      • GenotypeAssignmentMethod.java
                      • GenotypeLikelihoodCalculator.java
                    • validation
                      • AnnotateVcfWithBamDepth.java
                      • ConcordanceSummaryRecord.java
                      • FalsePositiveRecord.java
                      • EvaluateInfoFieldConcordance.java
                      • CalculateMixingFractions.java
                      • ConcordanceState.java
                      • Concordance.java
                      • basicshortmutpileup
                        • BetaBinomialDistribution.java
                        • BasicValidationResult.java
                        • ValidateBasicSomaticShortMutations.java
                        • PowerCalculationUtils.java
                        • AllelePileupCounter.java
                        • BasicSomaticShortMutationValidator.java
                      • MergeMutect2CallsWithMC3.java
                      • FilterAnalysisRecord.java
                      • CountFalsePositives.java
                      • MixingFraction.java
                      • RemoveNearbyIndels.java
                      • AnnotateVcfWithExpectedAlleleFraction.java
                      • InfoConcordanceRecord.java
                    • SplitIntervals.java
                    • CombineGVCFs.java
                    • MethylationTypeCaller.java
                    • vqsr
                      • VariantRecalibrationUtils.java
                      • CNNVariantWriteTensors.java
                      • TensorType.java
                      • VariantRecalibratorEngine.java
                      • VariantRecalibrator.java
                      • TruthSensitivityTranche.java
                      • Tranche.java
                      • VQSLODTranche.java
                      • FilterVariantTranches.java
                      • ApplyVQSR.java
                      • VariantRecalibratorArgumentCollection.java
                      • GaussianMixtureModel.java
                      • MultivariateGaussian.java
                      • CNNVariantTrain.java
                      • TrainingSet.java
                      • VariantDataManager.java
                      • GatherTranches.java
                      • VariantDatum.java
                      • TrancheManager.java
                      • CNNScoreVariants.java
                    • coverage
                      • CoverageUtils.java
                      • CoverageOutputWriter.java
                      • DepthOfCoverage.java
                      • DepthOfCoveragePartitionedDataStore.java
                      • DoCOutputType.java
                      • DepthOfCoverageStats.java
                    • realignmentfilter
                      • RealignmentEngine.java
                      • FilterAlignmentArtifacts.java
                      • RealignmentArgumentCollection.java
                    • fasta
                      • CountBasesInReference.java
                      • FastaAlternateReferenceMaker.java
                      • FastaReferenceMaker.java
                  • BwaMemIndexImageCreator.java
                  • HtsgetReader.java
                  • AnalyzeSaturationMutagenesis.java
                  • htsgetreader
                    • HtsgetResponse.java
                    • HtsgetRequestBuilder.java
                    • HtsgetRequestField.java
                    • HtsgetFormat.java
                    • HtsgetClass.java
                    • HtsgetErrorResponse.java
                  • spark
                    • utils
                      • SetSizeUtils.java
                      • HopscotchMultiMap.java
                      • HopscotchCollection.java
                      • ReadFilterSparkifier.java
                      • ReadTransformerSparkifier.java
                      • LongIterator.java
                      • HopscotchMap.java
                      • HopscotchSet.java
                      • LargeLongHopscotchSet.java
                      • LongBloomFilter.java
                      • IntHistogram.java
                      • LongHopscotchSet.java
                      • FlatMapGluer.java
                      • HopscotchUniqueMultiMap.java
                    • pathseq
                      • PSScoreArgumentCollection.java
                      • PSBuildReferenceTaxonomyUtils.java
                      • MarkedOpticalDuplicateReadFilter.java
                      • PathSeqBuildReferenceTaxonomy.java
                      • PSKmerCollection.java
                      • HostAlignmentReadFilter.java
                      • PathSeqFilterSpark.java
                      • PSPairedUnpairedSplitterSpark.java
                      • PSKmerSet.java
                      • PSBwaUtils.java
                      • PathSeqPipelineSpark.java
                      • PSTaxonomyConstants.java
                      • PSBwaArgumentCollection.java
                      • PathSeqScoreSpark.java
                      • PSFilterArgumentCollection.java
                      • PSBwaAlignerSpark.java
                      • PSFilter.java
                      • loggers
                        • PSFilterEmptyLogger.java
                        • PSScoreFileLogger.java
                        • PSFilterMetrics.java
                        • PSFilterFileLogger.java
                        • PSFilterLogger.java
                        • PSScoreLogger.java
                        • PSScoreMetrics.java
                      • PSBwaAligner.java
                      • PSUtils.java
                      • PSPathogenAlignmentHit.java
                      • PSTaxonomyDatabase.java
                      • ContainsKmerReadFilterSpark.java
                      • PSKmerUtils.java
                      • PathSeqBwaSpark.java
                      • PSTreeNode.java
                      • PSPathogenTaxonScore.java
                      • PathSeqBuildKmers.java
                      • PSPathogenReferenceTaxonProperties.java
                      • PSBwaFilter.java
                      • PSTree.java
                      • PSScorer.java
                      • ContainsKmerReadFilter.java
                      • PSKmerBloomFilter.java
                    • bwa
                      • BwaSpark.java
                      • BwaArgumentCollection.java
                      • BwaSparkEngine.java
                    • ApplyBQSRSpark.java
                    • RevertSamSpark.java
                    • sv
                      • utils
                        • SVVCFReader.java
                        • ExtractOriginalAlignmentRecordsByNameSpark.java
                        • PairedStrandedIntervalTree.java
                        • StrandedInterval.java
                        • TextMDCodec.java
                        • SVFileUtils.java
                        • SVKmerLong.java
                        • SVKmerShort.java
                        • GATKSVVCFConstants.java
                        • GATKSVVCFHeaderLines.java
                        • SVInterval.java
                        • SVVCFWriter.java
                        • ComplexityPartitioner.java
                        • SVLocation.java
                        • Strand.java
                        • SVContext.java
                        • SVReferenceUtils.java
                        • ExternalCommandlineProgramModule.java
                        • CNVInputReader.java
                        • KmerAndCount.java
                        • SVKmerizer.java
                        • PairedStrandedIntervals.java
                        • SingleSequenceReferenceAligner.java
                        • SVFastqUtils.java
                        • SVIntervalTree.java
                        • SVUtils.java
                        • SVKmer.java
                        • SVDUSTFilteredKmerizer.java
                      • InsertSizeDistribution.java
                      • discovery
                        • DiscoverVariantsFromContigAlignmentsSAMSpark.java
                        • SimpleSVType.java
                        • SvDiscoveryInputMetaData.java
                        • alignment
                          • AssemblyContigWithFineTunedAlignments.java
                          • AlignedContigGenerator.java
                          • ContigAlignmentsModifier.java
                          • AlignmentInterval.java
                          • AssemblyContigAlignmentsConfigPicker.java
                          • AlignedAssembly.java
                          • StrandSwitch.java
                          • AlignedContig.java
                        • SvType.java
                        • SvDiscoveryUtils.java
                        • SvDiscoverFromLocalAssemblyContigAlignmentsSpark.java
                        • AnnotatedVariantProducer.java
                        • BreakEndVariantType.java
                        • inference
                          • CpxVariantInterpreter.java
                          • BreakpointsInference.java
                          • NovelAdjacencyAndAltHaplotype.java
                          • SimpleNovelAdjacencyInterpreter.java
                          • BreakpointComplications.java
                          • SimpleChimera.java
                          • TypeInferredFromSimpleChimera.java
                          • CpxVariantType.java
                          • ContigChimericAlignmentIterativeInterpreter.java
                          • SimpleNovelAdjacencyAndChimericAlignmentEvidence.java
                          • CpxVariantReInterpreterSpark.java
                          • CpxVariantInducingAssemblyContig.java
                          • SegmentedCpxVariantSimpleVariantExtractor.java
                          • CpxVariantCanonicalRepresentation.java
                          • ImpreciseVariantDetector.java
                      • InsertSizeDistributionShape.java
                      • evidence
                        • ReadMetadata.java
                        • KmerCounter.java
                        • SVReadFilter.java
                        • FermiLiteAssemblyHandler.java
                        • BreakpointEvidence.java
                        • ReadsForQNamesFinder.java
                        • EvidenceFeatures.java
                        • AlignedAssemblyOrExcuse.java
                        • BreakpointDensityFilter.java
                        • LibraryStatistics.java
                        • FindBadGenomicKmersSpark.java
                        • ReadClassifier.java
                        • KmerCleaner.java
                        • QNameAndInterval.java
                        • QNameIntervalFinder.java
                        • PartitionCrossingChecker.java
                        • EvidenceTargetLink.java
                        • EvidenceTargetLinkClusterer.java
                        • BreakpointEvidenceClusterer.java
                        • ExtractSVEvidenceSpark.java
                        • TemplateFragmentOrdinal.java
                        • IntervalCoverageFinder.java
                        • CalcMetadataSpark.java
                        • QNamesForKmersFinder.java
                        • EvidenceOverlapChecker.java
                        • QNameFinder.java
                        • KSWindowFinder.java
                        • XGBoostEvidenceFilter.java
                        • QNameKmerizer.java
                        • FindBreakpointEvidenceSpark.java
                        • KmerAndInterval.java
                      • StructuralVariationDiscoveryPipelineSpark.java
                      • StructuralVariationDiscoveryArgumentCollection.java
                    • pipelines
                      • PrintVariantsSpark.java
                      • BQSRPipelineSpark.java
                      • ReadsPipelineSpark.java
                      • CountReadsSpark.java
                      • PrintReadsSpark.java
                      • BwaAndMarkDuplicatesPipelineSpark.java
                      • SortSamSpark.java
                      • FlagStatSpark.java
                      • CountBasesSpark.java
                      • metrics
                        • MeanQualityByCycleSpark.java
                        • QualityScoreDistributionSpark.java
                        • CollectInsertSizeMetricsSpark.java
                        • CollectMultipleMetricsSpark.java
                        • CollectBaseDistributionByCycleSpark.java
                        • MetricsCollectorSparkTool.java
                        • QualityYieldMetricsCollectorSpark.java
                        • InsertSizeMetricsCollectorSpark.java
                        • CollectQualityYieldMetricsSpark.java
                        • MetricsCollectorSpark.java
                      • CountVariantsSpark.java
                    • ParallelCopyGCSDirectoryIntoHDFSSpark.java
                    • validation
                      • CompareDuplicatesSpark.java
                    • BaseRecalibratorSpark.java
                    • PileupSpark.java
                    • transforms
                      • markduplicates
                        • MarkDuplicatesSpark.java
                        • MarkDuplicatesSparkUtils.java
                      • BaseRecalibratorSparkFn.java
                      • ApplyBQSRSparkFn.java
                    • CreateHadoopBamSplittingIndex.java
                  • PrintReads.java
                  • FixMisencodedBaseQualityReads.java
                  • funcotator
                    • FuncotatorEngine.java
                    • BaseFuncotatorArgumentCollection.java
                    • AnnotatedIntervalToSegmentVariantContextConverter.java
                    • AminoAcid.java
                    • Funcotator.java
                    • vcfOutput
                      • VcfOutputRenderer.java
                    • FuncotatorVariantArgumentCollection.java
                    • FilterFuncotations.java
                    • FlankSettings.java
                    • Funcotation.java
                    • FuncotatorArgumentDefinitions.java
                    • FuncotateSegments.java
                    • FuncotationMap.java
                    • DataSourceFuncotationFactory.java
                    • SequenceComparison.java
                    • metadata
                      • TumorNormalPair.java
                      • VcfFuncotationMetadata.java
                      • SamplePairExtractor.java
                      • FuncotationMetadata.java
                      • FuncotationMetadataUtils.java
                    • FuncotatorDataSourceDownloader.java
                    • FilterFuncotationsUtils.java
                    • simpletsvoutput
                      • SimpleTsvOutputRenderer.java
                    • StrandCorrectedAllele.java
                    • AliasProvider.java
                    • genelistoutput
                      • GeneListOutputRenderer.java
                    • ProteinChangeInfo.java
                    • filtrationRules
                      • AlleleFrequencyGnomadUtils.java
                      • AlleleFrequencyExacUtils.java
                      • ClinVarFilter.java
                      • FuncotationFilter.java
                      • ArHomvarFilter.java
                      • AutosomalRecessiveConstants.java
                      • TwoPassFuncotationFilter.java
                      • LmmFilter.java
                      • ArHetvarFilter.java
                      • AlleleFrequencyUtils.java
                      • LofFilter.java
                      • FuncotationFiltrationRule.java
                    • StrandCorrectedReferenceBases.java
                    • mafOutput
                      • MafOutputRendererConstants.java
                      • CustomMafFuncotationCreator.java
                      • MafOutputRenderer.java
                    • dataSources
                      • TableFuncotation.java
                      • DataSourceUtils.java
                      • vcf
                        • VcfFuncotationFactory.java
                      • xsv
                        • SimpleKeyXsvFuncotationFactory.java
                        • LocatableXsvFuncotationFactory.java
                      • gencode
                        • GencodeFuncotationFactory.java
                        • GencodeFuncotationBuilder.java
                        • GencodeFuncotation.java
                        • segment
                          • SegmentExonUtils.java
                          • SegmentExonOverlaps.java
                      • LocatableFuncotationCreator.java
                      • cosmic
                        • CosmicFuncotationFactory.java
                    • FuncotatorSegmentArgumentCollection.java
                    • OutputRenderer.java
                    • FuncotatorConstants.java
                    • FilterFuncotationsConstants.java
                    • FuncotatorUtils.java
                    • compositeoutput
                      • CompositeOutputRenderer.java
                    • TranscriptSelectionMode.java
                  • GetSampleName.java
                  • HaplotypeCallerSpark.java
                  • validation
                    • CompareMatrix.java
                    • validate-reads-spark-pipeline.sh
                    • CompareBaseQualities.java
                  • DownsampleableSparkReadShard.java
                  • readersplitters
                    • ReaderSplitter.java
                    • LibraryNameSplitter.java
                    • ReadGroupSplitter.java
                    • SampleNameSplitter.java
                    • ReadGroupIdSplitter.java
                  • ClipReads.java
                  • GatherVcfsCloud.java
                  • FlagStat.java
                  • SplitReads.java
                  • PrintBGZFBlockInformation.java
                  • CountReads.java
                  • ApplyBQSRArgumentCollection.java
                  • CountBases.java
                  • CompareIntervalLists.java
                • CommandLineArgumentValidatorMain.java
                • metrics
                  • InsertSizeMetrics.java
                  • PerUnitMetricCollector.java
                  • InsertSizeMetricsArgumentCollection.java
                  • QualityYieldMetricsArgumentCollection.java
                  • PerUnitInsertSizeMetricsCollector.java
                  • MetricsArgumentCollection.java
                  • QualityYieldMetrics.java
                  • MultiLevelCollector.java
                  • analysis
                    • BaseDistributionByCycleMetrics.java
                    • AlleleFrequencyQCMetric.java
                  • SAMRecordMultiLevelCollector.java
                  • MultiLevelReducibleCollector.java
                  • InsertSizeMetricsCollectorArgs.java
                  • InsertSizeMetricsCollector.java
                  • SAMRecordAndReference.java
                  • MultiLevelMetrics.java
                  • SAMRecordAndReferenceMultiLevelCollector.java
                  • MetricsUtils.java
                  • MetricAccumulationLevel.java
      • test
        • resources
          • fastaWithoutFai.fasta
          • dbsnp_132.b36.excluding_sites_after_129.chr1_1k.vcf.idx
          • wgs_calling_regions.v1.interval_list
          • Homo_sapiens_assembly19_chr1_1M.fasta.fai
          • problematicFASTA.fasta
          • problematicFASTA.fasta.fai
          • exampleFASTA.fasta.gz.fai
          • fastaWithoutDict.fasta.fai
          • pairhmm-testdata.txt
          • exampleFASTA.fasta.fai
          • hg19mini.fasta.gz.fai
          • fastaWithoutFai.dict
          • read_anonymizer_expected.sam
          • human_g1k_v37.chr17_1Mb.fasta.fai
          • exampleFASTA.fasta.gz
          • Homo_sapiens_assembly19_chr1_1M.dict
          • empty.vcf
          • hg19mini.fasta.gz.gzi
          • NA12878.chr17_69k_70k.dictFix.cram
          • hg19mini.dict
          • hg19micro.fasta.fai
          • empty.vcf.idx
          • exampleFASTA.dict
          • Homo_sapiens_assembly38_chrM_only.fasta
          • Homo_sapiens_assembly38_chrM_only.dict
          • oneSNP.vcf
          • iupacFASTA.fasta.fai
          • oneSNP.vcf.idx
          • NA12878.chr17_69k_70k.dictFix.bam.bai
          • picard_intervals.interval_list
          • picard_metrics_test.pre_adapter_detail_metrics
          • hg19mini.fasta.fai
          • problematicFASTA.dict
          • hg19mini.fasta.gz
          • iupacFASTA.fasta
          • iupacFASTA.dict
          • Homo_sapiens_assembly38_chrM_only.fasta.fai
          • small_unmerged_gatk_intervals.list
          • NA12878.chr17_69k_70k.dictFix.cram.crai
          • seqsToClip.fasta
          • human_g1k_v37.chr17_1Mb.dict
          • HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf
          • hg19micro.fasta
          • exampleFASTA.fasta.gz.gzi
          • hg19mini.interval_list
          • large
            • human_g1k_v37.20.21.fasta.pac
            • NA12878.prod.chr20snippet.g.vcf.gz.tbi
            • expected.NA12878.RNAseq.splitNcigarReads.maxBasesInOverhang5.bam
            • gencode.v19.LargeFile.gtf
            • NA12878.prod.chr20snippet.g.vcf.gz
            • multiSampleSubsetted.bam
            • human_g1k_v37.20.21.fasta.bwt
            • NA12878.RNAseq.bam
            • Homo_sapiens_assembly38.fasta.gz
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam.bai
            • GRCm38_primary_assembly_genome
              • chr14.GRCm38.primary_assembly.genome.fa.gz
              • chr14.GRCm38.primary_assembly.genome.fa.gz.gzi
              • chr14.GRCm38.primary_assembly.genome.dict
              • chr14.GRCm38.primary_assembly.genome.fa.gz.fai
            • human_g1k_v37.20.21.2bit
            • NA12878.phasedData.Chr20.vcf
            • dbsnp_138.b37.20.21.vcf.blockgz.gz.tbi
            • 1000G.phase3.broad.withGenotypes.chr20.10100000.vcf.idx
            • human_g1k_v37.20.21.dict
            • dbsnp_138.b37.1.1-65M.vcf.idx
            • NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.chr20.vcf
            • human_g1k_v37.20.21.fasta.amb
            • mutect
              • highDPMTsnippet.bai
              • dream_synthetic_bams
                • normal_3.bam
                • tumor_4.bam.bai
                • normal_1.bam
                • tumor_2.bam.bai
                • normal_1.bam.bai
                • tumor_4.bam
                • tumor_2.bam
                • tumor_3.bam
                • normal_3.bam.bai
                • normal.bam.bai
                • tumor_1.bam.bai
                • normal_4.bam.bai
                • tumor.bam
                • normal.bam
                • normal_2.bam.bai
                • tumor_1.bam
                • normal_4.bam
                • tumor_3.bam.bai
                • normal_2.bam
                • tumor.bam.bai
              • highDPMTsnippet.bam
            • ALL.20100201.chr20.subset.bi.sites.vcf
            • mitochondria_references
              • Homo_sapiens_assembly38.chrM.fasta.ann
              • Homo_sapiens_assembly38.chrM.fasta
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac
              • blacklist_sites.hg38.chrM.bed.idx
              • Homo_sapiens_assembly38.chrM.fasta.fai
              • Homo_sapiens_assembly38.chrM.dict
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai
              • ShiftBack.chain
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa
              • blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed
              • blacklist_sites.hg38.chrM.bed
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta
              • Homo_sapiens_assembly38.chrM.fasta.sa
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt
              • Homo_sapiens_assembly38.chrM.fasta.bwt
              • blacklist_sites.hg38.chrM.shifted_by_8000_bases.bed.idx
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann
              • non_control_region.chrM.interval_list
              • Homo_sapiens_assembly38.chrM.fasta.pac
              • Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict
              • control_region_shifted.chrM.interval_list
              • Homo_sapiens_assembly38.chrM.fasta.amb
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram
            • NA12878.RNAseq.bai
            • ReblockGVCF
              • spanDel.exome.chr20.vcf.idx
              • spanDel.exome.chr20.vcf
            • gencode.v26.primary_assembly.annotation.XYZ.gtf.idx
            • contaminated_bams
              • CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.AT.15PERCENT.bam.bai
              • CEUTrio.HiSeq.WGS.b37.NA12878.CONTAMINATED.WITH.HCC1143.NORMALS.AT.15PERCENT.bam
            • exampleLargeFile.txt
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.tiny.vcf
            • expected.NA12878.RNAseq.splitNcigarReads.maxMismatchesInOverhang0.bai
            • dbsnp_138.b37.1.1-65M.vcf
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.tiny.md.bam
            • CalculateGenotypePosteriors
              • expectedCGP_testUsingDiscoveredAF.vcf
              • expectedCGP_testMissingPriors.vcf
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam
            • testProductionGVCF.expected.g.vcf.gz.tbi
            • Homo_sapiens_assembly38.dict
            • cnv_somatic_workflows_test_files
              • HCC1143-t1-chr20-downsampled.deduplicated.bam.bai
              • SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai
              • SM-74P4M-v1-chr20-downsampled.deduplicated.bam
              • wgs-do-gc.pon.hdf5
              • common_snps_sample-chr20.interval_list
              • ice_targets_sample-chr20.interval_list
              • chr20.interval_list
              • wes-no-gc.pon.hdf5
              • SM-74NEG-v1-chr20-downsampled.deduplicated.cram
              • wgs-no-gc.pon.hdf5
              • wes-do-gc.pon.hdf5
              • HCC1143_BL-n1-chr20-downsampled.deduplicated.bam
              • human_g1k_v37.chr-20.truncated.fasta.fai
              • SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai
              • human_g1k_v37.chr-20.truncated.dict
              • HCC1143_BL-n1-chr20-downsampled.deduplicated.bam.bai
              • HCC1143-t1-chr20-downsampled.deduplicated.bam
              • human_g1k_v37.chr-20.truncated.fasta
            • testProductionGVCF.expected.g.vcf
            • Homo_sapiens_assembly38.20.21.2bit
            • NexPond-377866.NA12878.WEX.20.21.with.unmapped.bam.bai
            • NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.chr20.vcf.idx
            • K-562.duplicateMarked.chr20.bam
            • NA12878.alignedHg38.duplicateMarked.baseRealigned.bam
            • NA12878.phasedData.Chr20.vcf.idx
            • expected.NA12878.RNAseq.splitNcigarReads.doNotFixOverhangs.bam
            • ALL.20100201.chr20.subset.bi.sites.vcf.idx
            • human_g1k_v37.20.21.fasta.gz.gzi
            • NexPond-377866.NA12878.WEX.20.21.with.unmapped.bam
            • NA24385.vcf.gz.tbi
            • gvcfs
              • combined.gatk3.7_30_ga4f720357.expected.vcf
              • combined_with_genotypes.g.vcf.gz.tbi
              • HG00268.spaceInSampleName.g.vcf
              • HG00268_after_combine_gvcfs.g.vcf.gz
              • combined_multi_interval.gatk3.7.g.vcf.gz
              • HG00096.g.vcf.gz
              • HapMap5plex.ploidy10.b37.g.vcf
              • HG00096_after_combine_gvcfs.g.vcf.gz.tbi
              • HG00268.g.vcf.gz
              • combined_multi_interval.gatk3.7.g.vcf.gz.tbi
              • HapMap5plex.ploidy10.b37.g.vcf.idx
              • combined.gatk3.7.g.vcf.gz.tbi
              • NA19625.g.vcf.gz.tbi
              • combined_with_genotypes.g.vcf.gz
              • NA19625_after_combine_gvcfs.g.vcf.gz.tbi
              • combined.gatk3.7_sites_only.g.vcf.gz
              • combined.gatk3.7.smaller_interval.g.vcf
              • HG00096_after_combine_gvcfs.g.vcf.gz
              • NA19625.g.vcf.gz
              • CEUTrio.20.21.gatk3.4.g.vcf.idx
              • CEUTrio.20.21.gatk3.4.g.vcf
              • combined.gatk3.7.smaller_interval.g.vcf.idx
              • combined.gatk3.7_30_ga4f720357.g.vcf.gz
              • NA19625_after_combine_gvcfs.g.vcf.gz
              • HG00268.g.vcf.gz.tbi
              • HG00268_after_combine_gvcfs.g.vcf.gz.tbi
              • combined.gatk3.7_sites_only.g.vcf.gz.tbi
              • gatk3.7_30_ga4f720357.24_sample.21.g.vcf
              • combined.gatk3.7_30_ga4f720357.g.vcf.gz.tbi
              • combined.gatk3.7.g.vcf.gz
              • gatk3.7_30_ga4f720357.24_sample.21.expected.vcf
              • HG00096.g.vcf.gz.tbi
              • gatk3.7_30_ga4f720357.24_sample.21.g.vcf.idx
              • HG00268.spaceInSampleName.g.vcf.idx
            • ALL.20100201.chr20.subset.bc.sites.vcf.idx
            • human_g1k_v37.20.21.fasta.fai
            • snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf.idx
            • human_g1k_v37.20.21.fasta.sa
            • 1000G.phase3.broad.withGenotypes.chr20.10100000.vcf
            • expected.NA12878.RNAseq.splitNcigarReads.bai
            • Mills_and_1000G_gold_standard.indels.b37.sites.chr20.vcf.idx
            • human_g1k_v37.20.21.fasta.ann
            • Homo_sapiens_assembly19.fasta.gz.fai
            • multiSampleSubsetted.bam.bai
            • expected.NA12878.RNAseq.splitNcigarReads.maxMismatchesInOverhang0.bam
            • gencode.v26.primary_assembly.annotation.XYZ.gtf
            • human_g1k_v37.20.21.fasta.gz
            • Homo_sapiens_assembly38.fasta.gz.fai
            • funcotator
              • e.coli_K12_MG1655.NC_000913.3.dict
              • gencode.v19.chr_patch_hapl_scaff.chr3.gtf
              • gencode.v19.pc_transcripts.fasta.fai
              • e_coli.MG1655.expected_output.vcf
              • calledcopyratio_gatk_output_hg38_integration_test.seg
              • e.coli_K12_MG1655.NC_000913.3.fasta
              • small_ds_FILTER_test
                • gencode_pik3ca
                  • hg19
                    • gencode.v19.PIK3CA.gtf
                    • gencode.config
                    • gencode.v19.PIK3CA_transcript.fasta.fai
                    • gencode.v19.PIK3CA.gtf.idx
                    • gencode.v19.PIK3CA_transcript.dict
                    • gencode.v19.PIK3CA_transcript.fasta
                • dbSnp
                  • hg19
                    • dbSnp.config
                    • dbSnp.regressionTestSet.hg19.FILTER.vcf.gz.tbi
                    • dbSnp.regressionTestSet.hg19.FILTER.vcf.gz
              • gencode.v19.pc_transcripts.dict
              • funcotator_dataSources_cloud
                • gnomAD
                  • hg19
                    • gnomAD.config
                • gencode
                  • hg38
                    • gencode.config
                  • hg19
                    • gencode.config
                • oreganno
                  • hg38
                    • oreganno.config
                  • hg19
                    • oreganno.config
                • MANIFEST.txt
                • achilles
                  • hg38
                    • achilles.config
                  • hg19
                    • achilles.config
              • funcotator_dataSources
                • simple_uniprot
                  • hg38
                    • simple_uniprot.config
                    • simple_uniprot_Dec012014.tsv
                  • hg19
                    • simple_uniprot.config
                    • simple_uniprot_Dec012014.tsv
                • clinvar
                  • hg19
                    • clinvar_hgmd.tsv
                    • clinvar_hgmd.tsv.idx
                    • clinvar_hgmd.config
                • cancer_gene_census
                  • hg38
                    • cancer_gene_census.config
                    • CancerGeneCensus_Table_1_full_2012-03-15.txt
                  • hg19
                    • cancer_gene_census.config
                    • CancerGeneCensus_Table_1_full_2012-03-15.txt
                • hgnc
                  • hg38
                    • hgnc_download_Nov302017.tsv
                    • hgnc.config
                  • hg19
                    • hgnc_download_Nov302017.tsv
                    • hgnc.config
                • gencode
                  • hg38
                    • gencode.config
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.dict
                    • gencode.v28.regressionTestVariantSet.gtf
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.fa.fai
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.fa
                    • gencode.v28.regressionTestVariantSet.gtf.idx
                  • hg19
                    • gencode.v19.testVariantSubset.gtf
                    • gencode.config
                    • gencode.v19.testVariantSubset.pc_transcripts.dict
                    • gencode.v19.testVariantSubset.pc_transcripts.fa
                    • gencode.v19.testVariantSubset.gtf.idx
                    • gencode.v19.testVariantSubset.pc_transcripts.fa.fai
                • template.config
                • gencode_xhgnc
                  • hg38
                    • gencode_xhgnc.config
                    • gencode_xhgnc_v90_38.hg38.tsv
                  • hg19
                    • gencode_xhgnc.config
                    • gencode_xhgnc_v75_37.hg19.tsv
                • familial
                  • hg38
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                  • hg19
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                • cosmic_tissue
                  • hg38
                    • cosmic_tissue.config
                    • cosmic_tissue.tsv
                  • hg19
                    • cosmic_tissue.config
                    • cosmic_tissue.tsv
                • gencode_xrefseq
                  • hg38
                    • gencode_xrefseq_v90_38.tsv
                    • gencode_xrefseq.config
                  • hg19
                    • gencode_xrefseq_v75_37.tsv
                    • gencode_xrefseq.config
                • dna_repair_genes
                  • hg38
                    • dnaRepairGenes.20171221T103938.csv
                    • dnaRepairGenes.config
                  • hg19
                    • dnaRepairGenes.20171221T103938.csv
                    • dnaRepairGenes.config
                • cosmic
                  • hg19
                    • cosmic.config
                    • CosmicTest.db
                • achilles
                  • hg38
                    • achilles.config
                    • achilles_lineage_results.import.txt
                  • hg19
                    • achilles.config
                    • achilles_lineage_results.import.txt
                • cosmic_fusion
                  • hg38
                    • cosmic_fusion.config
                    • cosmic_fusion.tsv
                  • hg19
                    • cosmic_fusion.config
                    • cosmic_fusion.tsv
                • dbSnp
                  • hg38
                    • dbSnp.regressionTestSet.hg38.vcf.gz
                    • dbSnp.regressionTestSet.hg38.vcf.gz.tbi
                    • dbSNP.config
                  • hg19
                    • dbSnp.regressionTestSet.hg19.vcf.gz
                    • dbSnp.regressionTestSet.hg19.vcf.gz.tbi
                    • dbSNP.config
              • GRCh37.p13.chr19.tar.gz
              • small_ds_pik3ca
                • gencode_pik3ca
                  • hg38
                    • gencode_pik3ca.config
                    • gencode.v28.PIK3CA.gtf
                    • gencode.v28.PIK3CA_transcript.fasta
                    • gencode.v28.PIK3CA.gtf.idx
                    • gencode.v28.PIK3CA_transcript.dict
                    • gencode.v28.PIK3CA_transcript.fasta.fai
                  • hg19
                    • gencode.v19.PIK3CA.gtf
                    • gencode.config
                    • gencode.v19.PIK3CA_transcript.fasta.fai
                    • gencode.v19.PIK3CA.gtf.idx
                    • gencode.v19.PIK3CA_transcript.dict
                    • gencode.v19.PIK3CA_transcript.fasta
                • dummy_clinvar_pik3ca
                  • hg38
                    • dummy_clinvar_hg38_pik3ca.vcf
                    • dummy_clinvar_pik3ca.config
                    • dummy_clinvar_hg38_pik3ca.vcf.idx
                  • hg19
                    • dummy_clinvar_hg19_pik3ca.vcf
                    • dummy_clinvar_pik3ca.config
                    • dummy_clinvar_hg19_pik3ca.vcf.idx
              • small_ds_clinvar_hg19
                • gencode_pik3ca
                  • hg19
                    • gencode.v19.PIK3CA.gtf
                    • gencode.config
                    • gencode.v19.PIK3CA_transcript.fasta.fai
                    • gencode.v19.PIK3CA.gtf.idx
                    • gencode.v19.PIK3CA_transcript.dict
                    • gencode.v19.PIK3CA_transcript.fasta
                • clinvar
                  • hg19
                    • clinvar_hgmd.tsv
                    • clinvar_hgmd.tsv.idx
                    • clinvar_hgmd.config
              • ecoli_ds
                • README.txt
                • gencode
                  • ASM584v2
                    • gencode.config
                    • Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.cds.all.dict
                    • Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.44.gtf.idx
                    • Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.cds.all.fa.fai
                    • Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.cds.all.fa
                    • Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.44.gtf
              • modelFinal_gatk_output_hg38_integration_test.seg
              • gencode.v19.chr_patch_hapl_scaff.chr3.gtf.idx
              • pik3ca_muc16_all_transcripts_ds
                • gencode_pik3ca
                  • hg19
                    • gencode.v19.PIK3CA.gtf
                    • gencode.config
                    • gencode.v19.PIK3CA_transcript.fasta.fai
                    • gencode.v19.PIK3CA.gtf.idx
                    • gencode.v19.PIK3CA_transcript.dict
                    • gencode.v19.PIK3CA_transcript.fasta
                • gencode_muc16
                  • hg19
                    • gencode.config
                    • gencode.v19.MUC16.gtf.idx
                    • gencode.v19.MUC16_transcript.fasta
                    • gencode.v19.MUC16_transcript.fasta.fai
                    • gencode.v19.MUC16_transcript.dict
                    • gencode.v19.MUC16.gtf
              • hg38.3.tar.gz
              • dummyDataSources
                • dummySrc1
                  • hg38
                    • cancer_gene_census.config
                    • CancerGeneCensus_Table_1_full_2012-03-15.txt
                  • hg19
                    • dnaRepairGenes.config
                    • dnaRepairGenes.20180524T145835.csv
                • dummySrc3
                  • hg38
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                  • hg19
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                • README.txt
                • MANIFEST.txt
                • dummySrc2
                  • hg38
                    • gencode_xrefseq_v90_38.tsv
                    • gencode_xrefseq.config
                  • hg19
                    • gencode_xrefseq_v75_37.tsv
                    • gencode_xrefseq.config
              • vcfFuncotationOrderingBugRepro
                • gencode_pik3ca
                  • hg19
                    • gencode.v19.PIK3CA.gtf
                    • gencode.config
                    • gencode.v19.PIK3CA_transcript.fasta.fai
                    • gencode.v19.PIK3CA.gtf.idx
                    • gencode.v19.PIK3CA_transcript.dict
                    • gencode.v19.PIK3CA_transcript.fasta
                • dbSnp
                  • hg19
                    • dbSnp.config
                    • dbSnp.repro.vcf.idx
                    • dbSnp.repro.vcf
              • dummyDataSources.sha256
              • funcotator_dataSources_cloud_gnomad
                • simple_uniprot
                  • hg38
                    • simple_uniprot.config
                    • simple_uniprot_Dec012014.tsv
                  • hg19
                    • simple_uniprot.config
                    • simple_uniprot_Dec012014.tsv
                • clinvar
                  • hg19
                    • clinvar_hgmd.tsv
                    • clinvar_hgmd.tsv.idx
                    • clinvar_hgmd.config
                • gnomAD
                  • hg19
                    • gnomAD.config
                • cancer_gene_census
                  • hg38
                    • cancer_gene_census.config
                    • CancerGeneCensus_Table_1_full_2012-03-15.txt
                  • hg19
                    • cancer_gene_census.config
                    • CancerGeneCensus_Table_1_full_2012-03-15.txt
                • hgnc
                  • hg38
                    • hgnc_download_Nov302017.tsv
                    • hgnc.config
                  • hg19
                    • hgnc_download_Nov302017.tsv
                    • hgnc.config
                • gencode
                  • hg38
                    • gencode.config
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.dict
                    • gencode.v28.regressionTestVariantSet.gtf
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.fa.fai
                    • gencode.v28.regressionTestVariantSet.pc_transcripts.fa
                    • gencode.v28.regressionTestVariantSet.gtf.idx
                  • hg19
                    • gencode.config
                    • gencode.v19.regressionTestVariantSet.gtf
                    • gencode.v19.regressionTestVariantSet.pc_transcripts.fa
                    • gencode.v19.regressionTestVariantSet.gtf.idx
                    • gencode.v19.regressionTestVariantSet.pc_transcripts.fa.fai
                    • gencode.v19.regressionTestVariantSet.pc_transcripts.dict
                • template.config
                • gencode_xhgnc
                  • hg38
                    • gencode_xhgnc.config
                    • gencode_xhgnc_v90_38.hg38.tsv
                  • hg19
                    • gencode_xhgnc.config
                    • gencode_xhgnc_v75_37.hg19.tsv
                • familial
                  • hg38
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                  • hg19
                    • familial.config
                    • Familial_Cancer_Genes.no_dupes.tsv
                • cosmic_tissue
                  • hg38
                    • cosmic_tissue.config
                    • cosmic_tissue.tsv
                  • hg19
                    • cosmic_tissue.config
                    • cosmic_tissue.tsv
                • gencode_xrefseq
                  • hg38
                    • gencode_xrefseq_v90_38.tsv
                    • gencode_xrefseq.config
                  • hg19
                    • gencode_xrefseq_v75_37.tsv
                    • gencode_xrefseq.config
                • dna_repair_genes
                  • hg38
                    • dnaRepairGenes.20171221T103938.csv
                    • dnaRepairGenes.config
                  • hg19
                    • dnaRepairGenes.20171221T103938.csv
                    • dnaRepairGenes.config
                • cosmic
                  • hg19
                    • cosmic.config
                    • CosmicTest.db
                • achilles
                  • hg38
                    • achilles.config
                    • achilles_lineage_results.import.txt
                  • hg19
                    • achilles.config
                    • achilles_lineage_results.import.txt
                • cosmic_fusion
                  • hg38
                    • cosmic_fusion.config
                    • cosmic_fusion.tsv
                  • hg19
                    • cosmic_fusion.config
                    • cosmic_fusion.tsv
                • dbSnp
                  • hg38
                    • dbSnp.regressionTestSet.hg38.vcf.gz
                    • dbSnp.regressionTestSet.hg38.vcf.gz.tbi
                    • dbSNP.config
                  • hg19
                    • dbSnp.regressionTestSet.hg19.vcf.gz
                    • dbSnp.regressionTestSet.hg19.vcf.gz.tbi
                    • dbSNP.config
              • gencode.v19.pc_transcripts.fasta
              • dummyDataSources.tar.gz
              • b37.2.tar.gz
              • e.coli_K12_MG1655.NC_000913.3.fasta.fai
              • e_coli_K12_MG1655.vcf
              • b37.3.tar.gz
              • GRCh37.p13.chr3.tar.gz
            • sv
              • CpxVariantReInterpreterSparkIntegrationTest_complex_assembly.bam
              • SVIntegrationTest_hg19.bam.bai
              • forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf
              • SVIntegrationTest_hg19_umap_s100.bed.gz.tbi
              • SVIntegrationTest_hg19_umap_s50.bed.gz.tbi
              • forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_1_seg.vcf
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam.bai
              • SVIntegrationTest_hg19_gaps.bed.gz.tbi
              • SVIntegrationTest_hg19.bam
              • SVIntegrationTest_hg19_umap_s50.bed.gz
              • SVIntegrationTest_hg19_umap_s100.bed.gz
              • SVIntegrationTest_hg19_gaps.bed.gz
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_cpx_reinterpreted_simple_multi_seg.vcf
              • CpxVariantReInterpreterSparkIntegrationTest_complex_assembly.bam.bai
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_NonComplex.vcf
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest.bam
              • forBND_SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_merged_simple.vcf
              • SvDiscoverFromLocalAssemblyContigAlignmentsSparkIntegrationTest_Complex.vcf
            • NA12878.alignedHg38.duplicateMarked.baseRealigned.bam.bai
            • expected.NA12878.RNAseq.splitNcigarReads.doNotFixOverhangs.bai
            • genotypes_r27_nr.b37_fwd.subset.vcf.idx
            • expected.NA12878.RNAseq.splitNcigarReads.bam
            • K-562.duplicateMarked.chr20.bai
            • ALL.20100201.chr20.subset.bc.sites.vcf
            • Homo_sapiens_assembly19.fasta.gz
            • Homo_sapiens_assembly38.fasta.gz.gzi
            • very-small-gnomad.vcf
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.tiny.unaligned.bam
            • VQSR
              • indelRecal.vcf
              • phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf.idx
              • g94982_20_1m_10m_python_2dcnn.indels.vcf.gz.tbi
              • g94982_contig_20_start_bamout.bam
              • resource_fofn_index_travis.txt
              • g94982_20_1m_10m_python_2dcnn.vcf.gz.tbi
              • snpRecal.vcf.idx
              • emptyB37.vcf
              • resource_fofn_travis_dbsnp.txt
              • g94982_b37_chr20_1m_10m.vcf.gz
              • cnn_ref_model
                • 1d_cnn_mix_train_full_bn.json
                • 1d_cnn_mix_train_full_bn.hd5
              • giab_na12878_confident_chr20_1m_10m.bed
              • indels.0.tranches
              • resource_fofn_travis.txt
              • combined.phase1.chr20.raw.indels.filtered.sites.1M-10M.vcf
              • dbsnp_132_b37.leftAligned.20.1M-10M.vcf.idx
              • g94982_b37_chr20_1m_895.vcf.gz
              • emptyB37.vcf.idx
              • snpTranches.scattered.2.txt
              • g94982_b37_chr20_1m_10m.vcf
              • g94982_b37_chr20_1m_895_bamout.bai
              • g94982_b37_chr20_1m_8m_bamout.bam
              • g94982_20_1m_10m_python_2dcnn.snps.vcf.gz
              • recalibrated_chr20_start.vcf
              • dbsnp_132_b37.leftAligned.20.1M-10M.vcf
              • combined.phase1.chr20.raw.indels.filtered.sites.1M-10M.vcf.idx
              • giab_chr20_1m_10m.vcf.gz.tbi
              • g94982_contig_20_start_bamout.bai
              • contig20_conf_1m_10m.interval_list
              • g94982_20_1m_10m_python_2dcnn.indels.vcf.gz
              • cnn_read_model
                • small_2d.hd5
                • small_2d.json
              • sites_r27_nr.b37_fwd.20.1M-10M.vcf
              • g94982_20_1m_10m_python_2dcnn.snps.vcf.gz.tbi
              • sites_r27_nr.b37_fwd.20.1M-10M.vcf.idx
              • ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf.idx
              • indels.1.tranches
              • g94982_b37_chr20_1m_10m.vcf.gz.tbi
              • g94982_b37_chr20_1m_895.vcf.gz.tbi
              • indelRecal.vcf.idx
              • g94982_b37_chr20_1m_10m.vcf.tbi
              • giab_chr20_1m_10m.vcf.gz
              • snpTranches.scattered.txt
              • g94982_b37_chr20_1m_8m_bamout.bai
              • chr1snippet.doctoredMQ.sites_only.vcf.gz
              • ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf
              • snpRecal.vcf
              • expected
                • snpSampledRecal.vcf
                • g94982_20_1m_10m_tranched_95_99_99.9.vcf
                • g94982_20_1m_10m_tranched_99_99.5.vcf
                • cnn_1d_contig20_1m_10m_expected.vcf
                • cnn_2d_chr20_subset_expected.vcf
                • chr20_tiny_tf_python_cpu.vcf
                • SNPDefaultTranches.txt
                • SNPAlternateTranches.txt
                • nn_outy2d.vcf
                • indelTranches.txt
                • expected.AS.recal.vcf.idx
                • cnn_1d_chr20_subset_expected.vcf
                • chr20_tiny_tf_python_gpu2.vcf
                • snpRecal.scattered.vcf
                • expected.AS.recal.vcf
                • anno_order.tranches
                • snpSampledTranches.txt
                • snpSampledRecal.vcf.idx
                • chrM.vcf
                • g94982_20_1m_10m_tranche_defaults.vcf
                • snpApplyResult.vcf
                • snpTranches.gathered.txt
                • g94982_20_1m_10m_tranched_99_with_old_filters.vcf
                • anno_order.recal
                • chr20_tiny_th_python_cpu.vcf
                • cnn_1d_contig20_1m_10m_expected.vcf.idx
                • indels.gathered.tranches
                • indelApplyResult.vcf
                • snpRecal.scattered.vcf.idx
                • chr20_tiny_th_python_gpu.vcf
              • Omni25_sites_1525_samples.b37.20.1M-10M.vcf.idx
              • phase1.projectConsensus.chr20.1M-10M.raw.snps.vcf
              • g94982_20_1m_10m_python_2dcnn.vcf.gz
              • contig20_1m_10m.interval_list
              • chr1snippet.doctoredMQ.sites_only.vcf.gz.tbi
              • Omni25_sites_1525_samples.b37.20.1M-10M.vcf
              • g94982_b37_chr20_1m_895_bamout.bam
              • resource_fofn_index_travis_dbsnp.txt
            • gencode.v19.LargeFile.gtf.idx
            • Mills_and_1000G_gold_standard.indels.b37.sites.chr20.vcf
            • dbsnp_138.b37.20.21.vcf.idx
            • Homo_sapiens_assembly19.dict
            • human_g1k_v37.20.21.fasta.gz.fai
            • expected.NA12878.RNAseq.splitNcigarReads.maxBasesInOverhang5.bai
            • Homo_sapiens_assembly38.20.21.fasta.fai
            • human_g1k_v37.20.21.fasta
            • very-small-gnomad.vcf.idx
            • snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf
            • Homo_sapiens_assembly19.fasta.gz.gzi
            • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram.bai
            • Homo_sapiens_assembly38.20.21.dict
            • genotypes_r27_nr.b37_fwd.subset.vcf
            • dbsnp_138.b37.20.21.vcf.blockgz.gz
            • Homo_sapiens_assembly38.20.21.fasta
            • expected.NA12878.RNAseq.splitNcigarReads.noSecondaryAlignments.bam
            • cnv_germline_workflows_test_files
              • segmental-duplication-20xy.bed.gz
              • Homo_sapiens_assembly19.truncated.fasta.fai
              • SM-74NEG_20xy-downsampled.bam.bai
              • contig_ploidy_priors_chr20xy.tsv
              • wes-do-gc-gcnv-model-1.tar.gz
              • SM-74P2T_20xy-downsampled.bam.bai
              • Homo_sapiens_assembly19.truncated.dict
              • segmental-duplication-20xy.bed.gz.tbi
              • SM-74P2T_20xy-downsampled.bam
              • Homo_sapiens_assembly19.truncated.fasta
              • umap-k100-single-read-mappability-merged-20xy.bed.gz
              • SM-74P35_20xy-downsampled.bam
              • SM-74P35_20xy-downsampled.bam.bai
              • ice_targets_chr20xy.interval_list
              • chr20xy.interval_list
              • umap-k100-single-read-mappability-merged-20xy.bed.gz.tbi
              • SM-74NEG_20xy-downsampled.bam
              • wes-do-gc-contig-ploidy-model.tar.gz
              • ice_targets_chr20xy.preprocessed.filtered.interval_list
              • wes-do-gc-gcnv-model-0.tar.gz
            • NA24385.vcf.gz
            • expected.K-562.splitNCigarReads.chr20.bam
            • whole_exome_illumina_coding_v1.Homo_sapiens_assembly19.targets.interval_list
            • dbsnp_138.b37.20.21.vcf
            • expected.NA12878.RNAseq.splitNcigarReads.subSequenceTest.bam
          • hg19micro.dict
          • wgs_calling_regions.v1.chr20_chr21.interval_list
          • fastaWithoutDict.fasta
          • Homo_sapiens_assembly19.dict
          • HSA19.dbsnp135.chr1_1M.exome_intervals.modified.vcf.idx
          • exampleGATKReportv2.tbl
          • empty_intervals.list
          • joint_calling.chr1_1M.1kg_samples.10samples.noINFO.vcf.idx
          • hg19mini.fasta
          • Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
          • small_unmerged_picard_intervals.interval_list
          • readgroupblacklisttest.txt
          • exampleFASTA.fasta
          • read_anonymizer_test.sam
          • org
            • broadinstitute
              • hellbender
                • utils
                  • SequenceDictionaryUtils
                    • test_variants_for_index.vcf.bgz.tbi
                    • test_variants_for_index.vcf.bgz
                    • test2.vcf
                    • test2.vcf.idx
                    • test.vcf.idx
                    • test.sorted.bam
                    • test.intervals
                    • test2.dict
                    • test.fasta.fai
                    • test2.fasta.fai
                    • test2.intervals
                    • test2.sorted.bam
                    • test2.fasta
                    • test.fasta
                    • test.sorted.bam.bai
                    • test_variants_for_index.vcf.idx
                    • test_variants_for_index.vcf
                    • test2.sorted.bam.bai
                    • test.dict
                    • test.vcf
                  • recalibration
                    • HiSeq.1mb.1RG.empty.table
                    • bqsr.manyObservations.full.table
                    • bqsr.manyObservations.piece.table
                  • samples
                    • SampleDB
                      • testtrio.ped
                    • SampleUtils
                      • emptySamples.samples
                      • overlapsWithSamples2.samples
                      • samples1.samples
                      • samples2.samples
                  • haplotype
                    • HaplotypeBAMWriter
                      • expected
                        • testSAM.sam
                        • fromHeaderSAM.sam
                        • testBAM.bam
                  • interval
                    • intervals_from_features_test.vcf
                    • example_intervals.list
                    • unrecognized_format_file.xyz
                    • intervals_from_features_test.bed
                    • intervals_from_features_test_exclude.vcf
                  • variant
                    • writers
                      • small.g.vcf
                  • test
                    • SamAssertionUtilsUnitTest
                      • valid.cram
                      • file1_reorder_PG_header_lines.sam
                      • file1_reorder_read_attributes.sam
                      • file1_different_cigar.sam
                      • file1_different_basequals.sam
                      • file1.bam
                      • file1_new_read_attribute.sam
                      • file1_different_position.sam
                      • file1.bam.bai
                      • file1_different_bases.sam
                      • file1_different_version.sam
                      • fake_cram_with_bam_contents.cram
                      • file1_missing_read_attribute.sam
                      • file1.sam
                      • file1_different_attributes.sam
                      • file1_different_mappingQ.sam
                  • hdf5
                    • wes-no-gc.pon.hdf5
                  • mcmc
                    • means-truth-for-gibbs-sampler-copy-ratio-test.txt
                    • number-of-targets-per-segment-for-gibbs-sampler-copy-ratio-test.txt
                    • coverages-for-gibbs-sampler-copy-ratio-test.txt
                  • config
                    • BasicTestConfigWithClassPathOverrides.properties
                    • TestGATKConfigOverrides.properties
                    • ChildClassConfig.properties
                    • AdditionalTestOverrides.properties
                  • spark
                    • reads_data_source_test1.bam.headerless.part-r-00000
                  • codecs
                    • xsvLocatableTable
                      • xsv_locatable_test4.config
                      • xsv_locatable_test3.csv
                      • xsv_locatable_test.config
                      • xsv_locatable_test_same_startend.csv
                      • xsv_locatable_test3.config
                      • xsv_locatable_test_error_mixed_preamble.tsv
                      • xsv_locatable_test_fails_decode_checks.config
                      • xsv_locatable_test_mixed_encodings.csv
                      • xsv_locatable_test_samfileheader_multiple_columns_no_name.config
                      • xsv_locatable_test_samfileheader.config
                      • xsv_locatable_test_samfileheader_no_name.config
                      • xsv_locatable_test2.config
                      • xsv_locatable_test4.csv
                      • xsv_locatable_test_samfileheader_error_nothing_found.config
                      • xsv_locatable_test_samfileheader_error_contig_equals_end.config
                      • xsv_locatable_test_error_mixed_preamble.config
                      • xsv_locatable_test_fails_decode_checks2.config
                      • xsv_locatable_test_samfileheader.tsv
                      • xsv_locatable_test_no_config.tsv
                      • xsv_locatable_test_samfileheader_error_contig_equals_start.config
                      • xsv_locatable_test2.tsv
                      • xsv_locatable_test_same_startend.config
                      • xsv_locatable_test.csv
                      • xsv_locatable_test_mixed_encodings.config
                      • xsv_locatable_test_same_startend_no_name.config
                      • xsv_locatable_test_samfileheader_multiple_columns.config
                    • gtf
                      • gencode.invalid_malformed_header_desc.gtf
                      • gencode.v19.valid_gencode_file2.gtf
                      • gencode.invalid_malformed_header_date.gtf
                      • gencode.valid1.gtf
                      • gencode.invalid_malformed_header_prov.gtf
                      • gencode.v19.valid1.gtf
                      • gencode.invalid_malformed_header_form.gtf
                      • gencode.v19.and.this.is.a.valid.one.too.gtf
                      • gencode.and.this.is.a.valid.one.too.table.gtf
                      • gencode.invalid_malformed_header_cont.gtf
                      • gencode.invalid_short_header.gtf
                      • gencode.valid_gencode_file2.gtf
                      • gencode.invalid_malformed_header.gtf
                  • io
                    • resource.properties
                    • IOUtils
                      • isEmpty.txt
                      • isTSV.hdf
                      • isTSV.tsv
                      • isValidHDF5.hdf5
                      • isValidHDF5.ext
                      • isTSV.hdf5
                    • testResourceFile.txt
                  • IndexUtils
                    • test_variants_for_index.vcf.bgz.tbi
                    • test_variants_for_index.vcf.bgz
                    • test_variants_for_index.newerThanIndex.vcf.idx
                    • test_variants_for_index.g.vcf.idx
                    • test_variants_for_index.g.vcf
                    • test_bed_for_index.bed
                    • test_variants_for_index.newerThanIndex.vcf
                    • test_variants_for_index.vcf.idx
                    • test_variants_for_index.vcf
                    • test_bed_for_index.bed.idx
                  • read
                    • comparator_test_with_unmapped.bam.bai
                    • ReadUtils
                      • print_reads.fasta.fai
                      • valid.cram
                      • query_sorted.bam
                      • print_reads.fasta
                      • valid.sam
                      • print_reads.sam
                      • coordinate_sorted.bam
                      • fake_cram_with_bam_contents.cram
                  • nio
                    • private_file.txt
                    • private_file_2.txt
                  • testing
                    • fileWithComments.txt
                    • fileWithNoComments.txt
                    • fileWithDifferentComments.txt
                • cmdline
                  • GATKPlugin
                    • changePluginPackages.properties
                • engine
                  • samtoolsSliceMD5WithAmbiguityCodesTest.cram
                  • GCSTests
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals_with_unmapped.bai
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_wholefile.bam
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals.bam
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_unmapped_only.bam
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_single_interval.bam
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_single_interval.bai
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_single_interval.vcf.idx
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals.bai
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_multiple_intervals.vcf
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_wholefile.vcf.idx
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_wholefile.bai
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_unmapped_only.bai
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_single_interval.vcf
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_wholefile.vcf
                    • expected_VariantWalkerGCSSupportIntegrationTest_vcf_multiple_intervals.vcf.idx
                    • expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals_with_unmapped.bam
                  • reads_data_source_test3.bam.bai
                  • CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam.bai
                  • expected_testFeaturesAsIntervals_output.txt
                  • feature_data_source_test_withSequenceDict.vcf.idx
                  • unindexed.vcf
                  • minimal_table_file.table
                  • unsupported_format_file
                  • testPGOnByDefault.bam
                  • CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.bam
                  • cramtestWrongRef.fasta.fai
                  • expected_ReadWalkerIntegrationTest_testManuallySpecifiedIndices.txt
                  • ambiguityCodes.fasta
                  • minimal_bed_file.bed
                  • invalid_coord_sort_order.sam
                  • MultiVariantWalkerGroupedOnStart
                    • gvcfExample1.copy.vcf
                    • gvcfExample2.copy.vcf
                    • gvcfExample2.vcf
                    • gvcfExample1.vcf
                    • gvcfExample1.vcf.idx
                    • gvcfExample3.vcf
                  • unindexed.bam
                  • minimal_vcf4_file.vcf
                  • cramtestWrongRef.dict
                  • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam
                  • reads_data_source_test1_with_unmapped.bam
                  • feature_data_source_test.vcf
                  • feature_data_source_test.wo-idx.vcf
                  • cram_with_bai_index.cram
                  • VariantWalkerTest_VariantsWithReads.bam.bai
                  • cram_with_crai_index.cram
                  • minimal_vcf3_file.vcf
                  • expected_testFeatureSupportUsingVCF_output.txt
                  • CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram.crai
                  • reads_data_source_test1_unmapped2.intervals
                  • example_variants_withSequenceDict.vcf
                  • reads_data_source_test2.bam
                  • feature_data_source_test_with_bigHeader.vcf
                  • example_variants_noSequenceDict.vcf.idx
                  • cramtest.sam
                  • Homo_sapiens_assembly38.headerOnly.vcf.gz
                  • feature_data_source_test_withSequenceDict.vcf
                  • CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam.bai
                  • reads_data_source_test2.bam.bai
                  • cram_with_bai_index.cram.bai
                  • example_features.bed
                  • cram_with_crai_index.cram.crai
                  • minimal_bcf_file.bcf.idx
                  • reads_data_source_test1.bam
                  • VariantWalkerTest_VariantsWithReads.bam
                  • spark
                    • datasources
                      • ReadsSparkSource
                        • hdfs_file_test.bam
                        • hdfs_file_test.bai
                      • ReadsSparkSink
                        • directoryWithNoPartFiles
                          • _SUCCESS
                        • fragments_test
                          • part-r-00000
                          • part-r-00002
                          • part-r-00003
                          • part-r-00001
                    • validNoDict.fasta
                  • feature_data_source_test_gvcf.vcf.idx
                  • reads_data_source_test1.bam.bai
                  • feature_data_source_test.vcf.idx
                  • 8_mutect2_sorted.vcf.gz
                  • minimal_bcf_file.bcf
                  • minimal_vcf3_file.vcf.idx
                  • Homo_sapiens_assembly38.headerOnly.vcf.gz.tbi
                  • reads_data_source_test1_with_unmapped.bam.bai
                  • lexicographically_sorted_dict.vcf
                  • minimal_bed_file.bed.idx
                  • readIndexTest
                    • indices
                      • reads_data_source_test2.bam.bai
                      • reads_data_source_test1.bam.bai
                    • reads_data_source_test2.bam
                    • reads_data_source_test1.bam
                  • ambiguityCodes.fasta.fai
                  • ambiguityCodes.dict
                  • expected_testFeaturesAsIntervalsWithExclusion_output.txt
                  • feature_data_source_test_gvcf.vcf
                  • vcf_with_genotypes.vcf
                  • reads_data_source_test4.xor.bam
                  • reads_data_source_test1_unmapped.intervals
                  • CEUTrio.HiSeq.WGS.b37.NA12878.snippet_with_unmapped.cram
                  • MultiVariantDataSource
                    • splitVariants_2.vcf.idx
                    • splitVariants_1.vcf
                    • splitVariants_1.vcf.idx
                    • splitVariants_2.vcf
                    • baseVariants.vcf
                    • interleavedVariants_1_NoDict.vcf
                    • interleavedVariants_1.vcf
                    • interleavedVariants_2.vcf
                    • interleavedVariants_1_WithOverlap.vcf
                    • interleavedVariants_2.vcf.idx
                    • interleavedVariants_1_WithOverlap.vcf.idx
                    • interleavedVariants_2_NoDict.vcf
                    • baseVariantsAlternateDictionary.vcf
                    • baseVariantsConflictingDictionary.vcf
                    • interleavedVariants_2_WithOverlap.vcf.idx
                    • interleavedVariants_2_WithOverlap.vcf
                    • interleavedVariants_1.vcf.idx
                    • baseVariants.vcf.idx
                  • example_features.bed.idx
                  • minimal_vcf4_file.vcf.idx
                  • VariantWalkerTest_VariantsWithReads.vcf
                  • GenomicsDBIntegration
                    • tiny.g.vcf.idx
                    • intervalsRestrictedExpected.g.vcf
                    • tiny.g.vcf
                  • reads_data_source_test3.bam
                  • example_variants_withSequenceDict.vcf.idx
                  • reads_data_source_test4.xor.bam.bai
                  • cramtestWrongRef.fasta
                  • cramtest.cram
                  • FeatureInput
                    • vcfWithOutIndex.vcf
                    • vcfWithIndex.vcf.idx
                    • vcfWithIndex.vcf
                  • example_variants_noSequenceDict.vcf
                • tools
                  • valid.dict
                  • valid.fasta
                  • count_reads.cram
                  • expected.AnalyzeCovariatesIntegrationTest.csv.gz
                  • copynumber
                    • model-segments-wes-tumor-denoised-copy-ratios-SM-74P4M-v1-chr20-downsampled.deduplicated.denoisedCR.tsv
                    • annotate-intervals-hg19-segmental-duplication-20-21.bed.gz.tbi
                    • annotate-intervals-hg19-segmental-duplication-20-21-with-overlaps.bed.gz.tbi
                    • utils
                      • tag-germline-tumor-some-match-normal.seg
                      • combine-segment-breakpoints-alt-samheader.seg
                      • tag-germline-tumor-all-match-normal.seg
                      • combine-segment-breakpoints-comparison-no-samheader.seg
                      • combine-segment-breakpoints-comparison-ucsc-track.seg
                      • annotatedinterval
                        • annotated-interval-many-columns.seg
                        • annotated-interval-collection-named-cols.config
                        • annotated-interval-collection-index-cols.config
                        • annotated-interval-alt-samheader.seg
                        • old-header.config
                        • simple-annotated-interval-writer-replacement-header-comments.seg
                      • combine-segment-breakpoints-comparison-recapseg.seg
                      • combine-segment-breakpoints-comparison-jabba.seg
                      • tag-germline-header-normal.seg
                      • combine-segment-breakpoints-different-annotation-headers.seg
                      • merge-annotated-regions-simple-test.seg
                      • combine-segment-breakpoints-no-samheader.seg
                      • combine-segment-breakpoints-comparison-pcawg-consensus.seg
                      • tag-germline-no-match-normal.seg
                      • combine-segment-breakpoints-comparison-oncotator-gene-list.seg
                      • combine-segment-breakpoints-comparison.seg
                      • annotate-intervals-hg19-umap-k100-single-read-mappability-NaN-20-21.bed.gz
                      • merge-annotated-regions-by-annotation-legacy-test.seg
                      • tag-germline-tumor-split-some-match-normal.seg
                      • combine-segment-breakpoints.seg
                      • tag-germline-tumor-split-no-match-normal.seg
                      • combine-segment-breakpoints-comparison-pcawg-consensus-expected.seg
                      • combine-segment-breakpoints-comparison-ucsc-track-expected.seg
                      • combine-segment-breakpoints-comparison-jabba-expected.seg
                    • annotate-intervals-hg19-segmental-duplication-20-21.bed.gz
                    • call-copy-ratio-segments-segments.seg
                    • model-segments-wes-normal-allelic-counts-with-missing-sites.allelicCounts.tsv
                    • preprocess-intervals-test.interval_list
                    • denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5
                    • annotate-intervals-hg19-umap-k100-single-read-mappability-merged-20-21.bed.gz
                    • collect-read-counts-NA12878.bam.bai
                    • model-segments-wes-normal-allelic-counts-SM-74NEG-v1-chr20-downsampled.deduplicated.allelicCounts.tsv
                    • collect-allelic-counts-tumor.bam
                    • model-segments-wes-tumor-denoised-copy-ratios-with-sample-name-mismatch.denoisedCR.tsv
                    • gcnv-postprocess
                      • denoised_copy_ratios_SAMPLE_002.tsv
                      • intervals_output_SAMPLE_001.vcf
                      • shard_1-calls
                        • calling_config.json
                        • SAMPLE_2
                          • std_read_depth_s_log__.tsv
                          • log_c_emission_tc.tsv
                          • mu_psi_s_log__.tsv
                          • mu_z_su.tsv
                          • std_z_su.tsv
                          • log_q_c_tc.tsv
                          • std_denoised_copy_ratio_t.tsv
                          • mu_denoised_copy_ratio_t.tsv
                          • mu_read_depth_s_log__.tsv
                          • baseline_copy_number_t.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • SAMPLE_1
                          • std_read_depth_s_log__.tsv
                          • log_c_emission_tc.tsv
                          • mu_psi_s_log__.tsv
                          • mu_z_su.tsv
                          • std_z_su.tsv
                          • log_q_c_tc.tsv
                          • std_denoised_copy_ratio_t.tsv
                          • mu_denoised_copy_ratio_t.tsv
                          • mu_read_depth_s_log__.tsv
                          • baseline_copy_number_t.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • interval_list.tsv
                        • denoising_config.json
                        • SAMPLE_0
                          • std_read_depth_s_log__.tsv
                          • log_c_emission_tc.tsv
                          • mu_psi_s_log__.tsv
                          • mu_z_su.tsv
                          • std_z_su.tsv
                          • log_q_c_tc.tsv
                          • std_denoised_copy_ratio_t.tsv
                          • mu_denoised_copy_ratio_t.tsv
                          • mu_read_depth_s_log__.tsv
                          • baseline_copy_number_t.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • gcnvkernel_version.json
                      • shard_2-model
                        • mu_ard_u_log__.tsv
                        • mu_W_tu.tsv
                        • calling_config.json
                        • std_log_mean_bias_t.tsv
                        • std_ard_u_log__.tsv
                        • mu_log_mean_bias_t.tsv
                        • interval_list.tsv
                        • denoising_config.json
                        • log_q_tau_tk.tsv
                        • gcnvkernel_version.json
                        • std_psi_t_log__.tsv
                        • std_W_tu.tsv
                        • mu_psi_t_log__.tsv
                      • denoised_copy_ratios_SAMPLE_000.tsv
                      • shard_1-model
                        • mu_ard_u_log__.tsv
                        • mu_W_tu.tsv
                        • calling_config.json
                        • std_log_mean_bias_t.tsv
                        • std_ard_u_log__.tsv
                        • mu_log_mean_bias_t.tsv
                        • interval_list.tsv
                        • denoising_config.json
                        • log_q_tau_tk.tsv
                        • gcnvkernel_version.json
                        • std_psi_t_log__.tsv
                        • std_W_tu.tsv
                        • mu_psi_t_log__.tsv
                      • segments_output_SAMPLE_002.vcf
                      • ploidy-calls
                        • SAMPLE_2
                          • mu_psi_s_log__.tsv
                          • global_read_depth.tsv
                          • contig_ploidy.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • SAMPLE_1
                          • mu_psi_s_log__.tsv
                          • global_read_depth.tsv
                          • contig_ploidy.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • SAMPLE_0
                          • mu_psi_s_log__.tsv
                          • global_read_depth.tsv
                          • contig_ploidy.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                      • segments_output_SAMPLE_000.vcf
                      • shard_2-calls
                        • calling_config.json
                        • SAMPLE_2
                          • std_read_depth_s_log__.tsv
                          • log_c_emission_tc.tsv
                          • mu_psi_s_log__.tsv
                          • mu_z_su.tsv
                          • std_z_su.tsv
                          • log_q_c_tc.tsv
                          • std_denoised_copy_ratio_t.tsv
                          • mu_denoised_copy_ratio_t.tsv
                          • mu_read_depth_s_log__.tsv
                          • baseline_copy_number_t.tsv
                          • sample_name.txt
                          • std_psi_s_log__.tsv
                        • SAMPLE_1
                          • std_read_depth_s_log__.tsv
                          • log_c_emission_tc.tsv