├── .github └── workflows │ └── static.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── installer ├── README.txt ├── ReleaseNotes.txt ├── resources │ ├── common │ │ └── scripts │ │ │ ├── GRCh37.example.reference.txt │ │ │ ├── GRCh38.example.reference.txt │ │ │ ├── hg18.example.reference.txt │ │ │ ├── hg19.example.reference.txt │ │ │ └── rtg-bash-completion │ └── tools │ │ ├── RTGOperationsManual.pdf │ │ ├── RTGOperationsManual │ │ ├── _images │ │ │ ├── ceph-1463.png │ │ │ ├── chinese-trio.png │ │ │ ├── math │ │ │ │ ├── 67e012a427a90dc0c0f8a2d5939a95e5f6ffe591.png │ │ │ │ ├── 6c754ae3fc49dc56e236eb95ef00cfdcad3df594.png │ │ │ │ ├── 888f7c323ac0341871e867220ae2d76467d74d6e.png │ │ │ │ ├── b6f66d1803a9dcb5f12f25c57d4e43fb6584ca7e.png │ │ │ │ ├── b81c7a12342c0ee157b2c3f1bcfc4f91642187dc.png │ │ │ │ └── f13fefe97363643ae6879e8f163616d0cf50ab3f.png │ │ │ ├── rocplot_ps.png │ │ │ └── rocplot_roc.png │ │ ├── _sources │ │ │ ├── administration.rst.txt │ │ │ ├── appendix.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── overview.rst.txt │ │ │ ├── product_usage.rst.txt │ │ │ └── rtg_command_reference.rst.txt │ │ ├── _static │ │ │ ├── background_b01.png │ │ │ ├── basic.css │ │ │ ├── bizstyle.css │ │ │ ├── bizstyle.js │ │ │ ├── css3-mediaqueries.js │ │ │ ├── doctools.js │ │ │ ├── documentation_options.js │ │ │ ├── file.png │ │ │ ├── html_logo.png │ │ │ ├── language_data.js │ │ │ ├── latex_logo.png │ │ │ ├── minus.png │ │ │ ├── plus.png │ │ │ ├── pygments.css │ │ │ ├── searchtools.js │ │ │ └── sphinx_highlight.js │ │ ├── administration.html │ │ ├── appendix.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── overview.html │ │ ├── product_usage.html │ │ ├── rtg_command_reference.html │ │ ├── search.html │ │ └── searchindex.js │ │ └── scripts │ │ ├── README.txt │ │ └── demo-tools.sh ├── rtg └── rtg.bat ├── lib ├── RPlot.jar ├── asm-7.3.1.jar ├── asm-analysis-7.3.1.jar ├── asm-commons-7.3.1.jar ├── asm-tree-7.3.1.jar ├── asm-util-7.3.1.jar ├── commons-collections-3.2.1.jar ├── commons-compress-1.4.1.jar ├── commons-lang-2.4.jar ├── findbugs-annotations.jar ├── findbugs-jsr305.jar ├── gzipfix.jar ├── json-simple-1.1.1.jar ├── jumble-annotations.jar ├── nashorn-core-15.4.jar ├── sam-rtg-2.23.0.1-src.jar ├── sam-rtg-2.23.0.1.jar ├── snappy-java-1.1.4.jar ├── velocity-1.7.jar └── velocity-tools-generic.jar ├── rocplot-screencap.gif ├── src ├── main │ ├── java │ │ └── com │ │ │ └── rtg │ │ │ ├── AbstractCliEntry.java │ │ │ ├── Command.java │ │ │ ├── CommandCategory.java │ │ │ ├── CommandLookup.java │ │ │ ├── HelpCommand.java │ │ │ ├── LicenseCommand.java │ │ │ ├── ReleaseLevel.java │ │ │ ├── RtgTools.java │ │ │ ├── ToolsCommand.java │ │ │ ├── VersionCommand.java │ │ │ ├── alignment │ │ │ ├── ActionsHelper.java │ │ │ ├── ActionsValidator.java │ │ │ ├── GotohEditDistance.java │ │ │ ├── Partition.java │ │ │ ├── Slice.java │ │ │ ├── SplitAlleles.java │ │ │ └── UnidirectionalEditDistance.java │ │ │ ├── bed │ │ │ ├── BedHeader.java │ │ │ ├── BedRangeLoader.java │ │ │ ├── BedReader.java │ │ │ ├── BedRecord.java │ │ │ ├── BedUtils.java │ │ │ ├── BedWriter.java │ │ │ ├── NamedBedRangeLoader.java │ │ │ └── SimpleBedRangeLoader.java │ │ │ ├── graph │ │ │ ├── DataBundle.java │ │ │ ├── ParseRocFile.java │ │ │ ├── ProgressBarDelegate.java │ │ │ ├── ProgressDelegate.java │ │ │ ├── RocLinePanel.java │ │ │ ├── RocLinesPanel.java │ │ │ ├── RocPlot.java │ │ │ ├── RocPlotCli.java │ │ │ ├── RocPlotPalettes.java │ │ │ ├── RocPlotSettings.java │ │ │ └── RocPlotToFile.java │ │ │ ├── jmx │ │ │ ├── DiskStats.java │ │ │ ├── ExternalCommand.java │ │ │ ├── LocalStats.java │ │ │ ├── MBeanStats.java │ │ │ ├── MonStats.java │ │ │ ├── MonUtils.java │ │ │ ├── NetworkStats.java │ │ │ ├── ProgressStats.java │ │ │ └── RecordStats.java │ │ │ ├── launcher │ │ │ ├── AbstractCli.java │ │ │ ├── AbstractStatistics.java │ │ │ ├── CommandLineFiles.java │ │ │ ├── CommonFlags.java │ │ │ ├── LoggedCli.java │ │ │ ├── ModuleParams.java │ │ │ ├── NoStatistics.java │ │ │ ├── OutputDirParams.java │ │ │ ├── OutputModuleParams.java │ │ │ ├── OutputParams.java │ │ │ ├── ParamsCli.java │ │ │ ├── ParamsTask.java │ │ │ ├── ReaderParams.java │ │ │ ├── Statistics.java │ │ │ └── globals │ │ │ │ ├── GlobalFlags.java │ │ │ │ ├── GlobalFlagsInitializer.java │ │ │ │ └── ToolsGlobalFlags.java │ │ │ ├── mode │ │ │ ├── BidirectionalFrame.java │ │ │ ├── DNA.java │ │ │ ├── DNAFastaSymbolTable.java │ │ │ ├── DNARange.java │ │ │ ├── DNARangeAT.java │ │ │ ├── DNARangeNAT.java │ │ │ ├── DNASimple.java │ │ │ ├── DnaUtils.java │ │ │ ├── FastaSymbolTable.java │ │ │ ├── Frame.java │ │ │ ├── GeneralDNARange.java │ │ │ ├── IllegalBaseException.java │ │ │ ├── Protein.java │ │ │ ├── ProteinFastaSymbolTable.java │ │ │ ├── ProteinFrame.java │ │ │ ├── ProteinScoringMatrix.java │ │ │ ├── Residue.java │ │ │ ├── ScoringMatrix.java │ │ │ ├── SequenceMode.java │ │ │ ├── SequenceType.java │ │ │ ├── TranslatedFrame.java │ │ │ └── UnidirectionalFrame.java │ │ │ ├── reader │ │ │ ├── AbstractAsyncChunkWriter.java │ │ │ ├── AbstractSdfWriter.java │ │ │ ├── AbstractSequencesReader.java │ │ │ ├── AbstractStreamManager.java │ │ │ ├── AlternatingSequencesReader.java │ │ │ ├── AlternatingSequencesWriter.java │ │ │ ├── AnnotatedSequencesReader.java │ │ │ ├── Arm.java │ │ │ ├── ArrayNames.java │ │ │ ├── AsyncFastqSequenceWriter.java │ │ │ ├── Batch.java │ │ │ ├── BatchProcessor.java │ │ │ ├── BatchReorderingWriter.java │ │ │ ├── BestSumReadTrimmer.java │ │ │ ├── BlockingExecutor.java │ │ │ ├── CachingSequencesReader.java │ │ │ ├── Cg2Sdf.java │ │ │ ├── CgSamBamSequenceDataSource.java │ │ │ ├── CgSequenceDataSource.java │ │ │ ├── CgUtils.java │ │ │ ├── CompressedMemorySequencesReader.java │ │ │ ├── CompressedMemorySequencesReader2.java │ │ │ ├── CompressedMemorySequencesWriter.java │ │ │ ├── CompressedSequenceFilePair.java │ │ │ ├── ConcatSequenceDataSource.java │ │ │ ├── CorruptSdfException.java │ │ │ ├── DataFileIndex.java │ │ │ ├── DataFileOpener.java │ │ │ ├── DataFileOpenerFactory.java │ │ │ ├── DataInMemory.java │ │ │ ├── DataSourceDescription.java │ │ │ ├── DefaultReadTrimmer.java │ │ │ ├── DefaultSequencesIterator.java │ │ │ ├── DefaultSequencesReader.java │ │ │ ├── EmptyStringNames.java │ │ │ ├── FastaSequenceDataSource.java │ │ │ ├── FastaUtils.java │ │ │ ├── FastaWriter.java │ │ │ ├── FastaWriterWrapper.java │ │ │ ├── FastqIterator.java │ │ │ ├── FastqSequence.java │ │ │ ├── FastqSequenceDataSource.java │ │ │ ├── FastqTrim.java │ │ │ ├── FastqTrimProcessor.java │ │ │ ├── FastqUtils.java │ │ │ ├── FastqWriter.java │ │ │ ├── FastqWriterWrapper.java │ │ │ ├── FileBitwiseInputStream.java │ │ │ ├── FileBitwiseOutputStream.java │ │ │ ├── FileCompressedInputStream.java │ │ │ ├── FileCompressedOutputStream.java │ │ │ ├── FileStreamIterator.java │ │ │ ├── FirstBasesReadTrimmer.java │ │ │ ├── FormatCli.java │ │ │ ├── FullReadTrimmer.java │ │ │ ├── IndexFile.java │ │ │ ├── Label.java │ │ │ ├── LabelStreamManager.java │ │ │ ├── LastBasesReadTrimmer.java │ │ │ ├── MappedSamBamSequenceDataSource.java │ │ │ ├── MinLengthReadTrimmer.java │ │ │ ├── MultiReadTrimmer.java │ │ │ ├── NameDuplicateDetector.java │ │ │ ├── NameFilePair.java │ │ │ ├── NameWrapperFilter.java │ │ │ ├── Names.java │ │ │ ├── NamesInterface.java │ │ │ ├── NormalSequenceFilePair.java │ │ │ ├── NullReadTrimmer.java │ │ │ ├── PointerFileHandler.java │ │ │ ├── PointerFileLookup.java │ │ │ ├── PrereadArm.java │ │ │ ├── PrereadHashFunction.java │ │ │ ├── PrereadType.java │ │ │ ├── QualityFormat.java │ │ │ ├── ReadHelper.java │ │ │ ├── ReadTrimmer.java │ │ │ ├── ReaderUtils.java │ │ │ ├── ReverseComplementReadTrimmer.java │ │ │ ├── ReverseComplementingReader.java │ │ │ ├── RightSimpleNames.java │ │ │ ├── RollingIndex.java │ │ │ ├── SamBamSequenceDataSource.java │ │ │ ├── SamSequence.java │ │ │ ├── SamWriterWrapper.java │ │ │ ├── Sdf2Cg.java │ │ │ ├── Sdf2Fasta.java │ │ │ ├── Sdf2Fastq.java │ │ │ ├── Sdf2Quala.java │ │ │ ├── Sdf2Sam.java │ │ │ ├── SdfFileUtils.java │ │ │ ├── SdfId.java │ │ │ ├── SdfReaderWrapper.java │ │ │ ├── SdfSplitter.java │ │ │ ├── SdfStatistics.java │ │ │ ├── SdfSubseq.java │ │ │ ├── SdfSubset.java │ │ │ ├── SdfUtils.java │ │ │ ├── SdfVerifier.java │ │ │ ├── SdfWriter.java │ │ │ ├── SdfWriterWrapper.java │ │ │ ├── SequenceDataLoader.java │ │ │ ├── SequenceDataSource.java │ │ │ ├── SequenceFilePair.java │ │ │ ├── SequenceStreamManager.java │ │ │ ├── SequenceWriter.java │ │ │ ├── SequencesIterator.java │ │ │ ├── SequencesReader.java │ │ │ ├── SequencesReaderFactory.java │ │ │ ├── SequencesReaderReferenceSource.java │ │ │ ├── SequencesWriter.java │ │ │ ├── SimpleNames.java │ │ │ ├── SourceFormat.java │ │ │ ├── SourceTemplateReadWriter.java │ │ │ ├── TaxidWrapperFilter.java │ │ │ ├── TsvSequenceDataSource.java │ │ │ ├── TsvWriterWrapper.java │ │ │ ├── WrapperFilter.java │ │ │ ├── WriterWrapper.java │ │ │ └── package.html │ │ │ ├── reference │ │ │ ├── GenerateReferenceManifest.java │ │ │ ├── Ploidy.java │ │ │ ├── ReferenceDetector.java │ │ │ ├── ReferenceGenome.java │ │ │ ├── ReferenceManifest.java │ │ │ ├── ReferenceParse.java │ │ │ ├── ReferenceSequence.java │ │ │ ├── ReferenceTextBuilder.java │ │ │ ├── Sex.java │ │ │ └── SexMemo.java │ │ │ ├── relation │ │ │ ├── ChildFamilyLookup.java │ │ │ ├── Family.java │ │ │ ├── GenomeRelationships.java │ │ │ ├── LineageLookup.java │ │ │ ├── MultiFamilyOrdering.java │ │ │ ├── PedFileParser.java │ │ │ ├── PedFilterCli.java │ │ │ ├── PedStatsCli.java │ │ │ ├── PedigreeException.java │ │ │ ├── Relationship.java │ │ │ ├── RelationshipsFileParser.java │ │ │ └── VcfPedigreeParser.java │ │ │ ├── report │ │ │ ├── ReportUtils.java │ │ │ ├── RtgVelocityLogChute.java │ │ │ └── VelocityReportUtils.java │ │ │ ├── sam │ │ │ ├── AbstractSamRecordIterator.java │ │ │ ├── BadSuperCigarException.java │ │ │ ├── BamIndexMerge.java │ │ │ ├── BamIndexReader.java │ │ │ ├── BamIndexer.java │ │ │ ├── BamReader.java │ │ │ ├── BgzfInputStream.java │ │ │ ├── DefaultSamFilter.java │ │ │ ├── DuplicateSamFilter.java │ │ │ ├── FlushLocus.java │ │ │ ├── ForcedInitialiser.java │ │ │ ├── MappedParams.java │ │ │ ├── MateInfo.java │ │ │ ├── NoneFilter.java │ │ │ ├── ReadGroupUtils.java │ │ │ ├── ReaderRecord.java │ │ │ ├── ReaderWindow.java │ │ │ ├── RecordCounter.java │ │ │ ├── RecordIterator.java │ │ │ ├── SamBamBaseFile.java │ │ │ ├── SamBamConstants.java │ │ │ ├── SamBamReader.java │ │ │ ├── SamBamRecord.java │ │ │ ├── SamBamRecordImpl.java │ │ │ ├── SamClosedFileReader.java │ │ │ ├── SamCommandHelper.java │ │ │ ├── SamCompareUtils.java │ │ │ ├── SamFileAndRecord.java │ │ │ ├── SamFileReaderAdaptor.java │ │ │ ├── SamFilter.java │ │ │ ├── SamFilterChain.java │ │ │ ├── SamFilterIterator.java │ │ │ ├── SamFilterOptions.java │ │ │ ├── SamFilterParams.java │ │ │ ├── SamMultiRestrictingIterator.java │ │ │ ├── SamOutput.java │ │ │ ├── SamRangeUtils.java │ │ │ ├── SamReadingContext.java │ │ │ ├── SamRecordException.java │ │ │ ├── SamRegionRestriction.java │ │ │ ├── SamRestrictingIterator.java │ │ │ ├── SamUtils.java │ │ │ ├── SimpleRecordCounter.java │ │ │ ├── SingleMappedParams.java │ │ │ ├── SkipInvalidRecordsIterator.java │ │ │ └── SmartSamWriter.java │ │ │ ├── simulation │ │ │ ├── DistributionSampler.java │ │ │ ├── GaussianSampler.java │ │ │ ├── IntSampler.java │ │ │ ├── SimulationUtils.java │ │ │ ├── genome │ │ │ │ ├── GenomeSimulator.java │ │ │ │ ├── RandomDistribution.java │ │ │ │ └── SequenceGenerator.java │ │ │ ├── reads │ │ │ │ ├── AbstractIlluminaMachine.java │ │ │ │ ├── AbstractMachine.java │ │ │ │ ├── CgSimCli.java │ │ │ │ ├── CompleteGenomicsMachine.java │ │ │ │ ├── CompleteGenomicsV1Machine.java │ │ │ │ ├── CompleteGenomicsV2Machine.java │ │ │ │ ├── ErrorMachine.java │ │ │ │ ├── FastaReadWriter.java │ │ │ │ ├── FastqReadWriter.java │ │ │ │ ├── FilteringFragmenter.java │ │ │ │ ├── FourFiveFourPairedEndMachine.java │ │ │ │ ├── FourFiveFourSingleEndMachine.java │ │ │ │ ├── FragmentTooSmallException.java │ │ │ │ ├── GenomeFragmenter.java │ │ │ │ ├── IlluminaPairedEndMachine.java │ │ │ │ ├── IlluminaSingleEndMachine.java │ │ │ │ ├── IonTorrentSingleEndMachine.java │ │ │ │ ├── Machine.java │ │ │ │ ├── MinMaxGaussianSampler.java │ │ │ │ ├── ReadSimCli.java │ │ │ │ ├── ReadSimCliValidator.java │ │ │ │ ├── ReadWriter.java │ │ │ │ ├── SdfReadWriter.java │ │ │ │ ├── SingleEndRandomLengthMachine.java │ │ │ │ ├── TaxonomyDistribution.java │ │ │ │ └── UnknownBaseReadWriter.java │ │ │ └── variants │ │ │ │ ├── ChildSampleSimulator.java │ │ │ │ ├── ChildSampleSimulatorCli.java │ │ │ │ ├── CrossoverSelector.java │ │ │ │ ├── DeNovoSampleSimulator.java │ │ │ │ ├── DeNovoSampleSimulatorCli.java │ │ │ │ ├── FixedStepPopulationVariantGenerator.java │ │ │ │ ├── FixedStepPopulationVariantGeneratorCli.java │ │ │ │ ├── Mutator.java │ │ │ │ ├── MutatorResult.java │ │ │ │ ├── MutatorSingle.java │ │ │ │ ├── PedSampleSimulatorCli.java │ │ │ │ ├── PopulationMutatorPriors.java │ │ │ │ ├── PopulationVariantGenerator.java │ │ │ │ ├── PopulationVariantSimulatorCli.java │ │ │ │ ├── PriorPopulationVariantGenerator.java │ │ │ │ ├── SampleReplayer.java │ │ │ │ ├── SampleReplayerCli.java │ │ │ │ ├── SampleSimulator.java │ │ │ │ └── SampleSimulatorCli.java │ │ │ ├── tabix │ │ │ ├── AbstractIndexReader.java │ │ │ ├── AbstractPositionReader.java │ │ │ ├── AlleleCountsPositionReader.java │ │ │ ├── BgZip.java │ │ │ ├── BlockCompressedLineReader.java │ │ │ ├── BlockCompressedPositionReader.java │ │ │ ├── BrLineReader.java │ │ │ ├── ExtractCli.java │ │ │ ├── GenericPositionReader.java │ │ │ ├── IndexUtils.java │ │ │ ├── IndexerCli.java │ │ │ ├── IndexingStreamCreator.java │ │ │ ├── LineReader.java │ │ │ ├── LocusIndex.java │ │ │ ├── SamPositionReader.java │ │ │ ├── SequenceIndex.java │ │ │ ├── SequenceIndexContainer.java │ │ │ ├── TabixHeader.java │ │ │ ├── TabixIndexMerge.java │ │ │ ├── TabixIndexReader.java │ │ │ ├── TabixIndexer.java │ │ │ ├── TabixLineReader.java │ │ │ ├── UnindexableDataException.java │ │ │ ├── VcfPositionReader.java │ │ │ └── VirtualOffsets.java │ │ │ ├── taxonomy │ │ │ ├── SequenceToTaxonIds.java │ │ │ ├── TaxonNode.java │ │ │ ├── Taxonomy.java │ │ │ └── TaxonomyUtils.java │ │ │ ├── usage │ │ │ ├── FileUsageLoggingClient.java │ │ │ ├── HttpUsageLoggingClient.java │ │ │ ├── NullUsageLoggingClient.java │ │ │ ├── UsageConfiguration.java │ │ │ ├── UsageLogging.java │ │ │ ├── UsageLoggingClient.java │ │ │ ├── UsageMessage.java │ │ │ ├── UsageMetric.java │ │ │ ├── UsageServer.java │ │ │ └── UsageServerCli.java │ │ │ ├── util │ │ │ ├── AutoAddMap.java │ │ │ ├── BasicLinkedListNode.java │ │ │ ├── BasicLinkedListNodeIterator.java │ │ │ ├── ByteUtils.java │ │ │ ├── ChiSquared.java │ │ │ ├── ChooseMemory.java │ │ │ ├── ClassPathScanner.java │ │ │ ├── CompareHelper.java │ │ │ ├── Constants.java │ │ │ ├── ContingencyTable.java │ │ │ ├── Counter.java │ │ │ ├── DoubleCounter.java │ │ │ ├── DoubleMultiSet.java │ │ │ ├── EnumHelper.java │ │ │ ├── Environment.java │ │ │ ├── GeneralParser.java │ │ │ ├── Histogram.java │ │ │ ├── HistogramWithNegatives.java │ │ │ ├── HtmlReportHelper.java │ │ │ ├── IORunnable.java │ │ │ ├── IORunnableProxy.java │ │ │ ├── IntegerOrPercentage.java │ │ │ ├── InvalidParamsException.java │ │ │ ├── License.java │ │ │ ├── LongCounter.java │ │ │ ├── LongMultiSet.java │ │ │ ├── MD5Utils.java │ │ │ ├── MathUtils.java │ │ │ ├── MultiMap.java │ │ │ ├── MultiMapFactory.java │ │ │ ├── MultiSet.java │ │ │ ├── NullStreamUtils.java │ │ │ ├── ObjectParams.java │ │ │ ├── Pair.java │ │ │ ├── Params.java │ │ │ ├── ParamsBuilder.java │ │ │ ├── Permutation.java │ │ │ ├── PortableRandom.java │ │ │ ├── PosteriorUtils.java │ │ │ ├── ProgramState.java │ │ │ ├── PropertiesUtils.java │ │ │ ├── PseudoEnum.java │ │ │ ├── QuickSort.java │ │ │ ├── QuickSortDoubleIntProxy.java │ │ │ ├── QuickSortIntIntProxy.java │ │ │ ├── QuickSortLongLongProxy.java │ │ │ ├── ReorderingQueue.java │ │ │ ├── Resources.java │ │ │ ├── RstTable.java │ │ │ ├── SimpleThreadPool.java │ │ │ ├── SpawnJvm.java │ │ │ ├── StringUtils.java │ │ │ ├── TextTable.java │ │ │ ├── TsvParser.java │ │ │ ├── Utils.java │ │ │ ├── WorkerThread.java │ │ │ ├── arithcode │ │ │ │ ├── ArithCodeModel.java │ │ │ │ ├── ArithCoder.java │ │ │ │ ├── ArithDecoder.java │ │ │ │ ├── ArithEncoder.java │ │ │ │ ├── ArithModelBuilder.java │ │ │ │ ├── DetailedModel.java │ │ │ │ ├── Input.java │ │ │ │ ├── InputBytes.java │ │ │ │ ├── Order0ModelBuilder.java │ │ │ │ ├── Output.java │ │ │ │ ├── OutputBytes.java │ │ │ │ ├── StaticModel.java │ │ │ │ └── UniformModel.java │ │ │ ├── array │ │ │ │ ├── AbstractIndex.java │ │ │ │ ├── ArrayHandle.java │ │ │ │ ├── ArrayType.java │ │ │ │ ├── ArrayUtils.java │ │ │ │ ├── CommonIndex.java │ │ │ │ ├── ExtensibleIndex.java │ │ │ │ ├── ImmutableIntArray.java │ │ │ │ ├── IndexSorter.java │ │ │ │ ├── IndexType.java │ │ │ │ ├── SingleValueIntArray.java │ │ │ │ ├── Swapper.java │ │ │ │ ├── WrappedIntArray.java │ │ │ │ ├── atomic │ │ │ │ │ ├── AtomicIndex.java │ │ │ │ │ ├── AtomicIntChunks.java │ │ │ │ │ └── AtomicLongChunks.java │ │ │ │ ├── bitindex │ │ │ │ │ ├── BitCreate.java │ │ │ │ │ └── BitIndex.java │ │ │ │ ├── byteindex │ │ │ │ │ ├── ByteArray.java │ │ │ │ │ ├── ByteChunks.java │ │ │ │ │ ├── ByteCreate.java │ │ │ │ │ ├── ByteIndex.java │ │ │ │ │ └── package.html │ │ │ │ ├── intindex │ │ │ │ │ ├── IntArray.java │ │ │ │ │ ├── IntChunks.java │ │ │ │ │ ├── IntCreate.java │ │ │ │ │ ├── IntIndex.java │ │ │ │ │ └── package.html │ │ │ │ ├── longindex │ │ │ │ │ ├── LongArray.java │ │ │ │ │ ├── LongChunks.java │ │ │ │ │ ├── LongCreate.java │ │ │ │ │ ├── LongIndex.java │ │ │ │ │ └── package.html │ │ │ │ ├── objectindex │ │ │ │ │ ├── ObjectArray.java │ │ │ │ │ ├── ObjectChunks.java │ │ │ │ │ ├── ObjectCreate.java │ │ │ │ │ ├── ObjectIndex.java │ │ │ │ │ └── package.html │ │ │ │ ├── package.html │ │ │ │ ├── packedindex │ │ │ │ │ ├── PackedCreate.java │ │ │ │ │ └── PackedIndex.java │ │ │ │ ├── shortindex │ │ │ │ │ ├── ShortArray.java │ │ │ │ │ ├── ShortChunks.java │ │ │ │ │ ├── ShortCreate.java │ │ │ │ │ ├── ShortIndex.java │ │ │ │ │ └── package.html │ │ │ │ └── zeroindex │ │ │ │ │ ├── ZeroCreate.java │ │ │ │ │ └── ZeroIndex.java │ │ │ ├── bytecompression │ │ │ │ ├── ArithByteCompression.java │ │ │ │ ├── BitwiseByteArray.java │ │ │ │ ├── ByteArray.java │ │ │ │ ├── ByteBaseCompression.java │ │ │ │ ├── ByteCompression.java │ │ │ │ ├── CompressedByteArray.java │ │ │ │ ├── MultiByteArray.java │ │ │ │ └── SingleByteArray.java │ │ │ ├── cli │ │ │ │ ├── AnonymousFlag.java │ │ │ │ ├── CFlags.java │ │ │ │ ├── CommandLine.java │ │ │ │ ├── CommonFlagCategories.java │ │ │ │ ├── Flag.java │ │ │ │ ├── FlagCountException.java │ │ │ │ ├── FlagValue.java │ │ │ │ ├── InvalidFlagHandler.java │ │ │ │ ├── Switch.java │ │ │ │ ├── Validator.java │ │ │ │ ├── WrappingStringBuilder.java │ │ │ │ └── package.html │ │ │ ├── diagnostic │ │ │ │ ├── AbstractTimer.java │ │ │ │ ├── CliDiagnosticListener.java │ │ │ │ ├── Diagnostic.java │ │ │ │ ├── DiagnosticEvent.java │ │ │ │ ├── DiagnosticListener.java │ │ │ │ ├── DiagnosticType.java │ │ │ │ ├── ErrorEvent.java │ │ │ │ ├── ErrorType.java │ │ │ │ ├── InformationEvent.java │ │ │ │ ├── InformationType.java │ │ │ │ ├── ListenerType.java │ │ │ │ ├── NoTalkbackSlimException.java │ │ │ │ ├── OneShotTimer.java │ │ │ │ ├── ParallelProgress.java │ │ │ │ ├── SimpleTalkback.java │ │ │ │ ├── SlimException.java │ │ │ │ ├── Spy.java │ │ │ │ ├── SpyCounter.java │ │ │ │ ├── SpyHistogram.java │ │ │ │ ├── SpyTimer.java │ │ │ │ ├── Talkback.java │ │ │ │ ├── Timer.java │ │ │ │ ├── WarningEvent.java │ │ │ │ ├── WarningType.java │ │ │ │ └── Warnings.java │ │ │ ├── format │ │ │ │ ├── Bits.java │ │ │ │ ├── FloatValue.java │ │ │ │ ├── FormatInteger.java │ │ │ │ ├── FormatIntegerLeft.java │ │ │ │ ├── FormatReal.java │ │ │ │ ├── FormattedValue.java │ │ │ │ ├── NullValue.java │ │ │ │ └── package.html │ │ │ ├── gzip │ │ │ │ └── GzipUtils.java │ │ │ ├── integrity │ │ │ │ ├── Exam.java │ │ │ │ ├── IntegerRange.java │ │ │ │ ├── IntegralAbstract.java │ │ │ │ ├── Integrity.java │ │ │ │ └── package.html │ │ │ ├── intervals │ │ │ │ ├── Interval.java │ │ │ │ ├── IntervalComparator.java │ │ │ │ ├── JSReferenceRegions.java │ │ │ │ ├── LongRange.java │ │ │ │ ├── MergedIntervals.java │ │ │ │ ├── Range.java │ │ │ │ ├── RangeList.java │ │ │ │ ├── RangeMeta.java │ │ │ │ ├── ReferenceRanges.java │ │ │ │ ├── ReferenceRegions.java │ │ │ │ ├── RegionRestriction.java │ │ │ │ ├── SequenceIdLocus.java │ │ │ │ ├── SequenceIdLocusComparator.java │ │ │ │ ├── SequenceIdLocusSimple.java │ │ │ │ ├── SequenceNameLocus.java │ │ │ │ ├── SequenceNameLocusComparator.java │ │ │ │ ├── SequenceNameLocusSimple.java │ │ │ │ ├── SimpleRangeMeta.java │ │ │ │ └── StatusInterval.java │ │ │ ├── io │ │ │ │ ├── AdjustableGZIPOutputStream.java │ │ │ │ ├── AsynchInputStream.java │ │ │ │ ├── AsynchOutputStream.java │ │ │ │ ├── BaseFile.java │ │ │ │ ├── BufferedOutputStreamFix.java │ │ │ │ ├── BufferedRandomAccessFile.java │ │ │ │ ├── ByteArrayIOUtils.java │ │ │ │ ├── ClosedFileInputStream.java │ │ │ │ ├── ConcurrentByteQueue.java │ │ │ │ ├── FalseSeekableStream.java │ │ │ │ ├── FileUtils.java │ │ │ │ ├── GzipAsynchInputStream.java │ │ │ │ ├── GzipAsynchOutputStream.java │ │ │ │ ├── IOIterator.java │ │ │ │ ├── IOUtils.java │ │ │ │ ├── InputFileUtils.java │ │ │ │ ├── LineWriter.java │ │ │ │ ├── LogFile.java │ │ │ │ ├── LogSimple.java │ │ │ │ ├── LogStream.java │ │ │ │ ├── MemoryPrintStream.java │ │ │ │ ├── Partition.java │ │ │ │ ├── RandomAccessFileStream.java │ │ │ │ ├── RuntimeIOIterator.java │ │ │ │ ├── SeekableStream.java │ │ │ │ ├── SimpleArchive.java │ │ │ │ ├── bzip2 │ │ │ │ │ ├── BZip2Constants.java │ │ │ │ │ ├── CBZip2InputStream.java │ │ │ │ │ └── CRC.java │ │ │ │ └── package.html │ │ │ ├── iterators │ │ │ │ ├── ArrayToIterator.java │ │ │ │ ├── ComposeIterators.java │ │ │ │ ├── IteratorForEach.java │ │ │ │ ├── IteratorHelper.java │ │ │ │ ├── SubsampleIterator.java │ │ │ │ └── Transform.java │ │ │ ├── machine │ │ │ │ ├── MachineOrientation.java │ │ │ │ ├── MachineType.java │ │ │ │ └── PairOrientation.java │ │ │ └── test │ │ │ │ └── params │ │ │ │ ├── BuilderNotSet.java │ │ │ │ └── ParamsNoField.java │ │ │ ├── variant │ │ │ ├── AbstractMachineErrorParams.java │ │ │ ├── GenomePriorParams.java │ │ │ ├── GenomePriorParamsBuilder.java │ │ │ ├── MachineErrorParams.java │ │ │ ├── MachineErrorParamsBuilder.java │ │ │ ├── PhredScaler.java │ │ │ ├── cnv │ │ │ │ ├── CnaType.java │ │ │ │ ├── CnvRecordFilter.java │ │ │ │ └── cnveval │ │ │ │ │ ├── BedAnnotation.java │ │ │ │ │ ├── CnaRecordStats.java │ │ │ │ │ ├── CnaVariant.java │ │ │ │ │ ├── CnaVariantList.java │ │ │ │ │ ├── CnaVariantSet.java │ │ │ │ │ └── CnvEvalCli.java │ │ │ └── sv │ │ │ │ ├── VcfSvDecomposer.java │ │ │ │ └── bndeval │ │ │ │ ├── AbstractBreakpointGeometry.java │ │ │ │ ├── AnnotatingBndEvalVcfWriter.java │ │ │ │ ├── BndEvalCli.java │ │ │ │ ├── BndEvalVcfWriter.java │ │ │ │ ├── BndVariant.java │ │ │ │ ├── BreakpointGeometry.java │ │ │ │ ├── FlippedProxyBreakpointGeometry.java │ │ │ │ ├── Interval.java │ │ │ │ ├── Orientation.java │ │ │ │ └── SplitBndEvalVcfWriter.java │ │ │ ├── vcf │ │ │ ├── AbstractVcfFilter.java │ │ │ ├── Adjuster.java │ │ │ ├── AllMatchFilter.java │ │ │ ├── AltVariantTypeFilter.java │ │ │ ├── AnnotatingVcfWriter.java │ │ │ ├── ArrayVcfIterator.java │ │ │ ├── AssertVcfSorted.java │ │ │ ├── AsyncVcfWriter.java │ │ │ ├── BedVcfAnnotator.java │ │ │ ├── BreakpointAlt.java │ │ │ ├── ChildPhasingVcfAnnotator.java │ │ │ ├── ClusterAnnotator.java │ │ │ ├── Decomposer.java │ │ │ ├── DecomposingVcfIterator.java │ │ │ ├── DecomposingVcfWriter.java │ │ │ ├── DefaultVcfWriter.java │ │ │ ├── ExpressionInfoFilter.java │ │ │ ├── ExpressionSampleFilter.java │ │ │ ├── FilterVcfWriter.java │ │ │ ├── NamedRangesVcfAnnotator.java │ │ │ ├── NullVcfWriter.java │ │ │ ├── Operation.java │ │ │ ├── OperationDouble.java │ │ │ ├── OperationObject.java │ │ │ ├── PassOnlyFilter.java │ │ │ ├── PerSampleVariantStatistics.java │ │ │ ├── ReorderingVcfWriter.java │ │ │ ├── ScriptedVcfFilter.java │ │ │ ├── ScriptedVcfProcessor.java │ │ │ ├── SnpIntersection.java │ │ │ ├── StatisticsVcfWriter.java │ │ │ ├── SymbolicAlt.java │ │ │ ├── VariantStatistics.java │ │ │ ├── VariantType.java │ │ │ ├── VcfAltCleaner.java │ │ │ ├── VcfAnnotator.java │ │ │ ├── VcfAnnotatorCli.java │ │ │ ├── VcfAnnotatorFactory.java │ │ │ ├── VcfDecomposerCli.java │ │ │ ├── VcfFilter.java │ │ │ ├── VcfFilterCli.java │ │ │ ├── VcfFilterIterator.java │ │ │ ├── VcfFilterStatistics.java │ │ │ ├── VcfFilterStripper.java │ │ │ ├── VcfFilterTask.java │ │ │ ├── VcfFormatException.java │ │ │ ├── VcfFormatStripper.java │ │ │ ├── VcfGtMajorityMerger.java │ │ │ ├── VcfIdAnnotator.java │ │ │ ├── VcfIdCleaner.java │ │ │ ├── VcfInfoFilter.java │ │ │ ├── VcfInfoStripper.java │ │ │ ├── VcfIterator.java │ │ │ ├── VcfMerge.java │ │ │ ├── VcfParser.java │ │ │ ├── VcfQualCleaner.java │ │ │ ├── VcfReader.java │ │ │ ├── VcfReaderFactory.java │ │ │ ├── VcfRecord.java │ │ │ ├── VcfRecordMerger.java │ │ │ ├── VcfSameAltsMerger.java │ │ │ ├── VcfSampleFilter.java │ │ │ ├── VcfSampleNameRelabeller.java │ │ │ ├── VcfSampleStripper.java │ │ │ ├── VcfSortRefiner.java │ │ │ ├── VcfSplitCli.java │ │ │ ├── VcfStatsCli.java │ │ │ ├── VcfSubset.java │ │ │ ├── VcfSubsetParser.java │ │ │ ├── VcfUtils.java │ │ │ ├── VcfWriter.java │ │ │ ├── VcfWriterFactory.java │ │ │ ├── annotation │ │ │ │ ├── AbstractDerivedAnnotation.java │ │ │ │ ├── AbstractDerivedFormatAnnotation.java │ │ │ │ ├── AbstractDerivedInfoAnnotation.java │ │ │ │ ├── AbstractInbreedingCoefficientAnnotation.java │ │ │ │ ├── AlleleCountInGenotypesAnnotation.java │ │ │ │ ├── AltAlleleQualityAnnotation.java │ │ │ │ ├── ContraryObservationCounter.java │ │ │ │ ├── DerivedAnnotations.java │ │ │ │ ├── EquilibriumProbabilityAnnotation.java │ │ │ │ ├── Formatter.java │ │ │ │ ├── GenotypeQualityOverDepthAnnotation.java │ │ │ │ ├── InbreedingCoefficientAnnotation.java │ │ │ │ ├── LongestAlleleAnnotation.java │ │ │ │ ├── MeanQualityDifferenceAnnotation.java │ │ │ │ ├── NumberAllelesInGenotypesAnnotation.java │ │ │ │ ├── NumberOfAltAllelesAnnotation.java │ │ │ │ ├── PloidyAnnotation.java │ │ │ │ ├── QualOverDepthAnnotation.java │ │ │ │ ├── RefAltAnnotation.java │ │ │ │ ├── SimpleTandemRepeatAnnotator.java │ │ │ │ ├── SplitContraryObservationAnnotator.java │ │ │ │ ├── VariantAllelicFractionAnnotation.java │ │ │ │ ├── VariantMinorAllelicFractionAnnotation.java │ │ │ │ ├── VcfAnnotation.java │ │ │ │ └── ZygosityAnnotation.java │ │ │ ├── eval │ │ │ │ ├── Allele.java │ │ │ │ ├── AlleleAccumulator.java │ │ │ │ ├── AnnotatingEvalSynchronizer.java │ │ │ │ ├── CombinedEvalSynchronizer.java │ │ │ │ ├── CombinedRocFilter.java │ │ │ │ ├── EvalSynchronizer.java │ │ │ │ ├── ExpressionRocFilter.java │ │ │ │ ├── FMeasureThreshold.java │ │ │ │ ├── FixedScoreThreshold.java │ │ │ │ ├── Ga4ghEvalSynchronizer.java │ │ │ │ ├── Ga4ghLooseMatchFilter.java │ │ │ │ ├── GtIdVariant.java │ │ │ │ ├── HalfPath.java │ │ │ │ ├── HaplotypePlayback.java │ │ │ │ ├── InterleavingEvalSynchronizer.java │ │ │ │ ├── LoadedVariants.java │ │ │ │ ├── MaxCallsMinBaseline.java │ │ │ │ ├── MaxSumBoth.java │ │ │ │ ├── OrientedVariant.java │ │ │ │ ├── Orientor.java │ │ │ │ ├── ParentalVariant.java │ │ │ │ ├── Path.java │ │ │ │ ├── PathFinder.java │ │ │ │ ├── PathPreference.java │ │ │ │ ├── PhaseTransferEvalSynchronizer.java │ │ │ │ ├── PhasingEvaluator.java │ │ │ │ ├── PrecisionThreshold.java │ │ │ │ ├── RegionsRocFilter.java │ │ │ │ ├── RocContainer.java │ │ │ │ ├── RocFilter.java │ │ │ │ ├── RocFilterProxy.java │ │ │ │ ├── RocFlags.java │ │ │ │ ├── RocOnlyEvalSynchronizer.java │ │ │ │ ├── RocPoint.java │ │ │ │ ├── RocPointCriteria.java │ │ │ │ ├── RocScoreField.java │ │ │ │ ├── RocSlope.java │ │ │ │ ├── RocSortOrder.java │ │ │ │ ├── RocSortValueExtractor.java │ │ │ │ ├── RocUtils.java │ │ │ │ ├── SampleRecoder.java │ │ │ │ ├── SensitivityThreshold.java │ │ │ │ ├── SequenceEvaluator.java │ │ │ │ ├── SkippedVariantException.java │ │ │ │ ├── SplitEvalSynchronizer.java │ │ │ │ ├── SquashedAlleleAccumulator.java │ │ │ │ ├── TabixVcfRecordSet.java │ │ │ │ ├── TrioEvalSynchronizer.java │ │ │ │ ├── Variant.java │ │ │ │ ├── VariantFactory.java │ │ │ │ ├── VariantId.java │ │ │ │ ├── VariantSet.java │ │ │ │ ├── VariantSetType.java │ │ │ │ ├── Vcf2Rocplot.java │ │ │ │ ├── VcfEvalCli.java │ │ │ │ ├── VcfEvalParams.java │ │ │ │ ├── VcfEvalTask.java │ │ │ │ ├── VcfRecordSet.java │ │ │ │ ├── VcfRecordTabixCallable.java │ │ │ │ ├── WithInfoEvalSynchronizer.java │ │ │ │ └── WithRocsEvalSynchronizer.java │ │ │ ├── header │ │ │ │ ├── AltField.java │ │ │ │ ├── ContigField.java │ │ │ │ ├── FilterField.java │ │ │ │ ├── FormatField.java │ │ │ │ ├── IdField.java │ │ │ │ ├── InfoField.java │ │ │ │ ├── MetaType.java │ │ │ │ ├── PedigreeField.java │ │ │ │ ├── SampleField.java │ │ │ │ ├── TypedField.java │ │ │ │ ├── VcfHeader.java │ │ │ │ ├── VcfHeaderMerge.java │ │ │ │ ├── VcfNumber.java │ │ │ │ └── VcfNumberType.java │ │ │ └── mendelian │ │ │ │ ├── Genotype.java │ │ │ │ ├── GenotypeProportions.java │ │ │ │ ├── MendeliannessAnnotator.java │ │ │ │ ├── MendeliannessChecker.java │ │ │ │ └── TrioConcordance.java │ │ │ └── visualization │ │ │ ├── AnsiDisplayHelper.java │ │ │ ├── DisplayHelper.java │ │ │ └── HtmlDisplayHelper.java │ └── resources │ │ └── com │ │ └── rtg │ │ ├── graph │ │ ├── palettes.properties │ │ └── resources │ │ │ ├── realtimegenomics_logo.png │ │ │ └── realtimegenomics_logo_sm.png │ │ ├── mode │ │ ├── BLOSUM45 │ │ ├── BLOSUM45.properties │ │ ├── BLOSUM62 │ │ ├── BLOSUM62.properties │ │ ├── BLOSUM80 │ │ └── BLOSUM80.properties │ │ ├── reference │ │ └── resources │ │ │ ├── grch37-hgrc.manifest │ │ │ ├── grch37-hgrc.txt │ │ │ ├── grch37-ucsc.manifest │ │ │ ├── grch37-ucsc.txt │ │ │ ├── grch38-ucsc.manifest │ │ │ ├── grch38-ucsc.txt │ │ │ ├── grcm38.manifest │ │ │ ├── grcm38.txt │ │ │ ├── hg18.manifest │ │ │ ├── hg18.txt │ │ │ ├── manifest.list │ │ │ ├── namelookup │ │ │ ├── hgrc-numbers.manifest │ │ │ ├── hgrc-wz.manifest │ │ │ ├── hgrc-xy.manifest │ │ │ ├── numbers.list │ │ │ ├── sex.list │ │ │ ├── ucsc-numbers.manifest │ │ │ ├── ucsc-wz.manifest │ │ │ └── ucsc-xy.manifest │ │ │ ├── ncbim37.manifest │ │ │ └── ncbim37.txt │ │ ├── report │ │ └── resources │ │ │ ├── 07_ascending.gif │ │ │ ├── 07_descending.gif │ │ │ ├── blank.png │ │ │ ├── canvasXpress.min.js │ │ │ ├── check.png │ │ │ ├── cross.png │ │ │ ├── default.html │ │ │ ├── default.vm │ │ │ ├── excanvas.js │ │ │ ├── rtg.css │ │ │ ├── rtg_logo.png │ │ │ ├── table.css │ │ │ └── table.js │ │ ├── simulation │ │ └── variants │ │ │ └── alt.allele.frequency.counts.txt │ │ ├── util │ │ └── diagnostic │ │ │ └── Diagnostics.properties │ │ ├── variant │ │ └── priors │ │ │ ├── cnv │ │ │ └── cnv-default.properties │ │ │ ├── error │ │ │ ├── cg_real_errors.properties │ │ │ ├── cg_test_errors-080412.properties │ │ │ ├── cg_test_errors.properties │ │ │ ├── complete.properties │ │ │ ├── completegenomics.properties │ │ │ ├── default.properties │ │ │ ├── errorrate_0.001_indelrate_0.1_errors.properties │ │ │ ├── errorrate_0.01_indelrate_0.1_errors.properties │ │ │ ├── errorrate_0.01_indelrate_0.1_withMnps_errors.properties │ │ │ ├── illumina.properties │ │ │ ├── iontorrent.properties │ │ │ ├── ls454_pe.properties │ │ │ ├── ls454_se.properties │ │ │ └── no_errors.properties │ │ │ └── prior │ │ │ └── human.properties │ │ └── vcf │ │ ├── field_adjustment.properties │ │ └── resources │ │ └── vcf_filter_preamble.js └── test │ ├── java │ ├── AllTests.java │ ├── ClassPathSuite.java │ ├── FindTestClasses.java │ ├── OutputListener.java │ ├── RtgTestEntry.java │ └── com │ │ └── rtg │ │ ├── AbstractTest.java │ │ ├── CommandCategoryTest.java │ │ ├── CommandLookupTest.java │ │ ├── CommandTest.java │ │ ├── DummyCliEntryTest.java │ │ ├── ReleaseLevelTest.java │ │ ├── RtgToolsTest.java │ │ ├── ToolsCommandTest.java │ │ ├── VersionCommandTest.java │ │ ├── alignment │ │ ├── AbstractUnidirectionalEditDistanceTest.java │ │ ├── ActionsHelperTest.java │ │ ├── ActionsValidatorTest.java │ │ ├── GotohEditDistanceTest.java │ │ ├── PartitionTest.java │ │ ├── SliceTest.java │ │ └── SplitAllelesTest.java │ │ ├── bed │ │ ├── BedHeaderTest.java │ │ ├── BedReaderTest.java │ │ ├── BedRecordTest.java │ │ ├── BedUtilsTest.java │ │ ├── BedWriterTest.java │ │ ├── NamedBedRangeLoaderTest.java │ │ └── SimpleBedRangeLoaderTest.java │ │ ├── graph │ │ ├── DataBundleTest.java │ │ ├── ParseRocFileTest.java │ │ ├── RightMouseButtonFilterTest.java │ │ ├── RocPlotCliTest.java │ │ ├── RocPlotPalettesTest.java │ │ └── RocPlotToFileTest.java │ │ ├── jmx │ │ ├── DiskStatsTest.java │ │ ├── ExternalCommandTest.java │ │ ├── LocalStatsTest.java │ │ ├── MBeanStatsTest.java │ │ ├── MonUtilsTest.java │ │ ├── NetworkStatsTest.java │ │ ├── ProgressStatsTest.java │ │ └── RecordStatsTest.java │ │ ├── launcher │ │ ├── AbstractCliTest.java │ │ ├── AbstractEndToEndTest.java │ │ ├── AbstractNanoTest.java │ │ ├── CommandLineFilesTest.java │ │ ├── CommonFlagsTest.java │ │ ├── DummyCliTest.java │ │ ├── DummyStatisticsTest.java │ │ ├── LoggedCliTest.java │ │ ├── MainResult.java │ │ ├── MockCli.java │ │ ├── MockCliParams.java │ │ ├── MockReaderParams.java │ │ ├── MockTask.java │ │ ├── ModuleParamsTest.java │ │ ├── NoStatisticsTest.java │ │ ├── OutputModuleParamsTest.java │ │ ├── OutputParamsTest.java │ │ ├── ParamsCliTest.java │ │ ├── ParamsTaskTest.java │ │ └── globals │ │ │ └── GlobalFlagsTest.java │ │ ├── mode │ │ ├── BidirectionalFrameTest.java │ │ ├── DNAFastaSymbolTableTest.java │ │ ├── DNARangeATTest.java │ │ ├── DNARangeNATTest.java │ │ ├── DNARangeTest.java │ │ ├── DNASimpleTest.java │ │ ├── DNATest.java │ │ ├── DnaUtilsTest.java │ │ ├── GeneralDNARangeTest.java │ │ ├── IllegalBaseExceptionTest.java │ │ ├── ProteinFastaSymbolTableTest.java │ │ ├── ProteinFrameTest.java │ │ ├── ProteinScoringMatrixTest.java │ │ ├── ProteinTest.java │ │ ├── ScoringMatrixTest.java │ │ ├── SequenceModeTest.java │ │ ├── SequenceTypeTest.java │ │ ├── TranslatedFrameTest.java │ │ └── UnidirectionalFrameTest.java │ │ ├── reader │ │ ├── AbstractByteArrayRegression.java │ │ ├── AbstractFileStreamRegression.java │ │ ├── AbstractSequencesReaderTest.java │ │ ├── AlternatingSequencesReaderTest.java │ │ ├── AlternatingSequencesWriterTest.java │ │ ├── ArmTest.java │ │ ├── ArrayNamesTest.java │ │ ├── ArraySequencesReader.java │ │ ├── AsyncFastqSequenceWriterTest.java │ │ ├── BatchProcessorTest.java │ │ ├── BatchReorderingWriterTest.java │ │ ├── BatchTest.java │ │ ├── BestSumReadTrimmerTest.java │ │ ├── BlockingExecutorTest.java │ │ ├── CachingSequencesReaderTest.java │ │ ├── Cg2SdfTest.java │ │ ├── CgSamBamSequenceDataSourceTest.java │ │ ├── CgUtilsTest.java │ │ ├── CompressedMemorySequencesReader2Test.java │ │ ├── CompressedMemorySequencesReaderTest.java │ │ ├── CompressedMemorySequencesWriterTest.java │ │ ├── ConcatSequenceDataSourceTest.java │ │ ├── CorruptSdfExceptionTest.java │ │ ├── DataFileOpenerFactoryTest.java │ │ ├── DataInMemoryTest.java │ │ ├── DataSourceDescriptionTest.java │ │ ├── DefaultReadTrimmerTest.java │ │ ├── DefaultSequencesReaderTest.java │ │ ├── DummyAsyncChunkWriterTest.java │ │ ├── DummySequencesReader.java │ │ ├── EmptyStringNamesTest.java │ │ ├── FastaSequenceDataSourceTest.java │ │ ├── FastaUtilsTest.java │ │ ├── FastaWriterTest.java │ │ ├── FastqIteratorTest.java │ │ ├── FastqSequenceDataSourceTest.java │ │ ├── FastqSequenceTest.java │ │ ├── FastqTrimProcessorTest.java │ │ ├── FastqTrimTest.java │ │ ├── FastqUtilsTest.java │ │ ├── FastqWriterTest.java │ │ ├── FileBitwiseInputStreamTest.java │ │ ├── FileBitwiseOutputStreamTest.java │ │ ├── FileBitwiseStreamRegression.java │ │ ├── FileCompressedInputStreamTest.java │ │ ├── FileCompressedOutputStreamTest.java │ │ ├── FileCompressedStreamRegression.java │ │ ├── FileStreamIteratorTest.java │ │ ├── FirstBasesReadTrimmerTest.java │ │ ├── FormatCliTest.java │ │ ├── FullReadTrimmerTest.java │ │ ├── IndexFileTest.java │ │ ├── LabelTest.java │ │ ├── LargeBitwiseByteArrayRegression.java │ │ ├── LargeCompressedByteArrayRegression.java │ │ ├── LargeMultiByteArrayRegression.java │ │ ├── LastBasesReadTrimmerTest.java │ │ ├── MappedSamBamSequenceDataSourceTest.java │ │ ├── MinLengthReadTrimmerTest.java │ │ ├── MockArraySequencesReader.java │ │ ├── MockSequencesReader.java │ │ ├── MultiReadTrimmerTest.java │ │ ├── NameDuplicateDetectorTest.java │ │ ├── NameFilePairTest.java │ │ ├── NamesTest.java │ │ ├── NullReadTrimmerTest.java │ │ ├── PointerFileHandlerTest.java │ │ ├── PointerFileLookupTest.java │ │ ├── PrereadArmTest.java │ │ ├── PrereadHashFunctionTest.java │ │ ├── PrereadTypeTest.java │ │ ├── QualityFormatTest.java │ │ ├── ReadHelperTest.java │ │ ├── ReaderLongMock.java │ │ ├── ReaderTestUtils.java │ │ ├── ReaderUtilsTest.java │ │ ├── ReverseComplementReadTrimmerTest.java │ │ ├── ReverseComplementingReaderTest.java │ │ ├── RightSimpleNamesTest.java │ │ ├── SamBamSequenceDataSourceTest.java │ │ ├── Sdf2CgTest.java │ │ ├── Sdf2FastaTest.java │ │ ├── Sdf2FastqTest.java │ │ ├── Sdf2QualaTest.java │ │ ├── Sdf2SamTest.java │ │ ├── SdfFileUtilsTest.java │ │ ├── SdfIdTest.java │ │ ├── SdfSplitterTest.java │ │ ├── SdfStatisticsTest.java │ │ ├── SdfSubseqTest.java │ │ ├── SdfSubsetTest.java │ │ ├── SdfUtilsTest.java │ │ ├── SdfVerifierTest.java │ │ ├── SequenceDataLoaderTest.java │ │ ├── SequenceStreamManagerTest.java │ │ ├── SequencesReaderFactoryTest.java │ │ ├── SequencesReaderReferenceSourceTest.java │ │ ├── SequencesWriterTest.java │ │ ├── SimpleNamesTest.java │ │ ├── SourceFormatTest.java │ │ ├── SourceTemplateReadWriterTest.java │ │ └── TsvSequenceDataSourceTest.java │ │ ├── reference │ │ ├── GenerateReferenceManifestTest.java │ │ ├── PloidyTest.java │ │ ├── ReferenceDetectorTest.java │ │ ├── ReferenceGenomeTest.java │ │ ├── ReferenceManifestTest.java │ │ ├── ReferenceParseTest.java │ │ ├── ReferenceSequenceTest.java │ │ ├── ReferenceTextBuilderTest.java │ │ ├── SexMemoTest.java │ │ └── SexTest.java │ │ ├── relation │ │ ├── ChildFamilyLookupTest.java │ │ ├── FamilyTest.java │ │ ├── GenomeRelationshipsTest.java │ │ ├── LineageLookupTest.java │ │ ├── MultiFamilyOrderingTest.java │ │ ├── PedFileParserTest.java │ │ ├── PedFilterCliTest.java │ │ ├── PedStatsCliTest.java │ │ ├── RelationshipsFileParserTest.java │ │ └── VcfPedigreeParserTest.java │ │ ├── report │ │ ├── RtgVelocityLogChuteTest.java │ │ └── VelocityReportUtilsTest.java │ │ ├── sam │ │ ├── BadSuperCigarExceptionTest.java │ │ ├── BamIndexMergeTest.java │ │ ├── BamIndexReaderTest.java │ │ ├── BamIndexerTest.java │ │ ├── BamReaderTest.java │ │ ├── BgzfInputStreamTest.java │ │ ├── DefaultSamFilterTest.java │ │ ├── DuplicateSamFilterTest.java │ │ ├── FlushLocusTest.java │ │ ├── MappedParamsTest.java │ │ ├── MockSamBamRecord.java │ │ ├── NoneFilterTest.java │ │ ├── ReadGroupUtilsTest.java │ │ ├── SamBamBaseFileTest.java │ │ ├── SamBamReaderTest.java │ │ ├── SamBamRecordImplTest.java │ │ ├── SamClosedFileReaderTest.java │ │ ├── SamCommandHelperTest.java │ │ ├── SamCompareUtilsTest.java │ │ ├── SamFileAndRecordTest.java │ │ ├── SamFilterChainTest.java │ │ ├── SamFilterOptionsTest.java │ │ ├── SamFilterParamsTest.java │ │ ├── SamMultiRestrictingIteratorTest.java │ │ ├── SamOutputTest.java │ │ ├── SamRangeUtilsTest.java │ │ ├── SamReadingContextTest.java │ │ ├── SamRecordExceptionTest.java │ │ ├── SamRegionRestrictionTest.java │ │ ├── SamRestrictingIteratorTest.java │ │ ├── SamUtilsTest.java │ │ ├── SharedSamConstants.java │ │ ├── SingleMappedParamsTest.java │ │ ├── SkipInvalidRecordsIteratorTest.java │ │ └── SmartSamWriterTest.java │ │ ├── simulation │ │ ├── DistributionSamplerTest.java │ │ ├── GaussianSamplerTest.java │ │ ├── SimulationUtilsTest.java │ │ ├── genome │ │ │ ├── GenomeSimulatorTest.java │ │ │ ├── RandomDistributionTest.java │ │ │ └── SequenceGeneratorTest.java │ │ ├── reads │ │ │ ├── AbstractMachineTest.java │ │ │ ├── CgSimCliTest.java │ │ │ ├── CompleteGenomicsV1MachineTest.java │ │ │ ├── CompleteGenomicsV2MachineTest.java │ │ │ ├── DummyIlluminaMachineTest.java │ │ │ ├── DummyMachineTest.java │ │ │ ├── ErrorMachineTest.java │ │ │ ├── FastaReadWriterTest.java │ │ │ ├── FastqReadWriterTest.java │ │ │ ├── FilteringFragmenterTest.java │ │ │ ├── FourFiveFourPairedEndMachineTest.java │ │ │ ├── FourFiveFourSingleEndMachineTest.java │ │ │ ├── FragmentTooSmallExceptionTest.java │ │ │ ├── GenomeFragmenterTest.java │ │ │ ├── IlluminaPairedEndMachineTest.java │ │ │ ├── IlluminaSingleEndMachineTest.java │ │ │ ├── IonTorrentSingleEndMachineTest.java │ │ │ ├── MinMaxGaussianSamplerTest.java │ │ │ ├── ReadSimCliTest.java │ │ │ ├── ReadSimCliValidatorTest.java │ │ │ ├── SdfReadWriterTest.java │ │ │ ├── TaxonomyDistributionTest.java │ │ │ └── UnknownBaseReadWriterTest.java │ │ └── variants │ │ │ ├── ChildSampleSimulatorCliTest.java │ │ │ ├── ChildSampleSimulatorTest.java │ │ │ ├── CrossoverSelectorTest.java │ │ │ ├── DeNovoSampleSimulatorCliTest.java │ │ │ ├── DeNovoSampleSimulatorTest.java │ │ │ ├── FixedStepPopulationVariantGeneratorCliTest.java │ │ │ ├── FixedStepPopulationVariantGeneratorTest.java │ │ │ ├── MutatorResultTest.java │ │ │ ├── MutatorSingleTest.java │ │ │ ├── MutatorTest.java │ │ │ ├── PedSampleSimulatorCliTest.java │ │ │ ├── PopulationVariantGeneratorTest.java │ │ │ ├── PopulationVariantSimulatorCliTest.java │ │ │ ├── PriorPopulationVariantGeneratorTest.java │ │ │ ├── SampleReplayerCliTest.java │ │ │ ├── SampleReplayerTest.java │ │ │ ├── SampleSimulatorCliTest.java │ │ │ └── SampleSimulatorTest.java │ │ ├── tabix │ │ ├── AlleleCountsPositionReaderTest.java │ │ ├── BgZipTest.java │ │ ├── BlockCompressedLineReaderTest.java │ │ ├── BrLineReaderTest.java │ │ ├── ExtractCliTest.java │ │ ├── GenericPositionReaderTest.java │ │ ├── IndexTestUtils.java │ │ ├── IndexUtilsTest.java │ │ ├── IndexerCliTest.java │ │ ├── IndexingStreamCreatorTest.java │ │ ├── SamPositionReaderTest.java │ │ ├── SequenceIndexContainerTest.java │ │ ├── TabixHeaderTest.java │ │ ├── TabixIndexMergeTest.java │ │ ├── TabixIndexReaderTest.java │ │ ├── TabixIndexerTest.java │ │ ├── TabixLineReaderTest.java │ │ └── VcfPositionReaderTest.java │ │ ├── taxonomy │ │ ├── SequenceToTaxonIdsTest.java │ │ ├── TaxonNodeTest.java │ │ ├── TaxonomyTest.java │ │ └── TaxonomyUtilsTest.java │ │ ├── usage │ │ ├── FileUsageLoggingClientTest.java │ │ ├── HttpUsageLoggingClientTest.java │ │ ├── NullUsageLoggingClientTest.java │ │ ├── UsageConfigurationTest.java │ │ ├── UsageLoggingTest.java │ │ ├── UsageMessageTest.java │ │ ├── UsageMetricTest.java │ │ ├── UsageServerCliTest.java │ │ └── UsageServerTest.java │ │ ├── util │ │ ├── AutoAddMapTest.java │ │ ├── BasicLinkedListNodeTest.java │ │ ├── ByteUtilsTest.java │ │ ├── ChiSquaredTest.java │ │ ├── ChooseMemoryTest.java │ │ ├── ClassPathScannerTest.java │ │ ├── CompareHelperTest.java │ │ ├── ConstantsTest.java │ │ ├── ContingencyTableTest.java │ │ ├── DoubleMultiSetTest.java │ │ ├── EnumHelperTest.java │ │ ├── EnvironmentTest.java │ │ ├── HistogramTest.java │ │ ├── HistogramWithNegativesTest.java │ │ ├── HtmlReportHelperTest.java │ │ ├── IORunnableProxyTest.java │ │ ├── IntegerOrPercentageTest.java │ │ ├── InvalidParamsExceptionTest.java │ │ ├── LongMultiSetTest.java │ │ ├── MD5UtilsTest.java │ │ ├── MathUtilsTest.java │ │ ├── MultiMapTest.java │ │ ├── MultiSetTest.java │ │ ├── NullStreamUtilsTest.java │ │ ├── PairTest.java │ │ ├── ParamsBuilderTest.java │ │ ├── PermutationTest.java │ │ ├── PortableRandomTest.java │ │ ├── PosteriorUtilsTest.java │ │ ├── ProgramStateTest.java │ │ ├── PropertiesUtilsTest.java │ │ ├── QuickSortDoubleIntProxyTest.java │ │ ├── QuickSortIntIntProxyTest.java │ │ ├── QuickSortLongLongProxyTest.java │ │ ├── QuickSortTest.java │ │ ├── ReorderingQueueTest.java │ │ ├── ResourcesTest.java │ │ ├── RstTableTest.java │ │ ├── SimpleThreadPoolTest.java │ │ ├── SpawnJvmTest.java │ │ ├── StringUtilsTest.java │ │ ├── TestUtils.java │ │ ├── TextTableTest.java │ │ ├── TsvParserTest.java │ │ ├── UtilsTest.java │ │ ├── WorkerThreadTest.java │ │ ├── arithcode │ │ │ ├── ArithTest.java │ │ │ ├── BytesTest.java │ │ │ ├── Order0ModelBuilderTest.java │ │ │ ├── StaticModelTest.java │ │ │ └── UniformModelTest.java │ │ ├── array │ │ │ ├── AbstractCommonIndexRegression.java │ │ │ ├── AbstractCommonIndexTest.java │ │ │ ├── ArrayHandleTest.java │ │ │ ├── ArrayTypeTest.java │ │ │ ├── ArrayUtilsTest.java │ │ │ ├── DummyIndexTest.java │ │ │ ├── IndexSorterTest.java │ │ │ ├── IndexTypeTest.java │ │ │ ├── SingleValueIntArrayTest.java │ │ │ ├── WrappedIntArrayTest.java │ │ │ ├── atomic │ │ │ │ ├── AtomicIntChunksTest.java │ │ │ │ └── AtomicLongChunksTest.java │ │ │ ├── bitindex │ │ │ │ ├── BitCreateTest.java │ │ │ │ └── BitIndexTest.java │ │ │ ├── byteindex │ │ │ │ ├── AbstractByteIndexTest.java │ │ │ │ ├── ByteArrayTest.java │ │ │ │ ├── ByteChunksTest.java │ │ │ │ ├── ByteCreateTest.java │ │ │ │ └── ByteIndexTest.java │ │ │ ├── intindex │ │ │ │ ├── AbstractIntIndexTest.java │ │ │ │ ├── IntArrayTest.java │ │ │ │ ├── IntChunksTest.java │ │ │ │ ├── IntCreateTest.java │ │ │ │ └── IntIndexTest.java │ │ │ ├── longindex │ │ │ │ ├── AbstractLongIndexTest.java │ │ │ │ ├── LongArrayTest.java │ │ │ │ ├── LongChunksRegression.java │ │ │ │ ├── LongChunksTest.java │ │ │ │ ├── LongCreateTest.java │ │ │ │ ├── LongIndexTest.java │ │ │ │ └── SmallChunksTest.java │ │ │ ├── objectindex │ │ │ │ ├── AbstractObjectIndexTest.java │ │ │ │ ├── ObjectArrayTest.java │ │ │ │ ├── ObjectChunksRegression.java │ │ │ │ ├── ObjectChunksTest.java │ │ │ │ ├── ObjectCreateTest.java │ │ │ │ ├── ObjectIndexTest.java │ │ │ │ └── SmallChunksTest.java │ │ │ ├── packedindex │ │ │ │ ├── PackedCreateTest.java │ │ │ │ └── PackedIndexTest.java │ │ │ ├── shortindex │ │ │ │ ├── AbstractShortIndexTest.java │ │ │ │ ├── ShortArrayTest.java │ │ │ │ ├── ShortChunksRegression.java │ │ │ │ ├── ShortChunksTest.java │ │ │ │ ├── ShortCreateTest.java │ │ │ │ ├── ShortIndexTest.java │ │ │ │ └── SmallChunksTest.java │ │ │ └── zeroindex │ │ │ │ ├── ZeroCreateTest.java │ │ │ │ └── ZeroIndexTest.java │ │ ├── bytecompression │ │ │ ├── AbstractByteCompressionTest.java │ │ │ ├── ArithByteCompressionTest.java │ │ │ ├── BitwiseByteArrayTest.java │ │ │ ├── ByteArrayTest.java │ │ │ ├── ByteBaseCompressionTest.java │ │ │ ├── CompressedByteArrayTest.java │ │ │ ├── MultiByteArrayTest.java │ │ │ └── SingleByteArrayTest.java │ │ ├── cli │ │ │ ├── CFlagsTest.java │ │ │ ├── CheckSpelling.java │ │ │ ├── CommandLineTest.java │ │ │ ├── CommonFlagCategoriesTest.java │ │ │ ├── FlagCountExceptionTest.java │ │ │ ├── FlagTest.java │ │ │ ├── FlagValueTest.java │ │ │ ├── TestCFlags.java │ │ │ └── WrappingStringBuilderTest.java │ │ ├── diagnostic │ │ │ ├── AbstractDiagnosticEventTest.java │ │ │ ├── CliDiagnosticListenerTest.java │ │ │ ├── DiagnosticEventTest.java │ │ │ ├── DiagnosticTest.java │ │ │ ├── ErrorEventTest.java │ │ │ ├── ErrorTypeTest.java │ │ │ ├── InformationEventTest.java │ │ │ ├── InformationTypeTest.java │ │ │ ├── ListenerTypeTest.java │ │ │ ├── NoTalkbackSlimExceptionTest.java │ │ │ ├── OneShotTimerTest.java │ │ │ ├── ParallelProgressTest.java │ │ │ ├── SlimExceptionTest.java │ │ │ ├── SpyCounterTest.java │ │ │ ├── SpyHistogramTest.java │ │ │ ├── SpyTest.java │ │ │ ├── SpyTimerTest.java │ │ │ ├── TalkbackTest.java │ │ │ ├── TimerTest.java │ │ │ ├── WarningEventTest.java │ │ │ ├── WarningTypeTest.java │ │ │ └── WarningsTest.java │ │ ├── format │ │ │ ├── BitsTest.java │ │ │ ├── FloatValueTest.java │ │ │ ├── FormatIntegerLeftTest.java │ │ │ ├── FormatIntegerTest.java │ │ │ ├── FormatRealTest.java │ │ │ └── NullValueTest.java │ │ ├── gzip │ │ │ └── GzipUtilsTest.java │ │ ├── integrity │ │ │ ├── ExamTest.java │ │ │ ├── IntegerRangeTest.java │ │ │ └── IntegralAbstractTest.java │ │ ├── intervals │ │ │ ├── IntervalComparatorTest.java │ │ │ ├── JSReferenceRegionsTest.java │ │ │ ├── LongRangeTest.java │ │ │ ├── MergedIntervalsTest.java │ │ │ ├── RangeListTest.java │ │ │ ├── RangeTest.java │ │ │ ├── ReferenceRangesTest.java │ │ │ ├── ReferenceRegionsTest.java │ │ │ ├── RegionRestrictionTest.java │ │ │ ├── SequenceIdLocusComparatorTest.java │ │ │ ├── SequenceIdLocusSimpleTest.java │ │ │ ├── SequenceNameLocusComparatorTest.java │ │ │ ├── SequenceNameLocusSimpleTest.java │ │ │ ├── SimpleRangeMetaTest.java │ │ │ └── StatusIntervalTest.java │ │ ├── io │ │ │ ├── AdjustableGZIPOutputStreamTest.java │ │ │ ├── AsynchInputStreamTest.java │ │ │ ├── AsynchOutputStreamTest.java │ │ │ ├── BaseFileTest.java │ │ │ ├── BufferedOutputStreamFixTest.java │ │ │ ├── BufferedRandomAccessFileTest.java │ │ │ ├── ByteArrayIOUtilsTest.java │ │ │ ├── ClosedFileInputStreamTest.java │ │ │ ├── ConcurrentByteQueueTest.java │ │ │ ├── FalseSeekableStreamTest.java │ │ │ ├── FileUtilsTest.java │ │ │ ├── GzipAsynchInputStreamTest.java │ │ │ ├── GzipAsynchOutputStreamTest.java │ │ │ ├── IOUtilsTest.java │ │ │ ├── InputFileUtilsTest.java │ │ │ ├── LineWriterTest.java │ │ │ ├── LogFileTest.java │ │ │ ├── LogRecord.java │ │ │ ├── LogSimpleTest.java │ │ │ ├── MemoryPrintStreamTest.java │ │ │ ├── PartitionTest.java │ │ │ ├── RandomAccessFileStreamTest.java │ │ │ ├── RuntimeIOIteratorTest.java │ │ │ ├── SimpleArchiveTest.java │ │ │ ├── TestDirectory.java │ │ │ ├── TestDirectoryTest.java │ │ │ └── bzip2 │ │ │ │ ├── CBZip2InputStreamTest.java │ │ │ │ └── CRCTest.java │ │ ├── iterators │ │ │ ├── ArrayToIteratorTest.java │ │ │ ├── ComposeIteratorsTest.java │ │ │ ├── IteratorHelperTest.java │ │ │ ├── SubsampleIteratorTest.java │ │ │ └── TransformTest.java │ │ ├── machine │ │ │ ├── MachineOrientationTest.java │ │ │ ├── MachineTypeTest.java │ │ │ └── PairOrientationTest.java │ │ └── test │ │ │ ├── AbstractTempFileHandler.java │ │ │ ├── BgzipFileHelper.java │ │ │ ├── FileHelper.java │ │ │ ├── FileHelperTest.java │ │ │ ├── HttpServer.java │ │ │ ├── MockEventListener.java │ │ │ ├── NanoRegression.java │ │ │ ├── NotRandomRandom.java │ │ │ ├── NotRandomRandomTest.java │ │ │ ├── RandomByteGenerator.java │ │ │ ├── RandomDna.java │ │ │ ├── RandomDnaTest.java │ │ │ └── params │ │ │ └── TestParams.java │ │ ├── variant │ │ ├── GenomePriorParamsTest.java │ │ ├── MachineErrorParamsTest.java │ │ ├── cnv │ │ │ ├── CnaTypeTest.java │ │ │ ├── CnvRecordFilterTest.java │ │ │ └── cnveval │ │ │ │ ├── AbstractCnvEvalTest.java │ │ │ │ ├── CnaVariantListTest.java │ │ │ │ ├── CnaVariantSetTest.java │ │ │ │ ├── CnaVariantTest.java │ │ │ │ └── CnvEvalCliTest.java │ │ └── sv │ │ │ ├── VcfSvDecomposerTest.java │ │ │ └── bndeval │ │ │ ├── AbstractBndEvalTest.java │ │ │ ├── BndEvalCliTest.java │ │ │ ├── BndVariantTest.java │ │ │ ├── BreakpointGeometryTest.java │ │ │ ├── DummyBreakpointGeometryTest.java │ │ │ ├── FlippedProxyBreakpointGeometryTest.java │ │ │ ├── IntervalTest.java │ │ │ └── OrientationTest.java │ │ ├── vcf │ │ ├── AbstractVcfWriterTest.java │ │ ├── AdjusterTest.java │ │ ├── AllMatchFilterTest.java │ │ ├── AltVariantTypeFilterTest.java │ │ ├── AnnotatingVcfWriterTest.java │ │ ├── AssertVcfSortedTest.java │ │ ├── AsyncVcfWriterTest.java │ │ ├── BreakpointAltTest.java │ │ ├── ChildPhasingVcfAnnotatorTest.java │ │ ├── ClusterAnnotatorTest.java │ │ ├── DecomposingVcfIteratorTest.java │ │ ├── DefaultVcfWriterTest.java │ │ ├── ExpressionInfoFilterTest.java │ │ ├── ExpressionSampleFilterTest.java │ │ ├── FilterVcfWriterTest.java │ │ ├── NullVcfWriterTest.java │ │ ├── PassOnlyFilterTest.java │ │ ├── ReorderingVcfWriterTest.java │ │ ├── ScriptedVcfFilterTest.java │ │ ├── SnpIntersectionTest.java │ │ ├── StatisticsVcfWriterTest.java │ │ ├── SymbolicAltTest.java │ │ ├── VariantStatisticsTest.java │ │ ├── VariantTypeTest.java │ │ ├── VcfAltCleanerTest.java │ │ ├── VcfAnnotatorCliTest.java │ │ ├── VcfDecomposerCliTest.java │ │ ├── VcfFilterCliTest.java │ │ ├── VcfFilterCliValidatorTest.java │ │ ├── VcfFilterIteratorTest.java │ │ ├── VcfFilterStatisticsTest.java │ │ ├── VcfFilterStripperTest.java │ │ ├── VcfFormatStripperTest.java │ │ ├── VcfGtMajorityMergerTest.java │ │ ├── VcfIdCleanerTest.java │ │ ├── VcfInfoFilterTest.java │ │ ├── VcfInfoStripperTest.java │ │ ├── VcfMergeTest.java │ │ ├── VcfParserTest.java │ │ ├── VcfQualCleanerTest.java │ │ ├── VcfReaderTest.java │ │ ├── VcfRecordMergerTest.java │ │ ├── VcfRecordTest.java │ │ ├── VcfSameAltsMergerTest.java │ │ ├── VcfSampleNameRelabellerTest.java │ │ ├── VcfSampleStripperTest.java │ │ ├── VcfSortRefinerTest.java │ │ ├── VcfSplitCliTest.java │ │ ├── VcfStatsCliTest.java │ │ ├── VcfSubsetParserTest.java │ │ ├── VcfSubsetTest.java │ │ ├── VcfUtilsTest.java │ │ ├── annotation │ │ │ ├── AlleleCountInGenotypesAnnotationTest.java │ │ │ ├── AltAlleleQualityAnnotationTest.java │ │ │ ├── ContraryObservationCounterTest.java │ │ │ ├── DerivedAnnotationsTest.java │ │ │ ├── DummyDerivedFormatAnnotationTest.java │ │ │ ├── DummyDerivedInfoAnnotationTest.java │ │ │ ├── EquilibriumProbabilityAnnotationTest.java │ │ │ ├── FormatterTest.java │ │ │ ├── GenotypeQualityOverDepthAnnotationTest.java │ │ │ ├── InbreedingCoefficientAnnotationTest.java │ │ │ ├── LongestAlleleAnnotationTest.java │ │ │ ├── MeanQualityDifferenceAnnotationTest.java │ │ │ ├── NumberAllelesInGenotypesAnnotationTest.java │ │ │ ├── NumberOfAltAllelesAnnotationTest.java │ │ │ ├── PloidyAnnotationTest.java │ │ │ ├── QualOverDepthAnnotationTest.java │ │ │ ├── RefAltAnnotationTest.java │ │ │ ├── SimpleTandemRepeatAnnotatorTest.java │ │ │ ├── SplitContraryObservationAnnotatorTest.java │ │ │ ├── VariantAllelicFractionAnnotationTest.java │ │ │ ├── VariantMinorAllelicFractionAnnotationTest.java │ │ │ └── ZygosityAnnotationTest.java │ │ ├── eval │ │ │ ├── AbstractVcfEvalTest.java │ │ │ ├── AlleleAccumulatorTest.java │ │ │ ├── AnnotatingEvalSynchronizerTest.java │ │ │ ├── CombinedEvalSynchronizerTest.java │ │ │ ├── CombinedRocFilterTest.java │ │ │ ├── ExpressionRocFilterTest.java │ │ │ ├── FMeasureThresholdTest.java │ │ │ ├── FixedScoreThresholdTest.java │ │ │ ├── Ga4ghEvalSynchronizerTest.java │ │ │ ├── Ga4ghLooseMatchFilterTest.java │ │ │ ├── HalfPathTest.java │ │ │ ├── HaplotypePlaybackTest.java │ │ │ ├── MockVariant.java │ │ │ ├── OrientedVariantTest.java │ │ │ ├── OrientorTest.java │ │ │ ├── PathTest.java │ │ │ ├── PhaseTransferEvalSynchronizerTest.java │ │ │ ├── PhasingEvaluatorTest.java │ │ │ ├── PrecisionThresholdTest.java │ │ │ ├── RegionsRocFilterTest.java │ │ │ ├── RocContainerTest.java │ │ │ ├── RocFilterTest.java │ │ │ ├── RocOnlyEvalSynchronizerTest.java │ │ │ ├── RocPointTest.java │ │ │ ├── RocScoreFieldTest.java │ │ │ ├── RocSlopeTest.java │ │ │ ├── RocSortOrderTest.java │ │ │ ├── RocUtilsTest.java │ │ │ ├── SensitivityThresholdTest.java │ │ │ ├── SplitEvalSynchronizerTest.java │ │ │ ├── SquashedAlleleAccumulatorTest.java │ │ │ ├── TabixVcfRecordSetTest.java │ │ │ ├── TrioEvalSynchronizerTest.java │ │ │ ├── VariantFactoryTest.java │ │ │ ├── VariantSetTypeTest.java │ │ │ ├── VariantTest.java │ │ │ ├── Vcf2RocplotTest.java │ │ │ ├── VcfEvalCliTest.java │ │ │ ├── VcfEvalNanoTest.java │ │ │ ├── VcfEvalParamsTest.java │ │ │ ├── VcfEvalTaskTest.java │ │ │ └── VcfRecordTabixCallableTest.java │ │ ├── header │ │ │ ├── AltFieldTest.java │ │ │ ├── ContigFieldTest.java │ │ │ ├── FilterFieldTest.java │ │ │ ├── FormatFieldTest.java │ │ │ ├── InfoFieldTest.java │ │ │ ├── MetaTypeTest.java │ │ │ ├── PedigreeFieldTest.java │ │ │ ├── SampleFieldTest.java │ │ │ ├── VcfHeaderMergeTest.java │ │ │ ├── VcfHeaderTest.java │ │ │ ├── VcfNumberTest.java │ │ │ └── VcfNumberTypeTest.java │ │ └── mendelian │ │ │ ├── GenotypeProportionsTest.java │ │ │ ├── GenotypeTest.java │ │ │ ├── MendeliannessCheckerTest.java │ │ │ └── TrioConcordanceTest.java │ │ └── visualization │ │ ├── AnsiDisplayHelperTest.java │ │ ├── DisplayHelperTest.java │ │ └── HtmlDisplayHelperTest.java │ └── resources │ └── com │ └── rtg │ ├── alignment │ └── resources │ │ └── GotohEditDistanceDump.txt │ ├── graph │ └── resources │ │ ├── roc-nototal.tsv │ │ ├── roc.tsv │ │ └── roc2.tsv │ ├── mode │ ├── BLOSUM45TEST │ ├── BLOSUM45TEST.properties │ ├── BLOSUM45TESTPR │ ├── BLOSUM45TESTUNI │ ├── BLOSUM45TESTUNI.properties │ └── BLOSUM62CORRUPT │ ├── reader │ └── resources │ │ ├── cg2sdf-testns.txt │ │ ├── fastqtrim-e2e-rc.fastq │ │ ├── fastqtrim-e2e-trim-drop.fastq │ │ ├── fastqtrim-e2e-trim.fastq │ │ ├── format-cg-sam-v2.tsv │ │ ├── format-interleaved.txt │ │ ├── format-useprotein.txt │ │ ├── format-useq.txt │ │ ├── interleaved.fastq │ │ ├── mated-dups.sam │ │ ├── mated.sam │ │ ├── reads100.fastq │ │ ├── reads50_R1.fastq │ │ ├── reads50_R2.fastq │ │ ├── sample-cg-v2.sam │ │ ├── sample-v1.tsv │ │ ├── sample-v2.tsv │ │ ├── sample.tsv │ │ ├── sample.tsv.bz2 │ │ ├── sdf2cg-v1.tsv │ │ ├── sdf2cg-v2.tsv │ │ ├── sdf2sam-pe-sam │ │ ├── sdf2sam-se-sam │ │ ├── sdfsrc.fastq │ │ ├── sdfver10.arch │ │ ├── sdfver11.arch │ │ ├── sdfver12.arch │ │ ├── sdfver13.arch │ │ ├── sdfver4.arch │ │ ├── sdfver5.arch │ │ ├── sdfver6.arch │ │ ├── sdfver7.arch │ │ ├── sdfver8.arch │ │ ├── sdfver9.arch │ │ ├── sequences.fasta │ │ ├── taxonomy.tsv │ │ └── taxonomy_lookup.tsv │ ├── reference │ └── resources │ │ ├── testref-reference.txt │ │ ├── testref.fasta │ │ └── testref.manifest │ ├── relation │ └── resources │ │ ├── derived.vcf │ │ ├── dot.properties │ │ ├── octet.ped │ │ ├── pedfile │ │ ├── pedfilter-filtering-1.ped │ │ ├── pedfilter-filtering-2.ped │ │ ├── pedfilter-filtering-3.ped │ │ ├── pedfilter-toIds.ped │ │ ├── pedfilter-tovcf.txt │ │ ├── pedfromvcf │ │ ├── pednormal │ │ ├── pedstats-delim-c.txt │ │ ├── pedstats-delim-tab.txt │ │ ├── pedstats-female-ids.txt │ │ ├── pedstats-founder-ids.txt │ │ ├── pedstats-male-ids.txt │ │ ├── pedstats-maternal-ids.txt │ │ ├── pedstats-paternal-ids.txt │ │ ├── pedstats-primary-ids.txt │ │ ├── pedstats-todot-alt.txt │ │ ├── pedstats-todot-new.txt │ │ ├── pedstats-todot.txt │ │ ├── pop.ped │ │ ├── vcffromped.vcf │ │ └── vcfheader.vcf │ ├── report │ └── resources │ │ └── velocityTest.txt │ ├── sam │ └── resources │ │ ├── augmented.sam │ │ ├── bam.bam │ │ ├── bam.bam.bai │ │ ├── calibrate.bed │ │ ├── calibrated_mated.sam.gz │ │ ├── calibrated_mated.sam.gz.calibration │ │ ├── checklegacy │ │ ├── deduplicated-current.sam │ │ ├── deduplicated.sam │ │ ├── deduplicatedSE.sam │ │ ├── duplicates.sam │ │ ├── duplicatesSE.sam │ │ ├── failing.sam.gz │ │ ├── failing.sam.gz.tbi │ │ ├── indexmerge1.bam │ │ ├── indexmerge1.bam.bai │ │ ├── indexmerge2.bam │ │ ├── indexmerge2.bam.bai │ │ ├── indexmerge3.bam │ │ ├── indexmerge3.bam.bai │ │ ├── indexmerge4.bam │ │ ├── indexmerge4.bam.bai │ │ ├── mated.bam │ │ ├── mated.bam.bai │ │ ├── mated.sam │ │ ├── mergecombined.sam.gz │ │ ├── merged.bam.bai.debug │ │ ├── mergemated.sam │ │ ├── mergemated.sam.gz │ │ ├── mergeunmapped-aug.sam │ │ ├── mergeunmapped.sam.gz │ │ ├── mergeunmated.sam │ │ ├── mergeunmated.sam.gz │ │ ├── mixed.bam │ │ ├── mixed.bam.bai │ │ ├── mixed.sam.gz │ │ ├── mixed.sam.gz.tbi │ │ ├── mmmm.sam.gz │ │ ├── mmmm.sam.gz.tbi │ │ ├── multiRegionSequenceEnd.sam.gz │ │ ├── multiSequence.bam │ │ ├── multiSequence.bam.bai │ │ ├── readerWindow1.sam │ │ ├── readerWindow1.sam.gz │ │ ├── readerWindow1.sam.gz.tbi │ │ ├── readerWindow2.sam.gz │ │ ├── readerWindow2.sam.gz.tbi │ │ ├── readerWindow3.sam.gz │ │ ├── readerWindow3.sam.gz.tbi │ │ ├── readerWindowSmall.sam │ │ ├── readerWindowSmallGap.sam │ │ ├── readerWindowX4.sam.gz │ │ ├── readerWindowX4.sam.gz.tbi │ │ ├── readgroup_cg.txt │ │ ├── samoutput_expected_1.sam │ │ ├── sfm-exc-stdout │ │ ├── sfm-exc-unmappeddups │ │ ├── sfm-inc-stdout │ │ ├── sfm-inc-unmappeddups │ │ ├── snp_only.vcf.gz │ │ ├── snp_only.vcf.gz.tbi │ │ ├── tabix.sam.gz │ │ ├── tabix.sam.gz.tbi │ │ ├── tabixheader.sam.gz │ │ ├── tabixheader.sam.gz.tbi │ │ ├── test-multiregion.sam │ │ ├── test.cram │ │ ├── test.sam │ │ ├── test.sam.gz │ │ ├── test.sam.gz.tbi │ │ ├── test1_normal.sam │ │ ├── test2.bam │ │ ├── test2.bam.bai │ │ ├── test2.sam.gz │ │ ├── test2.sam.gz.tbi │ │ ├── test3.sam.gz │ │ ├── test3.sam.gz.tbi │ │ ├── tinyMappings.sam.gz │ │ ├── tinyTemplate.dwa │ │ ├── unmated-out-of-order.sam │ │ ├── unmated.sam │ │ ├── vcf.txt.gz │ │ └── vcf.txt.gz.tbi │ ├── simulation │ ├── reads │ │ └── resources │ │ │ ├── 454pe-results.fa │ │ │ ├── 454se-results.fa │ │ │ ├── cg-results.fa │ │ │ ├── cg-v2-results.fa │ │ │ └── cg-v2-results2.fa │ └── variants │ │ └── resources │ │ ├── childsim │ │ ├── pedsamplesim-summary.txt │ │ ├── pedsamplesim.vcf │ │ ├── popsim-simple.vcf │ │ ├── population_variant_gen_I.vcf │ │ ├── population_variant_gen_X.vcf │ │ ├── population_variant_gen_X_X.vcf │ │ ├── popvars │ │ └── samplereplayertest.vcf │ ├── tabix │ └── resources │ │ ├── alleleCounts.ac.gz │ │ ├── extract-header-only │ │ ├── extract-norestrict │ │ ├── extract-sam-multi │ │ ├── extract1000-5000 │ │ ├── extract500-1000 │ │ ├── extract500-1000-5000 │ │ ├── extract500-5000 │ │ ├── merged.sam.gz.tbi.debug │ │ ├── multiRegionSequenceEnd.bed.gz │ │ ├── tabixmerge1.sam.gz │ │ ├── tabixmerge1.sam.gz.tbi │ │ ├── tabixmerge2.sam.gz │ │ ├── tabixmerge2.sam.gz.tbi │ │ ├── tabixmerge3.sam.gz │ │ ├── tabixmerge3.sam.gz.tbi │ │ ├── tabixmerge4.sam.gz │ │ ├── tabixmerge4.sam.gz.tbi │ │ ├── tlr-multi-region │ │ └── tlr-single-region │ ├── taxonomy │ └── resources │ │ ├── tree1.tsv │ │ └── tree2.tsv │ ├── util │ ├── cli │ │ ├── spell.insensitive │ │ └── spell.sensitive │ ├── io │ │ └── bzip2 │ │ │ └── resources │ │ │ ├── sample3.ref │ │ │ ├── sample3.ref.bz2 │ │ │ ├── textfile │ │ │ ├── textfile.bz2 │ │ │ ├── textfilebad.bz2 │ │ │ └── textfilemulti.bz2 │ └── resources │ │ ├── ethwinout.txt │ │ ├── krona.xml │ │ ├── md5utils.txt │ │ ├── test.properties │ │ ├── tt-default.tsv │ │ ├── tt-default.txt │ │ ├── tt-indent-1center.txt │ │ ├── tt-indent-1left.txt │ │ ├── tt-indent.txt │ │ └── tt-mixed-alignments.txt │ ├── variant │ ├── cnv │ │ └── cnveval │ │ │ └── resources │ │ │ ├── cnveval_small_in_baseline.vcf │ │ │ ├── cnveval_small_in_calls.vcf │ │ │ ├── cnveval_small_in_regions.bed │ │ │ ├── cnveval_small_noroc_out_baseline.vcf │ │ │ ├── cnveval_small_noroc_out_calls.vcf │ │ │ ├── cnveval_small_noroc_out_summary.txt │ │ │ ├── cnveval_small_out_baseline.vcf │ │ │ ├── cnveval_small_out_calls.vcf │ │ │ ├── cnveval_small_out_del_roc.tsv │ │ │ ├── cnveval_small_out_dup_roc.tsv │ │ │ ├── cnveval_small_out_summary.txt │ │ │ └── cnveval_small_out_weighted_roc.tsv │ ├── priors │ │ ├── cnv │ │ │ └── testcnv-default.properties │ │ ├── error │ │ │ ├── testdummy_errors.properties │ │ │ └── testsequencer_errors.properties │ │ └── prior │ │ │ ├── testhumanprior.properties │ │ │ ├── testhumanpriorparams.properties │ │ │ ├── testprior.properties │ │ │ ├── testpriorbad1.properties │ │ │ ├── testpriorbad2.properties │ │ │ ├── testpriorbad3.properties │ │ │ └── testpriorbad4.properties │ └── sv │ │ └── bndeval │ │ └── resources │ │ ├── bndeval_small_all_out_fn.vcf │ │ ├── bndeval_small_all_out_fp.vcf │ │ ├── bndeval_small_all_out_summary.txt │ │ ├── bndeval_small_all_out_tp-baseline.vcf │ │ ├── bndeval_small_all_out_tp.vcf │ │ ├── bndeval_small_annotate_out_baseline.vcf │ │ ├── bndeval_small_annotate_out_calls.vcf │ │ ├── bndeval_small_annotate_out_summary.txt │ │ ├── bndeval_small_bidirectional2_in_baseline.vcf │ │ ├── bndeval_small_bidirectional2_in_calls.vcf │ │ ├── bndeval_small_bidirectional2_out_fn.vcf │ │ ├── bndeval_small_bidirectional2_out_fp.vcf │ │ ├── bndeval_small_bidirectional2_out_summary.txt │ │ ├── bndeval_small_bidirectional2_out_tp-baseline.vcf │ │ ├── bndeval_small_bidirectional2_out_tp.vcf │ │ ├── bndeval_small_bidirectional3_out_fn.vcf │ │ ├── bndeval_small_bidirectional3_out_fp.vcf │ │ ├── bndeval_small_bidirectional3_out_summary.txt │ │ ├── bndeval_small_bidirectional3_out_tp-baseline.vcf │ │ ├── bndeval_small_bidirectional3_out_tp.vcf │ │ ├── bndeval_small_bidirectional_annotate_out_baseline.vcf │ │ ├── bndeval_small_bidirectional_annotate_out_calls.vcf │ │ ├── bndeval_small_bidirectional_annotate_out_summary.txt │ │ ├── bndeval_small_bidirectional_in_baseline.vcf │ │ ├── bndeval_small_bidirectional_in_calls.vcf │ │ ├── bndeval_small_bidirectional_out_fn.vcf │ │ ├── bndeval_small_bidirectional_out_fp.vcf │ │ ├── bndeval_small_bidirectional_out_summary.txt │ │ ├── bndeval_small_bidirectional_out_tp-baseline.vcf │ │ ├── bndeval_small_bidirectional_out_tp.vcf │ │ ├── bndeval_small_default_out_fn.vcf │ │ ├── bndeval_small_default_out_fp.vcf │ │ ├── bndeval_small_default_out_summary.txt │ │ ├── bndeval_small_default_out_tp-baseline.vcf │ │ ├── bndeval_small_default_out_tp.vcf │ │ ├── bndeval_small_in_baseline.vcf │ │ ├── bndeval_small_in_calls.vcf │ │ ├── bndeval_small_tol_in_baseline.vcf │ │ ├── bndeval_small_tol_in_calls.vcf │ │ ├── bndeval_small_tol_out_fn.vcf │ │ ├── bndeval_small_tol_out_fp.vcf │ │ ├── bndeval_small_tol_out_summary.txt │ │ ├── bndeval_small_tol_out_tp-baseline.vcf │ │ └── bndeval_small_tol_out_tp.vcf │ └── vcf │ ├── annotation │ └── resources │ │ ├── coc_cof_rec.vcf │ │ └── scoc_cof_rec.vcf │ ├── eval │ └── resources │ │ ├── complexoverlap-hetero.tsv │ │ ├── complexoverlap-homo.tsv │ │ ├── complexoverlap-summary.txt │ │ ├── complexoverlap-weighted-rev.tsv │ │ ├── complexoverlap-weighted.tsv │ │ ├── ga4gh-loose-match-0_out.vcf │ │ ├── ga4gh-loose-match-1_out.vcf │ │ ├── ga4gh-loose-match-30_out.vcf │ │ ├── ga4gh-loose-match_in.vcf │ │ ├── obeyphasing │ │ ├── obeyphasing_in_baseline.vcf │ │ ├── obeyphasing_in_calls.vcf │ │ ├── obeyphasing_in_template.fa │ │ └── obeyphasing_out_tp.vcf │ │ ├── path-noinfite-roc.tsv │ │ ├── regions_roc_filter.bed │ │ ├── regions_roc_filter.vcf │ │ ├── roc-slope-0.txt │ │ ├── roc-slope-1.txt │ │ ├── roc-slope-2.txt │ │ ├── roc-slope-3.txt │ │ ├── roc-slope-3a.txt │ │ ├── rocempty-hetero.tsv │ │ ├── rocempty-homo.tsv │ │ ├── rocempty-summary.txt │ │ ├── rocempty-weighted-rev.tsv │ │ ├── rocempty-weighted.tsv │ │ ├── testroc-hetero.tsv │ │ ├── testroc-homo.tsv │ │ ├── testroc-summary.txt │ │ ├── testroc-weighted-rev.tsv │ │ ├── testroc-weighted.tsv │ │ ├── tricky-hetero.tsv │ │ ├── tricky-homo.tsv │ │ ├── tricky-summary.txt │ │ ├── tricky-weighted-rev.tsv │ │ ├── tricky-weighted.tsv │ │ ├── trickyxrx-hetero.tsv │ │ ├── trickyxrx-homo.tsv │ │ ├── trickyxrx-summary.txt │ │ ├── trickyxrx-weighted-rev.tsv │ │ ├── trickyxrx-weighted.tsv │ │ ├── vcf2rocplot │ │ ├── simple-region_out_summary.txt │ │ ├── simple-region_out_weighted_roc.tsv │ │ ├── simple_in_first.vcf │ │ ├── simple_in_second.vcf │ │ ├── simple_out_summary.txt │ │ └── simple_out_weighted_roc.tsv │ │ ├── vcfeval_all_matches_err.txt │ │ ├── vcfeval_all_matches_in_baseline.vcf │ │ ├── vcfeval_all_matches_in_calls.vcf │ │ ├── vcfeval_all_matches_in_template.fa │ │ ├── vcfeval_all_matches_out_output.vcf │ │ ├── vcfeval_annotate_in_baseline.vcf │ │ ├── vcfeval_annotate_in_calls.vcf │ │ ├── vcfeval_annotate_in_template.fa │ │ ├── vcfeval_annotate_out_baseline.vcf │ │ ├── vcfeval_annotate_out_calls.vcf │ │ ├── vcfeval_avoid_overlap │ │ ├── avoid_overlap_in_baseline.vcf │ │ ├── avoid_overlap_in_calls.vcf │ │ ├── avoid_overlap_in_template.fa │ │ ├── avoid_overlap_out_output.vcf │ │ └── avoid_overlap_out_summary.txt │ │ ├── vcfeval_combine2_in_baseline.vcf │ │ ├── vcfeval_combine2_in_calls.vcf │ │ ├── vcfeval_combine2_in_template.fa │ │ ├── vcfeval_combine2_out_output.vcf │ │ ├── vcfeval_combine_in_baseline.vcf │ │ ├── vcfeval_combine_in_calls.vcf │ │ ├── vcfeval_combine_in_template.fa │ │ ├── vcfeval_combine_out_output.vcf │ │ ├── vcfeval_ga4gh2_in_baseline.vcf │ │ ├── vcfeval_ga4gh2_in_calls.vcf │ │ ├── vcfeval_ga4gh2_in_template.fa │ │ ├── vcfeval_ga4gh2_out_output.vcf │ │ ├── vcfeval_ga4gh_in_baseline.vcf │ │ ├── vcfeval_ga4gh_in_calls.vcf │ │ ├── vcfeval_ga4gh_in_template.fa │ │ ├── vcfeval_ga4gh_out_output.vcf │ │ ├── vcfeval_nop │ │ ├── nop_in_baseline.vcf │ │ ├── nop_in_calls.vcf │ │ ├── nop_in_template.fa │ │ ├── nop_out_output.vcf │ │ └── nop_out_summary.txt │ │ ├── vcfeval_phase_transfer_in_baseline.vcf │ │ ├── vcfeval_phase_transfer_in_calls.vcf │ │ ├── vcfeval_phase_transfer_in_template.fa │ │ ├── vcfeval_phase_transfer_out_baseline.vcf │ │ ├── vcfeval_phase_transfer_out_calls.vcf │ │ ├── vcfeval_roc_only_in_baseline.vcf │ │ ├── vcfeval_roc_only_in_calls.vcf │ │ ├── vcfeval_roc_only_in_template.fa │ │ ├── vcfeval_roc_only_out_weighted_roc.tsv │ │ ├── vcfeval_roccrossjoin │ │ ├── vcfeval_roccrossjoin_in_baseline.vcf │ │ ├── vcfeval_roccrossjoin_in_calls.vcf │ │ ├── vcfeval_roccrossjoin_in_template.fa │ │ ├── vcfeval_roccrossjoin_out_test+indel_roc.tsv │ │ ├── vcfeval_roccrossjoin_out_test+snp_roc.tsv │ │ └── vcfeval_roccrossjoin_out_weighted_roc.tsv │ │ ├── vcfeval_small_alt │ │ ├── vcfeval_small_in_baseline.vcf │ │ ├── vcfeval_small_in_calls.vcf │ │ ├── vcfeval_small_in_template.fa │ │ ├── vcfeval_small_out_baseline.vcf │ │ └── vcfeval_small_out_calls.vcf │ │ ├── vcfeval_small_in_baseline.vcf │ │ ├── vcfeval_small_in_calls.vcf │ │ ├── vcfeval_small_in_template.fa │ │ ├── vcfeval_small_no_path │ │ ├── vcfeval_small_err.txt │ │ ├── vcfeval_small_in_baseline.vcf │ │ ├── vcfeval_small_in_calls.vcf │ │ └── vcfeval_small_in_template.fa │ │ ├── vcfeval_small_out_tp.vcf │ │ ├── vcfeval_small_out_weighted_roc.tsv │ │ ├── vcfeval_small_out_weighted_slope.tsv │ │ ├── vcfeval_small_recode_alleles.vcf │ │ ├── vcfeval_small_recode_in_empty.vcf │ │ ├── vcfeval_small_recode_in_samples.vcf │ │ ├── vcfeval_small_recode_in_template.fa │ │ ├── vcfeval_small_recode_recoded.vcf │ │ ├── vcfeval_small_region_in_baseline.vcf │ │ ├── vcfeval_small_region_in_calls.vcf │ │ ├── vcfeval_small_region_in_template.fa │ │ ├── vcfeval_small_region_out_weighted_roc.tsv │ │ ├── vcfeval_small_region_out_weighted_slope.tsv │ │ ├── vcfeval_small_samples_in_baseline.vcf │ │ ├── vcfeval_small_samples_in_calls.vcf │ │ ├── vcfeval_small_samples_in_template.fa │ │ ├── vcfeval_small_samples_out_weighted_roc.tsv │ │ ├── vcfeval_small_samples_out_weighted_slope.tsv │ │ ├── vcfeval_small_squash │ │ ├── vcfeval_small_in_baseline.vcf │ │ ├── vcfeval_small_in_calls.vcf │ │ ├── vcfeval_small_in_template.fa │ │ ├── vcfeval_small_out_tp.vcf │ │ └── vcfeval_small_out_weighted_roc.tsv │ │ ├── vcfeval_small_tricky │ │ ├── vcfeval_small_tricky_err.txt │ │ ├── vcfeval_small_tricky_in_baseline.vcf │ │ ├── vcfeval_small_tricky_in_calls.vcf │ │ ├── vcfeval_small_tricky_in_template.fa │ │ ├── vcfeval_small_tricky_out_tp.vcf │ │ └── vcfeval_small_tricky_out_weighted_roc.tsv │ │ ├── vcfeval_small_tricky2_err.txt │ │ ├── vcfeval_small_tricky2_in_baseline.vcf │ │ ├── vcfeval_small_tricky2_in_calls.vcf │ │ ├── vcfeval_small_tricky2_in_template.fa │ │ ├── vcfeval_small_tricky2_out_tp.vcf │ │ ├── vcfeval_small_tricky2_out_weighted_roc.tsv │ │ ├── vcfeval_small_tricky3_in_baseline.vcf │ │ ├── vcfeval_small_tricky3_in_calls.vcf │ │ ├── vcfeval_small_tricky3_in_template.fa │ │ ├── vcfeval_small_tricky3_out_tp.vcf │ │ ├── vcfeval_small_tricky3_out_weighted_roc.tsv │ │ ├── vcfeval_small_tricky4_in_baseline.vcf │ │ ├── vcfeval_small_tricky4_in_calls.vcf │ │ ├── vcfeval_small_tricky4_in_template.fa │ │ ├── vcfeval_small_tricky4_out_tp-baseline.vcf │ │ ├── vcfeval_small_tricky4_out_tp.vcf │ │ ├── vcfeval_small_trickysquash │ │ ├── trickysquash_in_baseline.vcf │ │ ├── trickysquash_in_calls.vcf │ │ ├── trickysquash_in_template.fa │ │ ├── trickysquash_out_baseline.vcf │ │ └── trickysquash_out_calls.vcf │ │ ├── vcfeval_small_updel │ │ ├── updel2_in_baseline.vcf │ │ ├── updel2_in_calls.vcf │ │ ├── updel2_in_template.fa │ │ ├── updel2_out_baseline.vcf │ │ ├── updel2_out_calls.vcf │ │ ├── updel3_in_baseline.vcf │ │ ├── updel3_in_calls.vcf │ │ ├── updel3_in_template.fa │ │ ├── updel3_out_baseline.vcf │ │ ├── updel3_out_calls.vcf │ │ ├── updel4_in_baseline.vcf │ │ ├── updel4_in_calls.vcf │ │ ├── updel4_in_template.fa │ │ ├── updel4_out_baseline.vcf │ │ ├── updel4_out_calls.vcf │ │ ├── updel5_in_baseline.vcf │ │ ├── updel5_in_calls.vcf │ │ ├── updel5_in_template.fa │ │ ├── updel5_out_baseline.vcf │ │ ├── updel5_out_calls.vcf │ │ ├── updel_in_baseline.vcf │ │ ├── updel_in_calls.vcf │ │ ├── updel_in_template.fa │ │ ├── updel_out_baseline.vcf │ │ └── updel_out_calls.vcf │ │ ├── vcfeval_split_in_baseline.vcf │ │ ├── vcfeval_split_in_calls.vcf │ │ ├── vcfeval_split_in_template.fa │ │ ├── vcfeval_split_no_roc_err.txt │ │ ├── vcfeval_split_no_roc_in_baseline.vcf │ │ ├── vcfeval_split_no_roc_in_calls.vcf │ │ ├── vcfeval_split_no_roc_in_template.fa │ │ ├── vcfeval_split_no_roc_out_fn.vcf │ │ ├── vcfeval_split_no_roc_out_fp.vcf │ │ ├── vcfeval_split_no_roc_out_phasing.txt │ │ ├── vcfeval_split_no_roc_out_summary.txt │ │ ├── vcfeval_split_no_roc_out_tp-baseline.vcf │ │ ├── vcfeval_split_no_roc_out_tp.vcf │ │ ├── vcfeval_split_out_fn.vcf │ │ ├── vcfeval_split_out_fp.vcf │ │ ├── vcfeval_split_out_phasing.txt │ │ ├── vcfeval_split_out_summary.txt │ │ ├── vcfeval_split_out_tp-baseline.vcf │ │ ├── vcfeval_split_out_tp.vcf │ │ ├── vcfeval_tetraploid │ │ ├── small_in_baseline.vcf │ │ ├── small_in_calls.vcf │ │ ├── small_in_template.fa │ │ ├── small_out_baseline.vcf │ │ └── small_out_calls.vcf │ │ ├── vcfeval_too_complex_end_err.txt │ │ ├── vcfeval_too_complex_end_in_baseline.vcf │ │ ├── vcfeval_too_complex_end_in_calls.vcf │ │ ├── vcfeval_too_complex_end_in_template.fa │ │ ├── vcfeval_too_complex_end_out_weighted_roc.tsv │ │ ├── vcfeval_too_complex_err.txt │ │ ├── vcfeval_too_complex_in_baseline.vcf │ │ ├── vcfeval_too_complex_in_calls.vcf │ │ ├── vcfeval_too_complex_in_template.fa │ │ ├── vcfeval_too_complex_out_weighted_roc.tsv │ │ ├── vcfeval_too_complex_out_weighted_slope.tsv │ │ ├── vcfeval_trio │ │ ├── mie_in_baseline.vcf │ │ ├── mie_in_calls.vcf │ │ ├── mie_in_template.fa │ │ ├── mie_out_output.vcf │ │ ├── ok_in_baseline.vcf │ │ ├── ok_in_calls.vcf │ │ ├── ok_in_template.fa │ │ └── ok_out_output.vcf │ │ └── vcfeval_triploid │ │ ├── small_in_baseline.vcf │ │ ├── small_in_calls.vcf │ │ ├── small_in_template.fa │ │ └── small_out_output.vcf │ ├── mendelian │ └── resources │ │ ├── gt_prop_biallelic_results.txt │ │ ├── gt_prop_can_results.txt │ │ ├── gt_prop_diploid_results.txt │ │ ├── gt_prop_ploidy_biallelic_results.txt │ │ ├── gt_prop_ploidy_can_results.txt │ │ ├── gt_prop_ploidy_diploid_results.txt │ │ ├── gt_prop_ploidy_results.txt │ │ ├── gt_prop_ploidy_test.vcf │ │ ├── gt_prop_results.txt │ │ ├── gt_prop_test.vcf │ │ ├── mendelian.annotated.vcf │ │ ├── mendelian.consistent.vcf │ │ ├── mendelian.inconsistent.vcf │ │ ├── mendelian.out.txt │ │ ├── mendelian2.out.txt │ │ └── merge.vcf │ └── resources │ ├── bedinput.txt │ ├── bedinputb.txt │ ├── exclude.bed │ ├── exclude.vcf │ ├── include.bed │ ├── include.vcf │ ├── snpAnnotate_small.bed │ ├── snpAnnotate_small.vcf │ ├── snpAnnotate_small_exp.vcf │ ├── snpAnnotate_small_ids.vcf │ ├── snpAnnotate_small_ids_exp.vcf │ ├── snpAnnotate_small_ids_vcf.vcf │ ├── snpAnnotate_small_vcf_ids_exp.vcf │ ├── snpfiltertest.vcf │ ├── snpfiltertest2.vcf │ ├── snpfiltertest2_exp.vcf │ ├── snpfiltertest2_exp.vcf.txt │ ├── snpfiltertest3.vcf │ ├── snpfiltertest3_exp.vcf │ ├── snpfiltertest3_exp.vcf.txt │ ├── snpfiltertest3_exp_all.vcf │ ├── snpfiltertest3_exp_all.vcf.txt │ ├── snpfiltertest4.vcf │ ├── snpfiltertest4_exp.vcf │ ├── snpfiltertest4_exp.vcf.txt │ ├── snpfiltertest4_exp_nonsnps.vcf │ ├── snpfiltertest4_exp_nonsnps.vcf.txt │ ├── snpfiltertest5.vcf │ ├── snpfiltertest5_DotPass_exp.vcf │ ├── snpfiltertest5_DotPass_exp.vcf.txt │ ├── snpfiltertest5_ac2_exp.vcf │ ├── snpfiltertest5_ac2_exp.vcf.txt │ ├── snpfiltertest5_ac3_exp.vcf │ ├── snpfiltertest5_ac3_exp.vcf.txt │ ├── snpfiltertest5_exp.vcf │ ├── snpfiltertest5_exp.vcf.txt │ ├── snpfiltertest5_exp_all.vcf │ ├── snpfiltertest5_exp_all.vcf.txt │ ├── snpfiltertest5_rx_exp.vcf │ ├── snpfiltertest5_rx_exp.vcf.txt │ ├── snpfiltertest6.vcf │ ├── snpfiltertest6_exp.vcf │ ├── snpfiltertest6_exp.vcf.txt │ ├── snpfiltertestASR_exp.vcf │ ├── snpfiltertestASR_exp.vcf.txt │ ├── snpfiltertestAVR.vcf │ ├── snpfiltertestAVR_AmMu3.vcf │ ├── snpfiltertestAVR_AmMu3.vcf.txt │ ├── snpfiltertestAVR_AmMu4.vcf │ ├── snpfiltertestAVR_AmMu4.vcf.txt │ ├── snpfiltertestAVR_AmMu5.vcf │ ├── snpfiltertestAVR_AmMu5.vcf.txt │ ├── snpfiltertestAVR_Avr7.vcf │ ├── snpfiltertestAVR_Avr7.vcf.txt │ ├── snpfiltertestAVR_exp.vcf │ ├── snpfiltertestAVR_exp.vcf.txt │ ├── snpfiltertestAVR_exp2.vcf │ ├── snpfiltertestAVR_exp2.vcf.txt │ ├── snpfiltertestAVR_exp3.vcf │ ├── snpfiltertestAVR_exp3.vcf.txt │ ├── snpfiltertestAVR_exp4.vcf │ ├── snpfiltertestAVR_exp4.vcf.txt │ ├── snpfiltertestAVR_exp5.vcf │ ├── snpfiltertestAVR_exp5.vcf.txt │ ├── snpfiltertestAVR_exp6.vcf │ ├── snpfiltertestAVR_exp6.vcf.txt │ ├── snpfiltertestAVR_exp7.vcf │ ├── snpfiltertestAVR_exp7.vcf.txt │ ├── snpfiltertestAVR_exp8.vcf │ ├── snpfiltertestAVR_exp8.vcf.txt │ ├── snpfiltertestRCE.vcf │ ├── snpfiltertestRCE_exp.vcf │ ├── snpfiltertestRCE_exp.vcf.txt │ ├── snpfiltertestSR.vcf │ ├── snpfiltertestSR_exp.vcf │ ├── snpfiltertestSR_exp.vcf.txt │ ├── snpfiltertest_DNP.vcf │ ├── snpfiltertest_DNP_exp.vcf │ ├── snpfiltertest_DNP_exp.vcf.txt │ ├── snpfiltertest_DNP_sample_exp.vcf │ ├── snpfiltertest_DNP_sample_exp.vcf.txt │ ├── snpfiltertest_complex.vcf │ ├── snpfiltertest_complex_exc.vcf │ ├── snpfiltertest_complex_inc.vcf │ ├── snpfiltertest_complex_inc_exc_bed.vcf │ ├── snpfiltertest_complex_inc_exc_bed.vcf.txt │ ├── snpfiltertest_complex_inc_exc_vcf.vcf │ ├── snpfiltertest_complex_inc_exc_vcf.vcf.txt │ ├── snpfiltertest_exp.vcf │ ├── snpfiltertest_exp.vcf.txt │ ├── snpfiltertest_exp_clear.vcf │ ├── snpfiltertest_exp_clear.vcf.txt │ ├── snpsA.vcf │ ├── snpsB.vcf │ ├── snps_complex.vcf │ ├── snpsannotatedb.txt │ ├── variantstatistics-known.txt │ ├── variantstatistics-novel.txt │ ├── variantstatistics.txt │ ├── variantstatistics2.txt │ ├── vcf-sort-tweak-2-out.vcf │ ├── vcf-sort-tweak-2.vcf │ ├── vcf-sort-tweak-out.vcf │ ├── vcf-sort-tweak.vcf │ ├── vcf.txt │ ├── vcfdecompose_in.vcf │ ├── vcfdecompose_out_indels.vcf │ ├── vcfdecompose_out_indels.vcf.txt │ ├── vcfdecompose_out_mnps.vcf │ ├── vcfdecompose_out_mnps.vcf.txt │ ├── vcfdecompose_out_noref.vcf │ ├── vcfdecompose_out_noref.vcf.txt │ ├── vcfdecompose_out_ref.vcf │ ├── vcfdecompose_out_ref.vcf.txt │ ├── vcfdecompose_splode1.vcf │ ├── vcfdensity_in.vcf │ ├── vcfdensity_out.vcf │ ├── vcffilterIndDens.vcf │ ├── vcffilterIndDens_exp.vcf │ ├── vcffilterIndDens_exp.vcf.txt │ ├── vcffilterNoGt.vcf │ ├── vcffilterNoGt_exp1.txt │ ├── vcffilterNoGt_exp2.txt │ ├── vcfmerge-f1.vcf │ ├── vcfmerge-f2.vcf │ ├── vcfmerge-f3.vcf │ ├── vcfmerge-mix-nosample-1.vcf │ ├── vcfmerge-mix-nosample-2.vcf │ ├── vcfmerge-na12880.vcf │ ├── vcfmerge-na12889.vcf │ ├── vcfmerge_out_drop.vcf │ ├── vcfmerge_out_force-all.vcf │ ├── vcfmerge_out_force1.vcf │ ├── vcfmerge_out_mix-nosample.vcf │ ├── vcfmerge_out_no-merge-alts.vcf │ ├── vcfmerge_out_no-merge.vcf │ ├── vcfmerge_out_numberformats.vcf │ ├── vcfmerge_out_preserve.vcf │ ├── vcfmerge_out_region5.vcf │ ├── vcfmerge_out_simple-rev.vcf │ ├── vcfmerge_out_simple.vcf │ ├── vcfmerge_stats.txt │ ├── vcfmerge_stats_drop.txt │ ├── vcfmerge_stats_force-all.txt │ ├── vcfmerge_stats_force1.txt │ ├── vcfmerge_stats_mix-nosample.txt │ ├── vcfmerge_stats_no-merge-alts.txt │ ├── vcfmerge_stats_no-merge.txt │ ├── vcfmerge_stats_numberformats.txt │ ├── vcfmerge_stats_preserve.txt │ ├── vcfmerge_stats_region5.txt │ ├── vcfmerge_stats_simple-rev.txt │ ├── vcfmerge_stats_simple.txt │ ├── vcfmerge_testSamePos.vcf │ ├── vcfmerge_testSamePosDiffRef.vcf │ ├── vcfmerge_testSamePosDiffRef_pa.vcf │ ├── vcfmerge_testSingle.vcf │ ├── vcfsplit-pop.vcf │ ├── vcfsplit_out_remove_daughter1.vcf │ ├── vcfsplit_out_remove_father.vcf │ ├── vcfsplit_out_select_son1.vcf │ ├── vcfsplit_out_select_son2.vcf │ ├── vcfsplit_out_simple_daughter1.vcf │ ├── vcfsplit_out_simple_daughter2.vcf │ ├── vcfsplit_out_simple_father.vcf │ ├── vcfsplit_out_simple_mother.vcf │ ├── 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