├── .github
└── workflows
│ └── static.yml
├── .gitignore
├── LICENSE.txt
├── README.md
├── build.xml
├── buildLib
├── ant-contrib-1.0b3.jar
└── handlechecker.jar
├── 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
│ ├── vcfsplit_out_simple_son1.vcf
│ ├── vcfsplit_out_simple_son2.vcf
│ ├── vcfstats-run1.txt
│ ├── vcfstats-run2.txt
│ ├── vcfstats-run3.txt
│ ├── vcfstats.vcf
│ ├── vcfsubset-keepfilter-pass.vcf
│ ├── vcfsubset-keepfilter.vcf
│ ├── vcfsubset-keepinfoACAN.vcf
│ ├── vcfsubset-keepsamples.vcf
│ ├── vcfsubset-multi.vcf
│ ├── vcfsubset-removeformat.vcf
│ └── vcfsubset.vcf
└── testLib
├── hamcrest-core-1.3.jar
├── junit-frames.xsl
├── junit.jar
├── junit.txt
├── spelling.jar
└── summary
└── junit-frames.xsl
/.gitignore:
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1 | # git ls-files --others --exclude-from=.git/info/exclude
2 | # Lines that start with '#' are comments.
3 | # For a project mostly in C, the following would be a good set of
4 | # exclude patterns (uncomment them if you want to use them):
5 | # *.[oa]
6 | # *~
7 |
8 | *.class
9 | *.aux
10 | *.log
11 | *.dvi
12 | *.pdf
13 | *.ps
14 | *.eps
15 | *.swp
16 | *.el
17 |
18 | *~
19 | #*#
20 | .#.*
21 |
22 | out
23 | bin
24 | build
25 | dist
26 | tmp
27 | .ant-targets-build.xml
28 | .settings
29 | *.classpath
30 | *.project
31 | /test/.checkstyle
32 | /.metadata
33 | /target
34 | /.idea
35 | *.iml
36 |
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1 | .. RTG Operations Manual documentation master file
2 |
3 | Table Of Contents
4 | =================
5 |
6 | .. toctree::
7 | :maxdepth: 3
8 |
9 | overview
10 | rtg_command_reference
11 | product_usage
12 | administration
13 | appendix
14 |
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1 | .. only:: core or extra
2 |
3 | .. include:: product_usage.inc.rst
4 |
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9 | SOURCELINK_SUFFIX: '.txt',
10 | NAVIGATION_WITH_KEYS: false,
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12 | ENABLE_SEARCH_SHORTCUTS: true,
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1 |
2 | Utility classes for managing large byte array like objects.
3 |
4 |
5 |
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1 |
2 | Utility classes for managing large int array like objects.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | Utility classes for managing large long array like objects.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | Utility classes for managing large Object array like objects.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | Utility classes for managing large array like objects.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | Utility classes for managing large short array like objects.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | Classes associated with parsing command line flags.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | String formatting utilities.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | John's stuff.
3 |
4 |
5 |
--------------------------------------------------------------------------------
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1 |
2 | I/O utility classes.
3 |
4 |
5 |
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1 | #
2 | # Expected value for score.
3 | EXPECTED = -0.2789
4 | # K in expect equation.
5 | K = 0.032
6 | # H is the relative entropy of the scoring matrix
7 | H = 0.10
8 | # LAMBDA in expect equation.
9 | LAMBDA = 0.195
10 | # Average score for two identical amino acids.
11 | HIT = 4.5
12 | # Average score for two different amino acids.
13 | MISS = -1.0
14 | # Score on opening a gap.
15 | GAP = -12.0
16 | # Score on extending a gap.
17 | EXTEND = -2.0
18 |
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/src/main/resources/com/rtg/mode/BLOSUM62.properties:
--------------------------------------------------------------------------------
1 | #
2 | # Expected value for score.
3 | EXPECTED = -0.5209
4 | # K in expect equation.
5 | K = 0.0410
6 | # H is the relative entropy of the scoring matrix
7 | H = 0.14
8 | # LAMBDA in expect equation.
9 | LAMBDA = 0.267
10 | # Average score for two identical amino acids.
11 | HIT = 4.5
12 | # Average score for two different amino acids.
13 | MISS = -1.0
14 | # Score on opening a gap.
15 | GAP = -10.0
16 | # Score on extending a gap.
17 | EXTEND = -1.0
18 |
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/src/main/resources/com/rtg/mode/BLOSUM80.properties:
--------------------------------------------------------------------------------
1 | #
2 | # Expected value for score.
3 | EXPECTED = -0.7442
4 | # K in expect equation.
5 | K = 0.071
6 | # H is the relative entropy of the scoring matrix
7 | H = 0.27
8 | # LAMBDA in expect equation.
9 | LAMBDA = 0.299
10 | # Average score for two identical amino acids.
11 | HIT = 4.5
12 | # Average score for two different amino acids.
13 | MISS = -1.0
14 | # Score on opening a gap.
15 | GAP = -9.0
16 | # Score on extending a gap.
17 | EXTEND = -1.0
18 |
--------------------------------------------------------------------------------
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2 | @desc Human GRCh37 with HGRC naming
3 | @source com/rtg/reference/resources/grch37-hgrc.txt
4 | @checks name length
5 | 1 249250621
6 | 2 243199373
7 | 3 198022430
8 | 4 191154276
9 | 5 180915260
10 | 6 171115067
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13 | 9 141213431
14 | 10 135534747
15 | 11 135006516
16 | 12 133851895
17 | 13 115169878
18 | 14 107349540
19 | 15 102531392
20 | 16 90354753
21 | 17 81195210
22 | 18 78077248
23 | 19 59128983
24 | 20 63025520
25 | 21 48129895
26 | 22 51304566
27 | X 155270560
28 | Y 59373566
29 | MT 16569
30 |
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2 | @desc Mouse GRCm38
3 | @source com/rtg/reference/resources/grcm38.txt
4 | @checks name length
5 | 1 195471971
6 | 2 182113224
7 | 3 160039680
8 | 4 156508116
9 | 5 151834684
10 | 6 149736546
11 | 7 145441459
12 | 8 129401213
13 | 9 124595110
14 | 10 130694993
15 | 11 122082543
16 | 12 120129022
17 | 13 120421639
18 | 14 124902244
19 | 15 104043685
20 | 16 98207768
21 | 17 94987271
22 | 18 90702639
23 | 19 61431566
24 | MT 16299
25 | X 171031299
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2 | grch37-ucsc.manifest
3 | grch38-ucsc.manifest
4 | hg18.manifest
5 | ncbim37.manifest
6 | grcm38.manifest
7 |
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2 | @desc Just Chr Names HGRC style
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4 | @checks name
5 | 1
6 | 2
7 | 3
8 | 4
9 | 5
10 | 6
11 | 7
12 | 8
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5 | chr1
6 | chr2
7 | chr3
8 | chr4
9 | chr5
10 | chr6
11 | chr7
12 | chr8
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2 | @desc Just Chr Names UCSC style
3 | @source NotAFile
4 | @checks name
5 | chrW
6 |
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3 | @source NotAFile
4 | @checks name
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2 | @desc Mouse NCBIM37
3 | @source com/rtg/reference/resources/ncbim37.txt
4 | @checks name length
5 | 1 197195432
6 | 2 181748087
7 | 3 159599783
8 | 4 155630120
9 | 5 152537259
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1 | #total baseline variants: 0
2 | #score true_positives false_positives
3 | 3.300 0.000 15
4 | 2.261 0.000 137
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/graph/resources/roc.tsv:
--------------------------------------------------------------------------------
1 | #total baseline variants: 3092754
2 | #score true_positives false_positives
3 | 3.300 0.000 15
4 | 2.261 70000.000 137
5 | 1.226 180000.000 516
6 | 0.700 406000.000 11337
7 | 0.533 1971000.000 1446920
8 | 0.333 2071000.000 1646920
9 | 0.200 2995295.000 1864591
10 |
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/src/test/resources/com/rtg/mode/BLOSUM45TEST.properties:
--------------------------------------------------------------------------------
1 | #
2 | # Expected value for score.
3 | #EXPECTED = -0.2789
4 | # K in expect equation.
5 | K = 0.0410
6 | # LAMBDA in expect equation.
7 | LAMBDA = 0.267
8 | # Average score for two identical amino acids.
9 | HIT = 4.5
10 | # Average score for two different amino acids.
11 | MISS = -1.0
12 | # Score on opening a gap.
13 | GAP = -10.0
14 | # Score on extending a gap.
15 | EXTEND = -1.0
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/mode/BLOSUM45TESTUNI.properties:
--------------------------------------------------------------------------------
1 | #
2 | # Expected value for score.
3 | #EXPECTED = -0.2789
4 | # K in expect equation.
5 | K = \uu
6 | # LAMBDA in expect equation.
7 | LAMBDA = 0.267
8 | # Average score for two identical amino acids.
9 | HIT = 4.5
10 | # Average score for two different amino acids.
11 | MISS = -1.0
12 | # Score on opening a gap.
13 | GAP = -10.0
14 | # Score on extending a gap.
15 | EXTEND = -1.0
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/cg2sdf-testns.txt:
--------------------------------------------------------------------------------
1 |
2 | Input Data
3 | Files : in.tsv
4 | Format : CG
5 | Type : DNA
6 | Number of pairs : 2
7 | Number of sequences: 4
8 | Total residues : 40
9 | Minimum length : 10
10 | Mean length : 10
11 | Maximum length : 10
12 |
13 | Output Data
14 | Number of pairs : 1
15 | Number of sequences: 2
16 | Total residues : 20
17 | Minimum length : 10
18 | Mean length : 10
19 | Maximum length : 10
20 |
21 | There were 1 pairs skipped due to filters
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/format-interleaved.txt:
--------------------------------------------------------------------------------
1 | Formatting interleaved paired-end FASTQ data
2 |
3 | Input Data
4 | Files : input.fastq
5 | Format : interleaved paired-end FASTQ
6 | Type : DNA
7 | Number of pairs : 20
8 | Number of sequences: 40
9 | Total residues : 4040
10 | Minimum length : 101
11 | Mean length : 101
12 | Maximum length : 101
13 |
14 | Output Data
15 | Number of pairs : 20
16 | Number of sequences: 40
17 | Total residues : 4040
18 | Minimum length : 101
19 | Mean length : 101
20 | Maximum length : 101
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/format-useprotein.txt:
--------------------------------------------------------------------------------
1 |
2 | Input Data
3 | Files : in.fasta
4 | Format : FASTA
5 | Type : PROTEIN
6 | Number of sequences: 1
7 | Total residues : 22
8 | Minimum length : 22
9 | Mean length : 22
10 | Maximum length : 22
11 |
12 | Output Data
13 | Number of sequences: 1
14 | Total residues : 22
15 | Minimum length : 22
16 | Mean length : 22
17 | Maximum length : 22
18 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/format-useq.txt:
--------------------------------------------------------------------------------
1 |
2 | Input Data
3 | Files : raw
4 | Format : FASTQ
5 | Type : DNA
6 | Number of sequences: 1
7 | Total residues : 5
8 | Minimum length : 5
9 | Mean length : 5
10 | Maximum length : 5
11 |
12 | Output Data
13 | Number of sequences: 1
14 | Total residues : 5
15 | Minimum length : 5
16 | Mean length : 5
17 | Maximum length : 5
18 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/sample.tsv:
--------------------------------------------------------------------------------
1 | #
2 | # Example header lines
3 |
4 | >flags reads scores
5 | 1 AAAAAAAAAACCCCCCCCCC ABCDEFGHIJJIHGFEDCBA
6 | 3 GGGGGGGGGGTTTTTTTTTT !"#$%&'()*+,-./01234
7 | 0 ATATATATATATATATATAT 56789:;<=>?@ABCDEFGH
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/sample.tsv.bz2:
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/src/test/resources/com/rtg/reader/resources/sdf2sam-pe-sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:unsorted
2 | name 77 * 0 0 * * 0 0 ACGTCG 123456
3 | name 141 * 0 0 * * 0 0 TTAATA 178876
4 | second 77 * 0 0 * * 0 0 ACGGGT 445565
5 | second 141 * 0 0 * * 0 0 CGGCCG 177888
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/sdf2sam-se-sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:unsorted
2 | name 4 * 0 0 * * 0 0 ACGTCG 123456
3 | second 4 * 0 0 * * 0 0 ACGGGT 445565
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/sdfsrc.fastq:
--------------------------------------------------------------------------------
1 | @foozlemcpants
2 | atcagcgactatcgatcagtcagatgcatgatcagcatctga
3 | +
4 | !$@#$%&*(SDASDASDAHJHKMJCSCDSAFDADKFJDA;';
5 | @pantsmcfoozle
6 | atcatcagtcagatgcatgatcagcatctgaagcgactatcg
7 | +
8 | !$@#$%DASDAHJHKMJCSC&*(SDASDSAFDADKFJDA;';
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/sdfver10.arch:
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/src/test/resources/com/rtg/reader/resources/sdfver11.arch:
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/src/test/resources/com/rtg/reader/resources/sdfver13.arch:
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/src/test/resources/com/rtg/reference/resources/testref-reference.txt:
--------------------------------------------------------------------------------
1 | version 1
2 | either def diploid linear
3 | either seq abcd diploid linear
4 | either seq moo diploid linear
5 | either seq lalala diploid linear
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reference/resources/testref.fasta:
--------------------------------------------------------------------------------
1 | >abcd
2 | acgatcagcatcgatcgatcagctagcatcgatttttcgagatcagtcagctagcat
3 | >test3
4 | tttagaggcagcatctgctcatcagcgactagctacgactgcat
5 | >moo
6 | ttttcgatacgagcgcgggggacgagcagcagtcactatcgagcgggcagctatataaaa
7 | >lalala
8 | tgcgtttgcaacggcgacgatataaaattctgcgcgcgagcgtactagctcat
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reference/resources/testref.manifest:
--------------------------------------------------------------------------------
1 | #ref-manifest v2.0
2 | @desc test manifest for testref.fasta
3 | @source com/rtg/reference/resources/testref-reference.txt
4 | @checks name length
5 | abcd 57
6 | moo 60
7 | lalala 53
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/derived.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##SAMPLE=
3 | ##SAMPLE=
4 | ##SAMPLE=
5 | ##SAMPLE=
6 | ##SAMPLE=
7 | ##SAMPLE=
8 | ##PEDIGREE=
9 | ##PEDIGREE=
10 | ##PEDIGREE=
11 | ##PEDIGREE=
12 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child child-cells1 child-cells2 child-cells3 father mother
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/dot.properties:
--------------------------------------------------------------------------------
1 | # Alternate display properties
2 | font=Helvetica
3 | invisible.node=[shape=point,style=filled,fillcolor="/greys9/8",label="",height=.001,width=.001]
4 | color=/greys9/8
5 | bgcolor=transparent
6 | male.fill=/rdylbu11/7:/rdylbu11/8
7 | female.fill=/rdpu9/2:/rdpu9/4
8 | unknown.fill=/greens9/2:/greens9/4
9 | disease.fill=/greys9/2:/greys9/4
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/octet.ped:
--------------------------------------------------------------------------------
1 | # PED format pedigree
2 | # fam-id ind-id pat-id mat-id sex phen
3 | 1 NA12880-1 NA12877-1 NA12878 2 0
4 | 0 NA12880-half NA12877-1 0 2 0
5 | 1 NA12883 NA12877-1 NA12878 1 0
6 | 1 NA12877-1 NA12889 NA12890 1 0
7 | 1 NA12878 NA12891-1 NA12892-1 2 0
8 | 0 NA12889 0 0 1 0
9 | 0 NA12890 0 0 2 0
10 | 0 NA12891-1 0 0 1 0
11 | 0 NA12892-1 0 0 2 0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfile:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
4 | #sex: 1=male; 2=female; 0=unknown
5 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
6 | #
7 | #fam-id ind-id pat-id mat-id sex phen
8 | 0 child father mother 1 2
9 | 0 father 0 0 1 2
10 | 0 mother 0 0 2 0
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfilter-filtering-1.ped:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
4 | #sex: 1=male; 2=female; 0=unknown
5 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
6 | #
7 | #fam-id ind-id pat-id mat-id sex phen
8 | 1 NA12877-1 0 0 1 0
9 | 1 NA12878 0 0 2 0
10 | 1 NA12880-1 NA12877-1 NA12878 2 0
11 | 1 NA12883 NA12877-1 NA12878 1 0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfilter-filtering-2.ped:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
4 | #sex: 1=male; 2=female; 0=unknown
5 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
6 | #
7 | #fam-id ind-id pat-id mat-id sex phen
8 | 1 NA12877-1 0 0 1 0
9 | 1 NA12878 0 0 2 0
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfilter-filtering-3.ped:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
4 | #sex: 1=male; 2=female; 0=unknown
5 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
6 | #
7 | #fam-id ind-id pat-id mat-id sex phen
8 | 1 NA12877-1 NA12889 0 1 0
9 | 1 NA12883 NA12877-1 0 1 0
10 | 0 NA12889 0 0 1 0
11 | 0 NA12891-1 0 0 1 0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfilter-toIds.ped:
--------------------------------------------------------------------------------
1 | NA12877-1,NA12878,NA12880-1,NA12880-half,NA12883,NA12889,NA12890,NA12891-1,NA12892-1
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfilter-tovcf.txt:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##source=[...]
4 | ##CL=[...]
5 | ##diseased=child,father
6 | ##SAMPLE=
7 | ##SAMPLE=
8 | ##SAMPLE=
9 | ##PEDIGREE=
10 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child father mother
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedfromvcf:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
4 | #sex: 1=male; 2=female; 0=unknown
5 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
6 | #
7 | #fam-id ind-id pat-id mat-id sex phen
8 | 0 sm-dad 0 0 1 0
9 | 0 sm-daughter1 sm-dad sm-mom 0 0
10 | 0 sm-daughter2 sm-dad sm-mom 0 0
11 | 0 sm-mom 0 0 2 0
12 | 0 sm-son1 sm-dad sm-mom 0 0
13 | 0 sm-son2 sm-dad sm-mom 0 0
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pednormal:
--------------------------------------------------------------------------------
1 | #PED format pedigree
2 | #
3 | #with an extra header comment
4 | #fam-id/ind-id/pat-id/mat-id: 0=unknown
5 | #sex: 1=male; 2=female; 0=unknown
6 | #phenotype: -9=missing, 0=missing; 1=unaffected; 2=affected
7 | #
8 | #fam-id ind-id pat-id mat-id sex phen
9 | 0 child father mother 1 2
10 | 0 father 0 0 1 2
11 | 0 mother 0 0 2 0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-delim-c.txt:
--------------------------------------------------------------------------------
1 | NA12877-1,NA12878,NA12880-1,NA12880-half,NA12883,NA12889,NA12890,NA12891-1,NA12892-1
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-delim-tab.txt:
--------------------------------------------------------------------------------
1 | NA12877-1 NA12878 NA12880-1 NA12880-half NA12883 NA12889 NA12890 NA12891-1 NA12892-1
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-female-ids.txt:
--------------------------------------------------------------------------------
1 | NA12878
2 | NA12880-1
3 | NA12880-half
4 | NA12890
5 | NA12892-1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-founder-ids.txt:
--------------------------------------------------------------------------------
1 | NA12889
2 | NA12890
3 | NA12891-1
4 | NA12892-1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-male-ids.txt:
--------------------------------------------------------------------------------
1 | NA12877-1
2 | NA12883
3 | NA12889
4 | NA12891-1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-maternal-ids.txt:
--------------------------------------------------------------------------------
1 | NA12878
2 | NA12890
3 | NA12892-1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-paternal-ids.txt:
--------------------------------------------------------------------------------
1 | NA12877-1
2 | NA12889
3 | NA12891-1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pedstats-primary-ids.txt:
--------------------------------------------------------------------------------
1 | NA12877-1
2 | NA12878
3 | NA12880-1
4 | NA12880-half
5 | NA12883
6 | NA12889
7 | NA12890
8 | NA12891-1
9 | NA12892-1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/pop.ped:
--------------------------------------------------------------------------------
1 | # PED format pedigree
2 | # fam-id ind-id pat-id mat-id sex phen
3 | 0 child father mother 1 2
4 | 0 mother 0 0 2 0
5 | 0 father 0 0 1 2
6 | 0 child2 father 0 2 2
7 | 0 child3 0 mother 1 0
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/relation/resources/vcffromped.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##diseased=child,child2,father
3 | ##SAMPLE=
4 | ##SAMPLE=
5 | ##SAMPLE=
6 | ##SAMPLE=
7 | ##SAMPLE=
8 | ##PEDIGREE=
9 | ##PEDIGREE=
10 | ##PEDIGREE=
11 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child child2 child3 father mother
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/report/resources/velocityTest.txt:
--------------------------------------------------------------------------------
1 | $aVariable
2 | textNextTo${bVariable}foo
3 |
4 | #if ($valExists)
5 | $valExists
6 | #end
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/bam.bam:
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/src/test/resources/com/rtg/sam/resources/calibrate.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 1442 1449 region
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/calibrated_mated.sam.gz:
--------------------------------------------------------------------------------
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/src/test/resources/com/rtg/sam/resources/calibrated_mated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.4 build b1400d0 (2011-12-22), calibrate v2.0
2 | #CL map -t ref -i reads -o map --sam-rg @RG\tID:TEST\tPL:ILLUMINA\tSM:test
3 | @mnp:TEST 0 7
4 | @nh:TEST 0 50
5 | @covar readgroup basequality sequence equal diff ins del
6 | TEST 20 simulatedSequence1 297 3 0 0
7 | TEST 20 simulatedSequence2 196 4 0 0
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/checklegacy:
--------------------------------------------------------------------------------
1 | 52 0 chr6 160560249 255 93M * 0 0 ACAGCAGCAGCAACAACAGTAACAACAGTAGAAATAAGTACAATAGCAATAACAACAGTAATAGCAACAGCAAAAACAATAGCAGCAGTAACA * AS:i:0 NM:i:0 IH:i:1
2 | 94 0 chr6 160560323 255 20M * 0 0 AACAATAGCAGCAGTAACAA * AS:i:0 NM:i:0 IH:i:1
3 | 78 16 chr6 160560324 255 51M * 0 0 ACAATAGCAGCAGTAACAATAACAACAGCAATAGCAGCAACAACAGCAACA * AS:i:0 NM:i:0 IH:i:1
4 | 87 16 chr6 160560357 255 51M * 0 0 GCAGCAACAACAGCAACAAGAAAAATGACAATAGCAGCAGCAACAACAGCA * AS:i:0 NM:i:0 IH:i:1
5 |
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
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/src/test/resources/com/rtg/sam/resources/indexmerge1.bam:
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/src/test/resources/com/rtg/sam/resources/indexmerge3.bam:
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/src/test/resources/com/rtg/sam/resources/readgroup_cg.txt:
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1 | @RG ID:RG23 SM:NA123 PL:COMPLETE
2 |
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/src/test/resources/com/rtg/sam/resources/samoutput_expected_1.sam:
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1 | @HD VN:1.6 SO:coordinate
2 | @SQ SN:seq LN:1000000
3 | read 0 seq 500000 0 4= * 0 0 ACGT ####
4 |
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/src/test/resources/com/rtg/sam/resources/sfm-exc-stdout:
--------------------------------------------------------------------------------
1 | SAM records read: 21
2 | SAM records written: 18
3 |
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/src/test/resources/com/rtg/sam/resources/sfm-inc-stdout:
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1 | SAM records read: 21
2 | SAM records written: 21
3 |
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/src/test/resources/com/rtg/simulation/reads/resources/454pe-results.fa:
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1 | >0 name/54/F/3./Left
2 | AAA
3 | >0 name/31/F/2./Right
4 | AA
5 | >1 name/32/R/1./Left
6 | T
7 | >1 name/54/R/3./Right
8 | TTT
9 | >2 name/54/F/3./Left
10 | AAA
11 | >2 name/31/F/1./Right
12 | A
13 |
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/src/test/resources/com/rtg/simulation/reads/resources/454se-results.fa:
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1 | >0 name/31/F/5.
2 | AAAAA
3 | >1 name/31/R/4.
4 | TTTT
5 | >2 name/32/F/4.
6 | AAAA
7 |
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/src/test/resources/com/rtg/simulation/reads/resources/cg-v2-results.fa:
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1 | >0 name/31/F/10.3B19./Left
2 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3 | >0 name/482/F/10.3B11.1X7./Right
4 | AAAAAAAAAAAAAAAAAAAAACAAAAAAA
5 | >1 name/31/F/7.1X2.2B19./Left
6 | AAAAAAATAAAAAAAAAAAAAAAAAAAAA
7 | >1 name/482/F/10.2B19./Right
8 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9 | >2 name/31/F/10.3B19./Left
10 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11 | >2 name/482/F/10.3B13.2X4./Right
12 | AAAAAAAAAAAAAAAAAAAAAAACGAAAA
13 | >3 name/505/R/13.1X1.1D4.4B10./Left
14 | TTTTTTTTTTTTTTTCTTTTTTTTTTTTT
15 | >3 name/54/R/5.1X13.2B10./Right
16 | TTTTTTTTTTTTTTTTTTTTTTTATTTTT
17 |
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/src/test/resources/com/rtg/tabix/resources/alleleCounts.ac.gz:
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/src/test/resources/com/rtg/tabix/resources/extract1000-5000:
--------------------------------------------------------------------------------
1 | simulatedSequence19 1302 . G A . PASS . GT:DP:RE:GQ:RS 1/0:37:0.736:275.0:A,17,0.338,G,20,0.398
2 | simulatedSequence19 3869 . T C . PASS . GT:DP:RE:GQ:RS 1/1:32:0.637:94.0:C,32,0.637
3 | simulatedSequence19 4367 . A C . PASS . GT:DP:RE:GQ:RS 1/1:34:0.677:99.0:C,34,0.677
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/tabix/resources/extract500-1000:
--------------------------------------------------------------------------------
1 | simulatedSequence19 583 . A T . PASS . GT:DP:RE:GQ:RS 0/1:23:0.458:185.0:A,11,0.219,T,12,0.239
2 | simulatedSequence19 637 . G C . PASS . GT:DP:RE:GQ:RS 1/0:27:0.537:53.0:C,7,0.139,G,20,0.398
3 | simulatedSequence19 737 . G C . PASS . GT:DP:RE:GQ:RS 1/1:27:0.537:74.0:C,26,0.517,T,1,0.020
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/tabix/resources/extract500-1000-5000:
--------------------------------------------------------------------------------
1 | simulatedSequence19 583 . A T . PASS . GT:DP:RE:GQ:RS 0/1:23:0.458:185.0:A,11,0.219,T,12,0.239
2 | simulatedSequence19 637 . G C . PASS . GT:DP:RE:GQ:RS 1/0:27:0.537:53.0:C,7,0.139,G,20,0.398
3 | simulatedSequence19 737 . G C . PASS . GT:DP:RE:GQ:RS 1/1:27:0.537:74.0:C,26,0.517,T,1,0.020
4 | simulatedSequence19 1302 . G A . PASS . GT:DP:RE:GQ:RS 1/0:37:0.736:275.0:A,17,0.338,G,20,0.398
5 | simulatedSequence19 3869 . T C . PASS . GT:DP:RE:GQ:RS 1/1:32:0.637:94.0:C,32,0.637
6 | simulatedSequence19 4367 . A C . PASS . GT:DP:RE:GQ:RS 1/1:34:0.677:99.0:C,34,0.677
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/tabix/resources/extract500-5000:
--------------------------------------------------------------------------------
1 | simulatedSequence19 583 . A T . PASS . GT:DP:RE:GQ:RS 0/1:23:0.458:185.0:A,11,0.219,T,12,0.239
2 | simulatedSequence19 637 . G C . PASS . GT:DP:RE:GQ:RS 1/0:27:0.537:53.0:C,7,0.139,G,20,0.398
3 | simulatedSequence19 737 . G C . PASS . GT:DP:RE:GQ:RS 1/1:27:0.537:74.0:C,26,0.517,T,1,0.020
4 | simulatedSequence19 1302 . G A . PASS . GT:DP:RE:GQ:RS 1/0:37:0.736:275.0:A,17,0.338,G,20,0.398
5 | simulatedSequence19 3869 . T C . PASS . GT:DP:RE:GQ:RS 1/1:32:0.637:94.0:C,32,0.637
6 | simulatedSequence19 4367 . A C . PASS . GT:DP:RE:GQ:RS 1/1:34:0.677:99.0:C,34,0.677
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/tabix/resources/multiRegionSequenceEnd.bed.gz:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge1.sam.gz:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge2.sam.gz:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge3.sam.gz:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge3.sam.gz.tbi:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge4.sam.gz:
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/src/test/resources/com/rtg/tabix/resources/tabixmerge4.sam.gz.tbi:
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/src/test/resources/com/rtg/tabix/resources/tlr-single-region:
--------------------------------------------------------------------------------
1 | simulatedSequence19 583 . A T . PASS . GT:DP:RE:GQ:RS 0/1:23:0.458:185.0:A,11,0.219,T,12,0.239
2 | simulatedSequence19 637 . G C . PASS . GT:DP:RE:GQ:RS 1/0:27:0.537:53.0:C,7,0.139,G,20,0.398
3 | simulatedSequence19 737 . G C . PASS . GT:DP:RE:GQ:RS 1/1:27:0.537:74.0:C,26,0.517,T,1,0.020
4 |
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/src/test/resources/com/rtg/util/cli/spell.insensitive:
--------------------------------------------------------------------------------
1 | fasta
2 | mapq
3 | fastq
4 | quala
5 | solexa
6 | solexa1
7 | illumina
8 | iontorrent
9 | pe
10 | se
11 | colorspace
12 | indel
13 | gzipped
14 | phred
15 | cgfastq
16 | blosum62
17 | blosum45
18 | blosum80
19 | contigs
20 | breakends
21 | breakend
22 | kmer
23 | denovo
24 | germline
25 | javascript
26 | rtg
27 | metagenomic
28 | unmergeable
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/io/bzip2/resources/sample3.ref.bz2:
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--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/io/bzip2/resources/textfile:
--------------------------------------------------------------------------------
1 | some generic text
2 | that we're going to compress
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/io/bzip2/resources/textfile.bz2:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-tools/f72c7991210776631b2ee36b8038a64b45deb6da/src/test/resources/com/rtg/util/io/bzip2/resources/textfile.bz2
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/src/test/resources/com/rtg/util/io/bzip2/resources/textfilebad.bz2:
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/src/test/resources/com/rtg/util/io/bzip2/resources/textfilemulti.bz2:
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/src/test/resources/com/rtg/util/resources/md5utils.txt:
--------------------------------------------------------------------------------
1 | #an example version file
2 | version 0.0 head
3 | date 2012/05/07 14:53:05 #another comment
4 | command rtg assemble -i previous -r lotsofreads.fasta
5 | guid 3F2504E0-4F89-11D3-9A0C-0305E82C3301
6 | contigOverlap 0
7 | inputguid 3F2504E0-4F89-11D3-9A0C-0305E82C3302
8 | inputguid 3F2504E0-4F89-11D3-9A0C-0305E82C3303
9 | #an example contig header
10 | contig cov Coverage of the contig
11 | contig tip Tip value
12 | contig foo
13 | #an example path header file
14 | path min Minimum coverage of the path
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/resources/test.properties:
--------------------------------------------------------------------------------
1 | #
2 | testing
3 | this as a resource
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/resources/tt-default.tsv:
--------------------------------------------------------------------------------
1 | #Depth Breadth Covered Size Non-N_Depth Non-N_Breadth Non-N_Covered Non-N_Size Name
2 | 0.0097 0.0087 2140198 247249719 0.0107 0.0095 2140198 224999719 chr1
3 | 0.0112 0.0093 1259191 135374737 0.0116 0.0096 1259191 131624728 chr10
4 | 0.0100 0.0093 1256531 134452384 0.0102 0.0096 1256531 131130753 chr11
5 | 0.0093 0.0088 1162746 132349534 0.0095 0.0089 1162746 130303032 chr12
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/resources/tt-indent-1center.txt:
--------------------------------------------------------------------------------
1 | 1: 4
2 | 2: 42
3 | 10: 24
4 | longer: 333
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/resources/tt-indent-1left.txt:
--------------------------------------------------------------------------------
1 | 1: 4
2 | 2: 42
3 | 10: 24
4 | longer: 333
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/resources/tt-indent.txt:
--------------------------------------------------------------------------------
1 | 1: 4
2 | 2: 42
3 | 10: 24
4 | longer: 333
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/cnveval/resources/cnveval_small_noroc_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 966 966 15 283 0.9847 0.7734 0.8664
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/cnveval/resources/cnveval_small_out_dup_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: DUP
4 | #total baseline variants: 1249
5 | #total call variants: 981
6 | #score field: SQS (INFO)
7 | #score true_positives_baseline false_positives true_positives_call
8 | 0.653 19.00 0.00 19.00
9 | 0.572 37.00 1.00 37.00
10 | 0.567 56.00 1.00 56.00
11 | 0.507 80.00 1.00 80.00
12 | 0.502 108.00 1.00 108.00
13 | 0.465 138.00 1.00 138.00
14 | 0.443 174.00 1.00 174.00
15 | 0.403 215.00 1.00 215.00
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/cnveval/resources/cnveval_small_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 0.403 966 966 15 283 0.9847 0.7734 0.8664
4 | None 966 966 15 283 0.9847 0.7734 0.8664
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/priors/error/testdummy_errors.properties:
--------------------------------------------------------------------------------
1 | #
2 | #Rate of snp error events (in read process not genome).
3 | error_mnp_event_rate = 0.005
4 | error_mnp_distribution = 0.50,0.20,0.20,0.10
5 |
6 | #Rate of insert errors (in read process not genome).
7 | error_ins_event_rate = 0.567890
8 |
9 | #Rate of insert errors (in read process not genome).
10 | error_del_event_rate = 0.123456
11 |
12 | #Distribution of machine errors for insertions and deletions (1..). These must sum to 1.0.
13 | error_ins_distribution = 0.99,0.01
14 | error_del_distribution = 0.01,0.99
15 |
16 | overlap = 0,0,1
17 | gap = 0,1,0
18 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/priors/prior/testpriorbad1.properties:
--------------------------------------------------------------------------------
1 | #
2 | #Priors for Diploid SNPs used for testing - missing one of the priors
3 |
4 | #Total prior for all classes of homozygous SNPs
5 | genome_snp_rate_homo = 0.0456
6 |
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/priors/prior/testpriorbad2.properties:
--------------------------------------------------------------------------------
1 | #
2 | #Priors for Diploid SNPs used for testing - illegal numeric value
3 |
4 | #Total prior for all classes of heterozygous SNPs
5 | genome_snp_rate_hetero = 0.!!3
6 |
7 | #Total prior for all classes of homozygous SNPs
8 | genome_snp_rate_homo = 0.0456
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/priors/prior/testpriorbad3.properties:
--------------------------------------------------------------------------------
1 | #
2 | #Priors for Diploid SNPs used for testing - negative prior
3 |
4 | #Total prior for all classes of heterozygous SNPs
5 | genome_snp_rate_hetero = -0.123
6 |
7 | #Total prior for all classes of homozygous SNPs
8 | genome_snp_rate_homo = 0.0456
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/priors/prior/testpriorbad4.properties:
--------------------------------------------------------------------------------
1 | #
2 | #Priors for Diploid SNPs used for testing - malformed unicode escape
3 |
4 | #Total prior for all classes of heterozygous SNPs
5 | genome_snp_rate_hetero = \uu
6 |
7 | #Total prior for all classes of homozygous SNPs
8 | genome_snp_rate_homo = 0.0456
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_all_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_all_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 2686.750 2 2 0 0 1.0000 1.0000 1.0000
4 | None 2 2 60 0 0.0323 1.0000 0.0625
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_all_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609947 . G [10:61638615[G 999 . .
7 | 10 61638615 . N [10:43609947[N 999 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_all_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638611[G 2686.75 . .
8 | 10 61638611 . G [10:43609952[G 2686.75 . .
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_annotate_out_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | ##INFO=
6 | ##INFO=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO
8 | 10 43609947 . G [10:61638615[G 999 . BASE=TP
9 | 10 61638615 . N [10:43609947[N 999 . BASE=TP
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_annotate_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 2 2 5 0 0.2857 1.0000 0.4444
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20170720
3 | ##reference=file:///rtgshare/data/human/ref/1000g_v37_phase2/hs37d5.fasta
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | 10 61638615 . N [10:43609947[N 999 . .
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609196 . C C[10:43609241[ 681.19 . .
8 | 10 43609241 . T ]10:43609196]T 681.19 . .
9 | 10 43615781 . C C[10:43615856[ 518.53 . .
10 | 10 43615856 . C ]10:43615781]C 518.53 . .
11 | 10 93589164 . T T]2:29446738] 519.24 . .
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 2686.750 1 2 0 0 1.0000 1.0000 1.0000
4 | None 1 2 5 0 0.2857 1.0000 0.4444
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 61638615 . N [10:43609947[N 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional2_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638611[G 2686.75 . .
8 | 10 61638611 . G [10:43609952[G 2686.75 . .
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional3_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional3_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609196 . C C[10:43609241[ 681.19 . .
8 | 10 43609241 . T ]10:43609196]T 681.19 . .
9 | 10 43615781 . C C[10:43615856[ 518.53 . .
10 | 10 43615856 . C ]10:43615781]C 518.53 . .
11 | 10 93589164 . T T]2:29446738] 519.24 . .
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional3_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 2686.750 2 2 0 0 1.0000 1.0000 1.0000
4 | None 2 2 5 0 0.2857 1.0000 0.4444
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional3_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609947 . G [10:61638615[G 999 . .
7 | 10 61638615 . N [10:43609947[N 999 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional3_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638611[G 2686.75 . .
8 | 10 61638611 . G [10:43609952[G 2686.75 . .
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_annotate_out_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | ##INFO=
6 | ##INFO=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO
8 | 10 43609947 . G [10:61638615[G 999 . BASE=TP
9 | 10 61638615 . N [10:43609947[N 999 . BASE=TP
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_annotate_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 2686.750 2 1 0 0 1.0000 1.0000 1.0000
4 | None 2 1 5 0 0.1667 1.0000 0.2857
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20170720
3 | ##reference=file:///rtgshare/data/human/ref/1000g_v37_phase2/hs37d5.fasta
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | 10 43609947 . G [10:61638615[G 999 . .
6 | 10 61638615 . N [10:43609947[N 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609196 . C C[10:43609241[ 681.19 . .
8 | 10 43609241 . T ]10:43609196]T 681.19 . .
9 | 10 43615781 . C C[10:43615856[ 518.53 . .
10 | 10 43615856 . C ]10:43615781]C 518.53 . .
11 | 10 93589164 . T T]2:29446738] 519.24 . .
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 2686.750 2 1 0 0 1.0000 1.0000 1.0000
4 | None 2 1 5 0 0.1667 1.0000 0.2857
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609947 . G [10:61638615[G 999 . .
7 | 10 61638615 . N [10:43609947[N 999 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_bidirectional_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638611[G 2686.75 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_default_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_default_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609196 . C C[10:43609241[ 681.19 . .
8 | 10 43609241 . T ]10:43609196]T 681.19 . .
9 | 10 43615781 . C C[10:43615856[ 518.53 . .
10 | 10 43615856 . C ]10:43615781]C 518.53 . .
11 | 10 93589164 . T T]2:29446738] 519.24 . .
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_default_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 2 2 5 0 0.2857 1.0000 0.4444
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_default_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609947 . G [10:61638615[G 999 . .
7 | 10 61638615 . N [10:43609947[N 999 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_default_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638611[G 2686.75 . .
8 | 10 61638611 . G [10:43609952[G 2686.75 . .
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20170720
3 | ##reference=file:///rtgshare/data/human/ref/1000g_v37_phase2/hs37d5.fasta
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | 10 43609947 . G [10:61638615[G 999 . .
6 | 10 61638615 . N [10:43609947[N 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20170720
3 | ##reference=file:///rtgshare/data/human/ref/1000g_v37_phase2/hs37d5.fasta
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | 10 43609947 . G [10:61638615[G 999 . .
6 | 10 61638615 . N [10:43609947[N 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=20170731
3 | ##FILTER=
4 | ##FILTER=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609952 . G [10:61638615[G 2686.75 . .
7 | 10 61638611 . G [10:43609947[G 2686.75 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 43609947 . G [10:61638615[G 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 43609952 . G [10:61638615[G 2686.75 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 1 1 1 1 0.5000 0.5000 0.5000
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##reference=[...]
4 | ##CL=[...]
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 10 61638615 . N [10:43609947[N 999 . .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/bndeval/resources/bndeval_small_tol_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=[...]
3 | ##CL=[...]
4 | ##FILTER=
5 | ##FILTER=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 10 61638611 . G [10:43609947[G 2686.75 . .
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/annotation/resources/coc_cof_rec.vcf:
--------------------------------------------------------------------------------
1 | seq 1 . A G . . . GT:SS:AD:COC:COF 0/0:.:9,1 0/1:2:6,6:1:0.100
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/annotation/resources/scoc_cof_rec.vcf:
--------------------------------------------------------------------------------
1 | seq 1 . A G . . . GT:SS:AD:OCOC:DCOC:OCOF:DCOF 0/0:.:9,1 0/1:2:6,6:1:0:0.100:0.000
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/complexoverlap-hetero.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HET (baseline rescaled)
3 | #total baseline variants: 0
4 | #total call variants: 0
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/complexoverlap-homo.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HOM (baseline rescaled)
3 | #total baseline variants: 2
4 | #total call variants: 2
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 25.600 1.00 0.00 1.00 1.00 1.0000 0.5000 0.6667
8 | 22.600 2.00 0.00 2.00 0.00 1.0000 1.0000 1.0000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/complexoverlap-summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 22.600 2 2 0 0 1.0000 1.0000 1.0000
4 | None 2 2 0 0 1.0000 1.0000 1.0000
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/complexoverlap-weighted-rev.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 2
4 | #total call variants: 2
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 22.600 1.00 0.00 1.00 1.00 1.0000 0.5000 0.6667
8 | 25.600 2.00 0.00 2.00 0.00 1.0000 1.0000 1.0000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/complexoverlap-weighted.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 2
4 | #total call variants: 2
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 25.600 1.00 0.00 1.00 1.00 1.0000 0.5000 0.6667
8 | 22.600 2.00 0.00 2.00 0.00 1.0000 1.0000 1.0000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/obeyphasing/obeyphasing_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
5 | template 2 . G T . PASS . GT 0|1
6 | template 4 . G T . PASS . GT 1|0
7 | template 6 . G T . PASS . GT 0|1
8 | template 8 . G T . PASS . GT 1|0
9 | template 10 . G T . PASS . GT 0|1
10 | template 12 . G T . PASS . GT 1|0
11 | template 14 . G T . PASS . GT 0|1
12 | template 16 . G T . PASS . GT 1|0
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/obeyphasing/obeyphasing_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
5 | template 2 . G T . PASS . GT 0/1
6 | template 4 . G T . PASS . GT 0/1
7 | template 6 . G T . PASS . GT 0|1
8 | template 8 . G T . PASS . GT 1|0
9 | template 10 . G T . PASS . GT 0|1
10 | template 12 . G T . PASS . GT 0|1
11 | template 14 . G T . PASS . GT 1|0
12 | template 16 . G T . PASS . GT 0|1
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/obeyphasing/obeyphasing_in_template.fa:
--------------------------------------------------------------------------------
1 | >template
2 | GGGGGGGGGGGGGGGGGGGG
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/obeyphasing/obeyphasing_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | ##contig=
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
6 | template 2 . G T . PASS . GT 0/1
7 | template 4 . G T . PASS . GT 0/1
8 | template 6 . G T . PASS . GT 0|1
9 | template 8 . G T . PASS . GT 1|0
10 | template 10 . G T . PASS . GT 0|1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/path-noinfite-roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 1
4 | #total call variants: 2
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 99.000 1.00 0.00 1.00 0.00 1.0000 1.0000 1.0000
8 | 75.000 1.00 1.00 1.00 0.00 0.5000 1.0000 0.6667
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/regions_roc_filter.bed:
--------------------------------------------------------------------------------
1 | chr1 100 110 region
2 | chr1 120 121 region
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/regions_roc_filter.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##FILTER=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | chr1 101 . AAAAAAAAAA C . PASS .
6 | chr1 121 . A C . PASS .
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/roc-slope-0.txt:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #posterior slope log-slope
3 | 10.00 1.00 0.000
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/roc-slope-1.txt:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #posterior slope log-slope
3 | 9.00 2.00 0.301
4 | 7.00 2.00 0.301
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/roc-slope-2.txt:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #posterior slope log-slope
3 | 9.00 2.50 0.398
4 | 5.00 2.50 0.398
5 | 5.00 1.00 0.000
6 | 3.00 1.00 0.000
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/roc-slope-3.txt:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #posterior slope log-slope
3 | 10.00 3.00 0.477
4 | 8.00 3.00 0.477
5 | 8.00 2.00 0.301
6 | 6.00 2.00 0.301
7 | 6.00 1.00 0.000
8 | 4.00 1.00 0.000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/roc-slope-3a.txt:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #posterior slope log-slope
3 | 10.00 3.00 0.477
4 | 8.00 3.00 0.477
5 | 8.00 2.00 0.301
6 | 6.00 2.00 0.301
7 | 6.00 1.00 0.000
8 | 4.00 1.00 0.000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/rocempty-hetero.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HET (baseline rescaled)
3 | #total baseline variants: 1
4 | #total call variants: 0
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | None 0.00 0.00 0.00 1.00 NaN 0.0000 NaN
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/rocempty-homo.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HOM (baseline rescaled)
3 | #total baseline variants: 0
4 | #total call variants: 1
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call
7 | None 0.00 1.00 0.00
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/rocempty-summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 0 0 1 1 0.0000 0.0000 0.0000
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/rocempty-weighted-rev.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 1
4 | #total call variants: 1
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | None 0.00 1.00 0.00 1.00 0.0000 0.0000 0.0000
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/rocempty-weighted.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 1
4 | #total call variants: 1
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | None 0.00 1.00 0.00 1.00 0.0000 0.0000 0.0000
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/testroc-hetero.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HET (baseline rescaled)
3 | #total baseline variants: 3
4 | #total call variants: 4
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 40.000 0.00 1.00 0.00 3.00 0.0000 0.0000 0.0000
8 | 30.004 1.00 1.00 1.00 2.00 0.5000 0.3333 0.4000
9 | 20.043 1.00 2.00 1.00 2.00 0.3333 0.3333 0.3333
10 | 10.414 2.00 2.00 2.00 1.00 0.5000 0.6667 0.5714
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/testroc-homo.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HOM (baseline rescaled)
3 | #total baseline variants: 3
4 | #total call variants: 2
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 50.000 1.00 0.00 1.00 2.00 1.0000 0.3333 0.5000
8 | None 1.00 1.00 1.00 2.00 0.5000 0.3333 0.4000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/testroc-summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 10.414 3 3 2 3 0.6000 0.5000 0.5455
4 | None 3 3 3 3 0.5000 0.5000 0.5000
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/testroc-weighted-rev.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 6
4 | #total call variants: 6
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 10.414 1.00 0.00 1.00 5.00 1.0000 0.1667 0.2857
8 | 20.043 1.00 1.00 1.00 5.00 0.5000 0.1667 0.2500
9 | 30.004 2.00 1.00 2.00 4.00 0.6667 0.3333 0.4444
10 | 40.000 2.00 2.00 2.00 4.00 0.5000 0.3333 0.4000
11 | 50.000 3.00 2.00 3.00 3.00 0.6000 0.5000 0.5455
12 | None 3.00 3.00 3.00 3.00 0.5000 0.5000 0.5000
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/testroc-weighted.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: ALL
3 | #total baseline variants: 6
4 | #total call variants: 6
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 50.000 1.00 0.00 1.00 5.00 1.0000 0.1667 0.2857
8 | 40.000 1.00 1.00 1.00 5.00 0.5000 0.1667 0.2500
9 | 30.004 2.00 1.00 2.00 4.00 0.6667 0.3333 0.4444
10 | 20.043 2.00 2.00 2.00 4.00 0.5000 0.3333 0.4000
11 | 10.414 3.00 2.00 3.00 3.00 0.6000 0.5000 0.5455
12 | None 3.00 3.00 3.00 3.00 0.5000 0.5000 0.5000
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/tricky-hetero.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HET (baseline rescaled)
3 | #total baseline variants: 1
4 | #total call variants: 1
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 100.000 1.00 0.00 1.00 0.00 1.0000 1.0000 1.0000
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/tricky-homo.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HOM (baseline rescaled)
3 | #total baseline variants: 6
4 | #total call variants: 6
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 90.000 0.00 1.00 0.00 6.00 0.0000 0.0000 0.0000
8 | 80.000 0.50 1.00 1.00 5.50 0.5000 0.0833 0.1429
9 | 40.000 1.00 1.00 2.00 5.00 0.6667 0.1667 0.2667
10 | 30.004 3.00 1.00 3.00 3.00 0.7500 0.5000 0.6000
11 | 20.043 4.00 1.00 4.00 2.00 0.8000 0.6667 0.7273
12 | 10.414 4.00 2.00 4.00 2.00 0.6667 0.6667 0.6667
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/tricky-summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 20.043 5 5 1 2 0.8333 0.7143 0.7692
4 | None 5 5 2 2 0.7143 0.7143 0.7143
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/trickyxrx-hetero.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HET (baseline rescaled)
3 | #total baseline variants: 1
4 | #total call variants: 1
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 100.000 1.00 0.00 1.00 0.00 1.0000 1.0000 1.0000
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/trickyxrx-homo.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #selection: HOM (baseline rescaled)
3 | #total baseline variants: 6
4 | #total call variants: 6
5 | #score field: GQ (FORMAT)
6 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
7 | 90.000 0.00 1.00 0.00 6.00 0.0000 0.0000 0.0000
8 | 80.000 0.50 1.00 1.00 5.50 0.5000 0.0833 0.1429
9 | 40.000 1.00 1.00 2.00 5.00 0.6667 0.1667 0.2667
10 | 30.004 3.00 1.00 3.00 3.00 0.7500 0.5000 0.6000
11 | 20.043 4.00 1.00 4.00 2.00 0.8000 0.6667 0.7273
12 | 10.414 4.00 2.00 4.00 2.00 0.6667 0.6667 0.6667
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/trickyxrx-summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 20.043 5 5 1 2 0.8333 0.7143 0.7692
4 | None 5 5 2 2 0.7143 0.7143 0.7143
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcf2rocplot/simple-region_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 6789.000 4 4 0 0 1.0000 1.0000 1.0000
4 | None 4 4 0 0 1.0000 1.0000 1.0000
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcf2rocplot/simple-region_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 13011.000 1.00 0.00 1.00 3.00 1.0000 0.2500 0.4000
9 | 12711.000 2.00 0.00 2.00 2.00 1.0000 0.5000 0.6667
10 | 11403.400 3.00 0.00 3.00 1.00 1.0000 0.7500 0.8571
11 | 6789.000 4.00 0.00 4.00 0.00 1.0000 1.0000 1.0000
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcf2rocplot/simple_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 410.000 9 7 0 4 1.0000 0.6923 0.8182
4 | None 13 11 0 0 1.0000 1.0000 1.0000
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_all_matches_err.txt:
--------------------------------------------------------------------------------
1 | VCF header does not contain a FORMAT field named GQ
2 | There were 19 variants not thresholded in ROC data files due to missing or invalid GQ (FORMAT) values.
3 | Could not select maximized F-measure threshold from ROC data, only un-thresholded statistics will be shown. Consider selecting a different scoring attribute with --vcf-score-field
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_annotate_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | AAAAAAAAAATAAAAAAAATAAATGGACCCCCCCCGG
3 | >14 [92085881,92085910]
4 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
5 | >18
6 | TGACGCTGGTGGATCACGATGTCAGGAGATC
7 | >21 [18693741,18693770]
8 | AATAAAAAAAAAATTTTTTTAATTGATTAT
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_avoid_overlap/avoid_overlap_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BASE QUERY
5 | 1-1 31 . ATCTATCATCTCTCTCTC A . . . GT 0/1 0/1
6 | 1-1 38 . ATCTCTCTC ATCTC . . . GT 0/1 0/1
7 | 1-1 44 . C A . . . GT 0/1 0/1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_avoid_overlap/avoid_overlap_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BASE QUERY
5 | 1-1 31 . ATCTATCATCTCTCTCTC A . . . GT 0/1 0/1
6 | 1-1 38 . ATCTCTCTC ATCTC . . . GT 0/1 0/1
7 | 1-1 44 . C A . . . GT 0/1 0/1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_avoid_overlap/avoid_overlap_in_template.fa:
--------------------------------------------------------------------------------
1 | >1-1 [4582951,4583010]
2 | TCTATCTATCTATCTATCTATCTATCATCTATCTATCATCTCTCTCTCTCTCTCTCTCTCNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_avoid_overlap/avoid_overlap_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 3 3 0 0 1.0000 1.0000 1.0000
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_combine2_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
5 | 1 68 . A AT . . . GT 1|1 .
6 | 1 69 . T TA . . . GT 1|1 .
7 | 1 70 . A T,TT . . . GT 2|2 1|1
8 | 1 83 . AAT A . . . GT 1|1 .
9 | 1 85 . T A . . . GT . 1|1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_combine2_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
5 | 1 68 . A AT . . . GT 1|1 .
6 | 1 69 . T TA . . . GT 1|1 .
7 | 1 70 . A T,TT . . . GT 2|2 1|1
8 | 1 83 . AAT A . . . GT 1|1 .
9 | 1 85 . T A . . . GT . 1|1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_combine2_in_template.fa:
--------------------------------------------------------------------------------
1 | >1 [7964301,7964400]
2 | GGATAGCTTGAGCCCAAGAGTTTGAGTCCAGCCTGGGCAACACAATGGGACCAGGTCTCTACAAAAAATAAAAAAAAAAAAAAATAATAAGCTGGGCATGNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_combine_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | AAAAAAAAAATAAAAAAAATAAATGGACCCCCCCCGG
3 | >14 [92085881,92085910]
4 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
5 | >18
6 | TGACGCTGGTGGATCACGATGTCAGGAGATC
7 | >21 [18693741,18693770]
8 | AATAAAAAAAAAATTTTTTTAATTGATTAT
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_ga4gh2_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
5 | 1 68 . A AT . . . GT 1|1 .
6 | 1 69 . T TA . . . GT 1|1 .
7 | 1 70 . A T,TT . . . GT 2|2 1|1
8 | 1 83 . AAT A . . . GT 1|1 .
9 | 1 85 . T A . . . GT . 1|1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_ga4gh2_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
5 | 1 68 . A AT . PASS . GT 1|1 .
6 | 1 69 . T TA . F1 . GT 1|1 .
7 | 1 70 . A T,TT . F1;F2 . GT 2|2 1|1
8 | 1 83 . AAT A . . . GT 1|1 .
9 | 1 85 . T A . . . GT . 1|1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_ga4gh2_in_template.fa:
--------------------------------------------------------------------------------
1 | >1 [7964301,7964400]
2 | GGATAGCTTGAGCCCAAGAGTTTGAGTCCAGCCTGGGCAACACAATGGGACCAGGTCTCTACAAAAAATAAAAAAAAAAAAAAATAATAAGCTGGGCATGNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_ga4gh_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | AAAAAAAAAATAAAAAAAATAAATGGACCCCCCCCGG
3 | >14 [92085881,92085910]
4 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
5 | >15 [92085881,92085910]
6 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
7 | >18
8 | TGACGCTGGTGGATCACGATGTCAGGAGATC
9 | >21 [18693741,18693770]
10 | AATAAAAAAAAAATTTTTTTAATTGATTAT
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_nop/nop_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=20160824
3 | ##contig=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT INTEGRATION
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_nop/nop_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##reference=hg19
3 | ##contig=
4 | ##FORMAT=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002
7 | chr6 7 . A A,T 8247.77 . . GT:GQ 2/1:99
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_nop/nop_in_template.fa:
--------------------------------------------------------------------------------
1 | >chr6 29696990-29696999
2 | TTTAAAATTTNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_nop/nop_out_summary.txt:
--------------------------------------------------------------------------------
1 | 0 total baseline variants, no summary statistics available
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_phase_transfer_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | AAAAAAAAAATAAAAAAAATAAATGGACCCCCCCCGG
3 | >14 [92085881,92085910]
4 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
5 | >18
6 | TGACGCTGGTGGATCACGATGTCAGGAGATC
7 | >21 [18693741,18693770]
8 | AATAAAAAAAAAATTTTTTTAATTGATTAT
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roc_only_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roc_only_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G 1 FAIL . GT 1/1 2/2
9 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
10 | chr2 200 . A C 2 PASS . GT 1/1 .
11 | chr2 900 . A G 3 PASS . GT . 1/1
12 | chr3 200 . A G 4 PASS . GT . 1/1
13 | chr3 300 . A C 5 PASS . GT 1/1 .
14 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roc_only_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 6.000 1.00 0.00 1.00 3.00 1.0000 0.2500 0.4000
9 | 5.000 2.00 0.00 2.00 2.00 1.0000 0.5000 0.6667
10 | 2.000 3.00 0.00 3.00 1.00 1.0000 0.7500 0.8571
11 | 1.000 4.00 0.00 4.00 0.00 1.0000 1.0000 1.0000
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##INFO=
4 | ##contig=
5 | ##contig=
6 | ##contig=
7 | ##contig=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT syndip
9 | chr1 11 . T A . . TEST=4 GT 0|1
10 | chr2 12 . G GA . . . GT 1|1
11 | chr3 13 . T C . . TEST=7 GT 1|0
12 | chr4 14 . A G . . TEST=8 GT 0|1
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##INFO=
4 | ##contig=
5 | ##contig=
6 | ##contig=
7 | ##contig=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT syndip
9 | chr1 11 . T A . . TEST=1 GT 0|1
10 | chr2 12 . G GA . . . GT 1|1
11 | chr3 13 . T G . . TEST=2 GT 1|0
12 | chr4 14 . A G . . TEST=9 GT 0|1
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_in_template.fa:
--------------------------------------------------------------------------------
1 | >chr1
2 | TGCTGCATCGTG
3 | >chr2
4 | AGCTGCTGCTAGG
5 | >chr3
6 | GCGCGTAGCGAGTCC
7 | >chr4
8 | TTTTGGGGCCCTGAAAA
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_out_test+indel_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: test+INDEL
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: GQ (FORMAT)
7 | #score true_positives_baseline false_positives true_positives_call
8 | None 0.00 0.00 0.00
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_out_test+snp_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: test+SNP
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: GQ (FORMAT)
7 | #score true_positives_baseline false_positives true_positives_call
8 | None 1.00 0.00 1.00
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_roccrossjoin/vcfeval_roccrossjoin_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: GQ (FORMAT)
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | None 3.00 1.00 3.00 1.00 0.7500 0.7500 0.7500
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_alt/vcfeval_small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_no_path/vcfeval_small_err.txt:
--------------------------------------------------------------------------------
1 | During ALT comparison some ROC data files will not be produced: [SNP, NON_SNP], producing ROC data for: [ALL]
2 | Error: VCF record ALT allele with ID 1 is the same as REF, record: chr2 200 . A A 2 PASS . GT 1/1 .
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_no_path/vcfeval_small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
10 | chr2 200 . A C 2 PASS . GT 1/1 .
11 | chr3 300 . A C 5 PASS . GT 1/1 .
12 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 5
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 7.000 0.00 1.00 0.00 4.00 0.0000 0.0000 0.0000
9 | 6.000 1.00 1.00 1.00 3.00 0.5000 0.2500 0.3333
10 | 5.000 2.00 1.00 2.00 2.00 0.6667 0.5000 0.5714
11 | 2.000 3.00 1.00 3.00 1.00 0.7500 0.7500 0.7500
12 | 1.000 4.00 1.00 4.00 0.00 0.8000 1.0000 0.8889
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_out_weighted_slope.tsv:
--------------------------------------------------------------------------------
1 | #posterior slope log-slope
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_recode_alleles.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##INFO=
4 | ##INFO=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO
6 | 22 21 . C CCCT . . STATUS=B-TP=22:22-22 (*:CCTx)
7 | 22 25 . T C . . STATUS=B-TP=22:25-26 (*:Cx)
8 | 22 27 . AATGGTG A . . STATUS=B-TP=22:28-34 (*:x)
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_recode_in_empty.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##INFO=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_recode_in_samples.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##INFO=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4
5 | 22 21 . C CCCT . . AC=3 GT ./1 . 1/1 .
6 | 22 23 . ATTTA CTC . . AC=3 GT . 1/0 . 1/1
7 | 22 25 . T C . . AC=3 GT ./1 . 1/1 .
8 | 22 27 . AATGGTG A . . AC=3 GT ./1 . 1/1 .
9 | 22 30 . GGTG CTA . . AC=3 GT . 1/0 . 1/1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_recode_in_template.fa:
--------------------------------------------------------------------------------
1 | >22 [23748501,23748550]
2 | TTCTGATGAGGGTGCCAAGACCATTTAATGGTGAAAGAACAATCTTTTCGNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_region_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_region_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
9 | chr2 200 . A C 2 PASS . GT 1/1 .
10 | chr2 900 . A G 3 PASS . GT . 1/1
11 | chr3 200 . A G 4 PASS . GT . 1/1
12 | chr3 300 . A C 5 PASS . GT 1/1 .
13 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_region_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 1
5 | #total call variants: 1
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 2.000 1.00 0.00 1.00 0.00 1.0000 1.0000 1.0000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_region_out_weighted_slope.tsv:
--------------------------------------------------------------------------------
1 | #posterior slope log-slope
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_samples_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 1/1
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 1/1
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_samples_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
9 | chr2 200 . A C 2 PASS . GT 1/1 .
10 | chr2 900 . A G 3 PASS . GT . 1/1
11 | chr3 200 . A G 4 PASS . GT . 1/1
12 | chr3 300 . A C 5 PASS . GT 1/1 .
13 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_samples_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 6
5 | #total call variants: 4
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 6.000 0.00 1.00 0.00 6.00 0.0000 0.0000 0.0000
9 | 5.000 1.00 1.00 1.00 5.00 0.5000 0.1667 0.2500
10 | 2.000 2.00 1.00 2.00 4.00 0.6667 0.3333 0.4444
11 | 1.000 2.00 2.00 2.00 4.00 0.5000 0.3333 0.4000
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_samples_out_weighted_slope.tsv:
--------------------------------------------------------------------------------
1 | #posterior slope log-slope
2 | 6.00 2.00 0.301
3 | 2.00 2.00 0.301
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_squash/vcfeval_small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_squash/vcfeval_small_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
10 | chr2 200 . A C 2 PASS . GT 1/1 .
11 | chr3 300 . A C 5 PASS . GT 1/1 .
12 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_squash/vcfeval_small_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 5
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 7.000 0.00 1.00 0.00 4.00 0.0000 0.0000 0.0000
9 | 6.000 1.00 1.00 1.00 3.00 0.5000 0.2500 0.3333
10 | 5.000 2.00 1.00 2.00 2.00 0.6667 0.5000 0.5714
11 | 2.000 3.00 1.00 3.00 1.00 0.7500 0.7500 0.7500
12 | 1.000 4.00 1.00 4.00 0.00 0.8000 1.0000 0.8889
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_err.txt:
--------------------------------------------------------------------------------
1 | There were 3 baseline variants skipped due to being too long, overlapping or starting outside the expected reference sequence length.
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##contig=
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
6 | 14 17 . TAA T . PASS . GT 1/1
7 | 14 19 . A ATTTT,ATTTTT,T . PASS . GT 1/2
8 | 21 13 . ATT A . PASS . GT 0/1
9 | 21 14 . T A . PASS . GT 0/1
10 | 21 15 . T A,TAAA . PASS . GT 2/1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##contig=
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
6 | 14 18 . AA TTTT,TTTTT 410 PASS . GT 2|1
7 | 21 3 . T TA 578 PASS . GT 1/0
8 | 21 14 . TT AA 578 PASS . GT 1/1
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_in_template.fa:
--------------------------------------------------------------------------------
1 | >14 [92085881,92085910]
2 | AAATAAGCCTTTTTTTTAAAAAAAAAATAG
3 | >21 [18693741,18693770]
4 | AATAAAAAAAAAATTTTTTTAATTGATTAT
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | ##contig=
4 | ##contig=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
7 | 14 18 . AA TTTT,TTTTT 410 PASS . GT 2|1
8 | 21 3 . T TA 578 PASS . GT 1/0
9 | 21 14 . TT AA 578 PASS . GT 1/1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky/vcfeval_small_tricky_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 5
5 | #total call variants: 3
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 578.000 3.00 0.00 2.00 2.00 1.0000 0.6000 0.7500
9 | 410.000 5.00 0.00 3.00 0.00 1.0000 1.0000 1.0000
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_err.txt:
--------------------------------------------------------------------------------
1 | During ALT comparison some ROC data files will not be produced: [SNP, NON_SNP], producing ROC data for: [ALL]
2 | There were 4 variants not thresholded in ROC data files due to missing or invalid QUAL values.
3 | Could not select maximized F-measure threshold from ROC data, only un-thresholded statistics will be shown. Consider selecting a different scoring attribute with --vcf-score-field
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT dummy
5 | 1 1 . A AT . . . GT .
6 | 1 2 . A T . . . GT 0|1
7 | 1 4 . A AT . . . GT .
8 | 1 6 . A T . . . GT 0|1
9 | 1 11 . T A . . . GT 0|1
10 | 1 11 . TAA T . . . GT .
11 | 1 13 . A T . . . GT 0|1
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
5 | 1 2 . A T . . . GT 0|1
6 | 1 6 . A T . . . GT 0|1
7 | 1 11 . T A . . . GT 0|1
8 | 1 13 . A T . . . GT 0|1
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | AAAAAAAAAATAAAAAAAATAAATGGACCCCCCCCGG
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | ##contig=
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
6 | 1 2 . A T . . . GT 0|1
7 | 1 6 . A T . . . GT 0|1
8 | 1 11 . T A . . . GT 0|1
9 | 1 13 . A T . . . GT 0|1
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky2_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 7
5 | #total call variants: 4
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | None 5.00 0.00 4.00 2.00 1.0000 0.7143 0.8333
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky3_in_template.fa:
--------------------------------------------------------------------------------
1 | >18
2 | TGACGCTGGTGGATCACGATGTCAGGAGATC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky3_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=[...]
3 | ##source=[...]
4 | ##CL=[...]
5 | ##contig=
6 | ##FORMAT=
7 | ##SAMPLE=
8 | ##SAMPLE=
9 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 dummy
10 | 18 3 . AC TG 37499 PASS . GT 1|1 .
11 | 18 7 . T G 37499 PASS . GT 1|1 .
12 | 18 10 . TG CA 37499 PASS . GT 1|1 .
13 | 18 20 . T G 11403.4 PASS . GT 1|1 1/1
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky3_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 4
5 | #total call variants: 4
6 | #score field: QUAL
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 37499.000 3.00 0.00 3.00 1.00 1.0000 0.7500 0.8571
9 | 11403.400 4.00 0.00 4.00 0.00 1.0000 1.0000 1.0000
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky4_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
3 | chrQ 3 . A AA . PASS . GT 0/1
4 | chrQ 5 . A T . PASS . GT 0/1
5 | chrQ 7 . AA A . PASS . GT 0/1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky4_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
3 | chrQ 5 . A T . PASS . GT 0/1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky4_in_template.fa:
--------------------------------------------------------------------------------
1 | >chrQ
2 | CAAAAAAAAAAAAT
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky4_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
4 | chrQ 3 . A AA . PASS . GT 0/1
5 | chrQ 5 . A T . PASS . GT 0/1
6 | chrQ 7 . AA A . PASS . GT 0/1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_tricky4_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
4 | chrQ 5 . A T . PASS . GT 0/1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_trickysquash/trickysquash_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHMI_CHMI3_WGS2
5 | 1-1 41 . G GTATA . . . GT 0/1
6 | 1-1 60 . T TA . . . GT 0/1
7 | 1-1 61 . T TATA . . . GT 0/1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_trickysquash/trickysquash_in_template.fa:
--------------------------------------------------------------------------------
1 | >1-1 [84765300,84765380]
2 | ATGGCAAACAGTTTGTTGGAGGGAGTGTGTGAGTACTAGTGTATATATATATATATATATTTATTTATTTATTTATTTATANNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel2_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT syndip
4 | 2-1 11 . TG T . . . GT 0|1
5 | 2-1 12 . G C,* . . . GT 1|2
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel2_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHMI_CHMI3_WGS2
5 | 2-1 11 . TG T,TC . . . GT 2|1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel2_in_template.fa:
--------------------------------------------------------------------------------
1 | >2-1 [79133093,79133122]
2 | TTTCCATGTTTGTATTCTAAAGAGAACTGCNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel3_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT syndip
4 | 2-1 11 . TGTA T . . . GT .|1
5 | 2-1 12 . GT C,* . . . GT 1|2
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel3_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHMI_CHMI3_WGS2
5 | 2-1 11 . TGTA T,TCA . . . GT 2|1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel3_in_template.fa:
--------------------------------------------------------------------------------
1 | >2-1 [79133093,79133122]
2 | TTTCCATGTTTGTATTCTAAAGAGAACTGCNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel4_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=20160824
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG001
5 | 1-1 16 . CGGA CA,C . . . GT 2|1
6 | 1-1 19 . AG A . . . GT 0|1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel4_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##reference=human_g1k_v37
3 | ##octopus_version=0.5.2-beta
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
6 | 1-1 16 . CGG C,* . . . GT 1|2
7 | 1-1 16 . CGGA C . . . GT .|1
8 | 1-1 19 . AG A,*G . . . GT 1|2
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel4_in_template.fa:
--------------------------------------------------------------------------------
1 | >1-1 [63493020,63493050]
2 | GCCCCCAGGAGCTGGCGGAGGAGGAGGAGGANNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel5_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=20160824
3 | ##FORMAT=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG001
5 | 1-1 32 . CTTA C . . . GT 0|1
6 | 1-1 35 . AT A . . . GT 1|0
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel5_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.3
2 | ##reference=human_g1k_v37
3 | ##octopus_version=0.5.2-beta
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
6 | 1-1 32 . CTTA C . . . GT 0|1
7 | 1-1 35 . AT A,*T . . . GT 1|2
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel5_in_template.fa:
--------------------------------------------------------------------------------
1 | >1-1 [165488640,165488700]
2 | AAGCTGTTTAGTTTAATTACGTCCCATTTGTCTTATTTTTTTTTTTTTTTGCAATTGCTTTNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT syndip
4 | 2-1 11 . TG T . . . GT 0|1
5 | 2-1 12 . G C,* . . . GT 1|2
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FORMAT=
3 | ##reference=file:///dsde/working/CHM/58re/37m/ref.fa
4 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CHMI_CHMI3_WGS2
5 | 2-1 12 . G C . . . GT 0/1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_small_updel/updel_in_template.fa:
--------------------------------------------------------------------------------
1 | >2-1 [79133093,79133122]
2 | TTTCCATGTTTGTATTCTAAAGAGAACTGCNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 1/1
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 1/1
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
9 | chr2 200 . A C 2 PASS . GT 1/1 .
10 | chr2 900 . A G 3 PASS . GT . 1/1
11 | chr3 200 . A G 4 PASS . GT . 1/1
12 | chr3 300 . A C 5 PASS . GT 1/1 .
13 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_err.txt:
--------------------------------------------------------------------------------
1 | During ALT comparison no ROC data will be produced, as a sample is required by the selected ROC score field: GQ (FORMAT)
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 1/1
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 1/1
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
9 | chr2 200 . A C 2 PASS . GT 1/1 .
10 | chr2 900 . A G 3 PASS . GT . 1/1
11 | chr3 200 . A G 4 PASS . GT . 1/1
12 | chr3 300 . A C 5 PASS . GT 1/1 .
13 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_phasing.txt:
--------------------------------------------------------------------------------
1 | Correct phasings: 0
2 | Incorrect phasings: 0
3 | Unresolvable phasings: 0
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | None 6 6 0 0 1.0000 1.0000 1.0000
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G . PASS . GT 1/1 2/2
10 | chr2 200 . A C . PASS . GT 1/1 1/1
11 | chr2 900 . A G . PASS . GT . 1/1
12 | chr3 200 . A G . PASS . GT . 1/1
13 | chr3 300 . A C . PASS . GT 1/1 1/1
14 | chr3 500 . A C,G . PASS . GT 1/1 2/2
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_no_roc_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
10 | chr2 200 . A C 2 PASS . GT 1/1 .
11 | chr2 900 . A G 3 PASS . GT . 1/1
12 | chr3 200 . A G 4 PASS . GT . 1/1
13 | chr3 300 . A C 5 PASS . GT 1/1 .
14 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_fn.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_fp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_phasing.txt:
--------------------------------------------------------------------------------
1 | Correct phasings: 0
2 | Incorrect phasings: 0
3 | Unresolvable phasings: 0
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_summary.txt:
--------------------------------------------------------------------------------
1 | Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure
2 | ----------------------------------------------------------------------------------------------------
3 | 1.000 4 4 0 0 1.0000 1.0000 1.0000
4 | None 4 4 0 0 1.0000 1.0000 1.0000
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_tp-baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G . PASS . GT 1/1 2/2
10 | chr2 200 . A C . PASS . GT 1/1 1/1
11 | chr3 300 . A C . PASS . GT 1/1 1/1
12 | chr3 500 . A C,G . PASS . GT 1/1 2/2
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_split_out_tp.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
9 | chr2 100 . A C,G 1 PASS . GT 1/1 2/2
10 | chr2 200 . A C 2 PASS . GT 1/1 .
11 | chr3 300 . A C 5 PASS . GT 1/1 .
12 | chr3 500 . A C,G 6 PASS . GT 1/1 2/2
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_tetraploid/small_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##fileDate=20200911
3 | ##CL=vcffilter -i /home/len/dan-tetraploid.baseline.vcf.gz -o - --region chr22:21110600+100 -j start='21110600' -j chr='chr22-1' -j "\nfunction record() {\n if (has(INFO.END)) {\n INFO.END = INFO.END - start + 1;\n }\n CHR = chr;\n POS = POS - start + 1;\n return true;\n}"
4 | ##FORMAT=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878_NA24385
6 | chr22 10 . G C . . . GT 0|0|0|1
7 | chr22 82 . CAAAA CAAA,C,CAA . . . GT 1|2|3|1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_tetraploid/small_in_template.fa:
--------------------------------------------------------------------------------
1 | >chr22
2 | TGAGCCCGTGAGGTGGAGGCTGCAGTGAGCCGAGATCATGCCACTGCACTCCAGCCTGGGCAACAGAGCAAGACTTTGTCTCAAAAAAAAAAAAAAAAAANNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_end_err.txt:
--------------------------------------------------------------------------------
1 | VCF header does not contain a FORMAT field named GQ
2 | Evaluation too complex (50002 unresolved paths, 189621 iterations) at reference region 11:3795-3836. Variants in this region will not be included in results.
3 | There were 2 variants not thresholded in ROC data files due to missing or invalid GQ (FORMAT) values.
4 | Could not select maximized F-measure threshold from ROC data, only un-thresholded statistics will be shown. Consider selecting a different scoring attribute with --vcf-score-field
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_end_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20140319
3 | ##contig=
4 | ##FILTER=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
7 | 11 1881 . A ATT . PASS . GT 0|1
8 | 11 3532 . G GC . PASS . GT 1/1
9 | 11 3795 . AACACACACAC A,AACACACAC . PASS . GT 1|2
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_end_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 2
5 | #total call variants: 2
6 | #score field: GQ (FORMAT)
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | None 1.00 1.00 1.00 1.00 0.5000 0.5000 0.5000
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_err.txt:
--------------------------------------------------------------------------------
1 | Evaluation too complex (50002 unresolved paths, 153183 iterations) at reference region 11:3795-3833. Variants in this region will not be included in results.
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_out_weighted_roc.tsv:
--------------------------------------------------------------------------------
1 | #Version [...]
2 | #CL [...]
3 | #selection: ALL
4 | #total baseline variants: 3
5 | #total call variants: 4
6 | #score field: GQ (FORMAT)
7 | #score true_positives_baseline false_positives true_positives_call false_negatives precision sensitivity f_measure
8 | 23.000 0.00 1.00 0.00 3.00 0.0000 0.0000 0.0000
9 | 18.000 1.00 1.00 1.00 2.00 0.5000 0.3333 0.4000
10 | 6.000 2.00 1.00 2.00 1.00 0.6667 0.6667 0.6667
11 | 1.000 2.00 2.00 2.00 1.00 0.5000 0.6667 0.5714
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_too_complex_out_weighted_slope.tsv:
--------------------------------------------------------------------------------
1 | #posterior slope log-slope
2 | 23.00 2.00 0.301
3 | 6.00 2.00 0.301
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/mie_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FILTER=
3 | ##FORMAT=
4 | ##FORMAT=
5 | ##PEDIGREE=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother child
7 | 1 6 . T G . . . GT 0/1 0/1 1/1
8 | 1 10 . T TGG . . . GT . . 1/1
9 | 1 13 . G GG . . . GT 1/1 . .
10 | 1 19 . T GT . . . GT . 1/1 .
11 | 1 23 . T G . . . GT 0/1 0/1 1/1
12 | 1 27 . T G . . . GT:FT 0/1:FAIL 0/1 1/1
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/mie_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FILTER=
3 | ##FORMAT=
4 | ##FORMAT=
5 | ##PEDIGREE=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother child
7 | 1 6 . T G . . . GT 0/1 0/1 1/1
8 | 1 10 . T TGG . . . GT . . 1/1
9 | 1 13 . G GG . . . GT 1/1 . .
10 | 1 19 . T GT . . . GT . 1/1 .
11 | 1 23 . T G . . . GT 0/1 0/1 1/1
12 | 1 27 . T G . . . GT:FT 0/1 0/1 1/1:FAIL
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/mie_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | ATGCATGCATGGGGGGGGTGCATGCATGC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/ok_in_baseline.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FILTER=
3 | ##FORMAT=
4 | ##PEDIGREE=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother child
6 | 1 6 . T G . . . GT 0/1 0/1 1/1
7 | 1 10 . T TG . . . GT . . 1/1
8 | 1 13 . G GG . . . GT 1/0 . .
9 | 1 19 . T GT . . . GT . 0/1 .
10 | 1 22 . T G . . . GT 0/1 0/1 1/1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/ok_in_calls.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.2
2 | ##FILTER=
3 | ##FORMAT=
4 | ##PEDIGREE=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT father mother child
6 | 1 6 . T G . . . GT 0/1 0/1 1/1
7 | 1 10 . T TG . . . GT . . 1/1
8 | 1 13 . G GG . . . GT 1/0 . .
9 | 1 19 . T GT . . . GT . 0/1 .
10 | 1 22 . T G . . . GT 0/1 0/1 1/1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_trio/ok_in_template.fa:
--------------------------------------------------------------------------------
1 | >1
2 | ATGCATGCATGGGGGGGGTGCATGC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/eval/resources/vcfeval_triploid/small_in_template.fa:
--------------------------------------------------------------------------------
1 | >chr01-1 11900-12199
2 | CCATCAGTGAATGTTTGGAATCGTAATGTGATATTATTTTTGCTAATTCAAATTGAAGAGTAATATTAAATCGAACTATTTTTTATGTTGGATACATAGTATATTATTTTTTTCATAATTAGCAGCTTTGTATTAATTGCCATTATCATTAATATTGGTACATCACTATTATTAAAATCGATATTATCGATAATATAATTACACTTAGAAGGATATAGGGTTAAGTGGAGTGAAAATTAGATTTCTATGAGATAGGAATCAAAACTATTAACCTCACATGAGGTTTGTGAATAAATAATTNNNNNNNNNN
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_biallelic_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 0/1 0/1 0/1 6 85.71% 50.00%
3 | 0/1 0/1 1/1 1 14.29% 8.33%
4 |
5 | 0/0 1/1 0/1 2 100.00% 16.67%
6 |
7 | 0/1 1/1 0/1 1 50.00% 8.33%
8 | 0/1 1/1 1/1 1 50.00% 8.33%
9 |
10 | 0/0 0/1 0/1 1 100.00% 8.33%
11 |
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_can_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 0/1 0/1 0/1 6 85.71% 46.15%
3 | 0/1 0/1 1/1 1 14.29% 7.69%
4 |
5 | 0/0 1/1 0/1 2 66.67% 15.38%
6 | 0/0 1/1 1/2 1 33.33% 7.69% INCONSISTENT
7 |
8 | 0/1 1/1 0/1 1 50.00% 7.69%
9 | 0/1 1/1 1/1 1 50.00% 7.69%
10 |
11 | 0/0 0/1 0/1 1 100.00% 7.69%
12 |
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_diploid_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 0/1 0/1 0/1 6 85.71% 46.15%
3 | 0/1 0/1 1/1 1 14.29% 7.69%
4 |
5 | 0/0 1/1 0/1 2 66.67% 15.38%
6 | 0/0 1/1 1/2 1 33.33% 7.69% INCONSISTENT
7 |
8 | 0/1 1/1 0/1 1 50.00% 7.69%
9 | 0/1 1/1 1/1 1 50.00% 7.69%
10 |
11 | 0/0 0/1 0/1 1 100.00% 7.69%
12 |
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_ploidy_biallelic_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 1 1/1 0/1 1 50.00% 20.00% INCONSISTENT
3 | 1 1/1 1/1 1 50.00% 20.00%
4 |
5 | . 1 0 1 50.00% 20.00% INCONSISTENT
6 | . 1 1 1 50.00% 20.00% INCONSISTENT
7 |
8 | 0/1 0/1 0/1 1 100.00% 20.00%
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_ploidy_can_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 1 1/1 0/1 1 50.00% 14.29% INCONSISTENT
3 | 1 1/1 1/1 1 50.00% 14.29%
4 |
5 | . 1 0 1 50.00% 14.29% INCONSISTENT
6 | . 1 1 1 50.00% 14.29% INCONSISTENT
7 |
8 | 0/0 1/1 1/2 1 100.00% 14.29% INCONSISTENT
9 |
10 | 0/1 0/1 0/1 1 100.00% 14.29%
11 |
12 | 0/1 0/2 0/2 1 100.00% 14.29%
13 |
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_ploidy_diploid_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 0/0 1/1 1/2 1 100.00% 33.33% INCONSISTENT
3 |
4 | 0/1 0/1 0/1 1 100.00% 33.33%
5 |
6 | 0/1 0/2 0/2 1 100.00% 33.33%
7 |
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_ploidy_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 1 1/1 0/1 1 50.00% 14.29% INCONSISTENT
3 | 1 1/1 1/1 1 50.00% 14.29%
4 |
5 | . 1 0 1 50.00% 14.29% INCONSISTENT
6 | . 1 1 1 50.00% 14.29% INCONSISTENT
7 |
8 | 0/0 1/1 1/2 1 100.00% 14.29% INCONSISTENT
9 |
10 | 0/1 0/1 0/1 1 100.00% 14.29%
11 |
12 | 0/1 0/2 0/2 1 100.00% 14.29%
13 |
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/gt_prop_results.txt:
--------------------------------------------------------------------------------
1 | Parental Child Count Local Global
2 | 0/1 0/1 0/1 6 85.71% 46.15%
3 | 0/1 0/1 1/1 1 14.29% 7.69%
4 |
5 | 0/0 1/1 0/1 2 66.67% 15.38%
6 | 0/0 1/1 1/2 1 33.33% 7.69% INCONSISTENT
7 |
8 | 0/1 1/1 0/1 1 50.00% 7.69%
9 | 0/1 1/1 1/1 1 50.00% 7.69%
10 |
11 | 0/0 0/1 0/1 1 100.00% 7.69%
12 |
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/mendelian.out.txt:
--------------------------------------------------------------------------------
1 | Checking:
2 | Family: [NA19239 + NA19238] -> [NA19240]
3 | Concordance NA19240: F:22/23 (95.65%) M:20/20 (100.00%) F+M:20/22 (90.91%)
4 | 6/41 (14.63%) records did not conform to expected call ploidy
5 | 32/41 (78.05%) records were variant in at least 1 family member and checked for Mendelian constraints
6 | 9/32 (28.13%) records had indeterminate consistency status due to incomplete calls
7 | 1/32 (3.13%) records were not adequately checked due to a child call that was neither haploid nor diploid
8 | 2/32 (6.25%) records contained a violation of Mendelian constraints
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/mendelian/resources/mendelian2.out.txt:
--------------------------------------------------------------------------------
1 | Checking:
2 | Family: [NA19239 + NA19238] -> [NA19240]
3 | 36 non-pass records were skipped
4 | Concordance NA19240: F:2/2 (100.00%) M:2/2 (100.00%) F+M:2/2 (100.00%)
5 | 0/5 (0.00%) records did not conform to expected call ploidy
6 | 2/5 (40.00%) records were variant in at least 1 family member and checked for Mendelian constraints
7 | 0/2 (0.00%) records contained a violation of Mendelian constraints
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/bedinput.txt:
--------------------------------------------------------------------------------
1 | #Comment
2 |
3 | chr1 0 3701 annotation1
4 | chr1 3700 4792 annotation2
5 | chr1 4769 4792 annotation3 annotation4
6 | chr2 0 3333 annotationNonExistant
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/bedinputb.txt:
--------------------------------------------------------------------------------
1 | chr1 206307328 206307328 rs35720470
2 | chr1 223739903 223739928 rs59122179
3 | chr1 433 433 rs56289060
4 | chr1 491 492 rs55998931
5 | chr1 518 519 rs62636508
6 | chr1 582 583 rs58108140
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/exclude.bed:
--------------------------------------------------------------------------------
1 | g1 10 14 foo
2 | g1 75 87 foo
3 | g1 97 98 foo
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/exclude.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##FORMAT=
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
4 | g1 11 . AAAA G . PASS . GT 1/1
5 | g1 76 . AAAAAAAAAAAA G . PASS . GT 1/1
6 | g1 98 . A G . PASS . GT 1/1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/include.bed:
--------------------------------------------------------------------------------
1 | g1 7 12 foo
2 | g1 54 80 foo
3 | g1 89 107 foo
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/include.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##FORMAT=
3 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample
4 | g1 8 . AAAAA G . PASS . GT 1/1
5 | g1 55 . AAAAAAAAAAAAAAAAAAAAAAAAAA G . PASS . GT 1/1
6 | g1 90 . AAAAAAAAAAAAAAAAAA G . PASS . GT 1/1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small.bed:
--------------------------------------------------------------------------------
1 | browser position chr1:762097-762217
2 | track db="hg19" name="Human All Exon V4 plus UTRs" description="" visibility=2 color=0,128,0 useScore=1
3 | chr1 433 434 notHere1
4 | chr1 491 492 notHere2
5 | chr2 0 899 label1 EXTRAINFOSHOULDNOTSHOWUP
6 | chr2 200 900 label2
7 | chr3 299 300 label3
8 | chr3 99 399 label4
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small_exp.vcf:
--------------------------------------------------------------------------------
1 | chr2 100 . A C,G . PASS ANN=label1;NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
2 | chr2 200 . A C . PASS ANN=label1;NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
3 | chr2 900 . A G . PASS ANN=label2;NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
4 | chr3 200 . A G . PASS ANN=label4;NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
5 | chr3 300 . A C . PASS ANN=label3,label4;NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
6 | chr3 500 . A C,G . PASS NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small_ids.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##contig=
5 | ##contig=
6 | ##FORMAT=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
8 | chr2 100 . A C,G . PASS . GT 1/1 2/2
9 | chr2 200 . A C . PASS . GT 1/1 .
10 | chr2 900 . A G . PASS . GT . 1/1
11 | chr3 200 . A G . PASS . GT . 1/1
12 | chr3 300 . A C . PASS . GT 1/1 .
13 | chr3 500 . A C,G . PASS . GT 1/1 2/2
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small_ids_exp.vcf:
--------------------------------------------------------------------------------
1 | chr2 100 label1 A C,G . PASS NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
2 | chr2 200 label1 A C . PASS NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
3 | chr2 900 label2 A G . PASS NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
4 | chr3 200 label4 A G . PASS NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
5 | chr3 300 label3;label4 A C . PASS NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
6 | chr3 500 . A C,G . PASS NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpAnnotate_small_vcf_ids_exp.vcf:
--------------------------------------------------------------------------------
1 | chr2 100 label1 A C,G . PASS NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
2 | chr2 200 label1 A C . PASS NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
3 | chr2 900 label2 A G . PASS NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
4 | chr3 200 label4 A G . PASS NAA=1;AC=2;AN=2 GT:ZY:PD . 1/1:o:d
5 | chr3 300 label3;label4 A C . PASS NAA=1;AC=2;AN=2 GT:ZY:PD 1/1:o:d .
6 | chr3 500 . A C,G . PASS NAA=2;AC=2,2;AN=4 GT:ZY:PD 1/1:o:d 2/2:o:d
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest2_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to OC : 7
4 | Remaining records : 13
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest3_exp.vcf:
--------------------------------------------------------------------------------
1 | chr16 33856224 . C G . PASS . GT:DP:RE:GQ:RS 0/1:67:1.990:169.0:A,1,0.001,C,54,1.873,G,12,0.116
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest3_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 15
3 | Filtered due to RC : 3
4 | Filtered due to RX : 9
5 | Filtered due to a1000.0 : 1
6 | Filtered due to same as reference : 1
7 | Remaining records : 1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest3_exp_all.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 15
3 | Remaining records : 15
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest4_exp.vcf:
--------------------------------------------------------------------------------
1 | chr16 33856224 . C G . PASS . GT:DP:RE:GQ:RS 0/1:67:1.990:169.0:A,1,0.001,C,54,1.873,G,12,0.116
2 | chr16 33856229 . C G . PASS . GT:DP:RE:GQ:RS 1/1:67:1.990:169.0:A,1,0.001,C,54,1.873,G,12,0.116
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest4_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 21
3 | Filtered due to not a SNP : 7
4 | Filtered due to not in keep set : 12
5 | Remaining records : 2
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest4_exp_nonsnps.vcf:
--------------------------------------------------------------------------------
1 | chr16 33856085 . TTG AAC . PASS . GT:DP:RE:GQ 1/1:152:0.000:3.0
2 | chr16 33856087 . NT N . PASS . GT:DP:RE:GQ 1/1:152:0.000:3.0
3 | chr16 33856090 . N NT . PASS . GT:DP:RE:GQ 1/0:152:0.000:3.0
4 | chr16 33856095 . NAG N . PASS . GT:DP:RE:GQ 0/1:152:0.000:3.0
5 | chr16 33856271 . NG NGG . PASS . GT:DP:RE:GQ 1/1:215:0.000:3.0
6 | chr16 33856279 . NG NGG,NT . PASS . GT:DP:RE:GQ 1/2:215:0.000:3.0
7 | chr16 33856294 . NT NA,NTT . PASS . GT:DP:RE:GQ 1/2:215:0.000:3.0
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest4_exp_nonsnps.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 21
3 | Filtered due to simple SNP : 2
4 | Filtered due to not in keep set : 12
5 | Remaining records : 7
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_DotPass_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 22 . G A,T 27.9 c100 . GT:DP:RE:AR:AB:GQ 1/2:10:0.000:0.101:0.000:27.9
2 | g1 23 . G T 27.9 RX . GT:DP:RE:AR:AB:GQ 0/1:10:0.000:0.101:0.500:27.9
3 | g1 24 . G T 27.9 RC . GT:DP:RE:AR:AB:GQ 1/0:10:0.000:0.101:0.500:27.9
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_DotPass_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Filtered due to . : 4
4 | Filtered due to PASS : 35
5 | Remaining records : 3
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_ac2_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Filtered due to allele count : 30
4 | Remaining records : 12
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_ac3_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 22 . G A,T 27.9 c100 . GT:DP:RE:AR:AB:GQ 1/2:10:0.000:0.101:0.000:27.9
2 | g1 27 . G A,T 27.9 PASS . GT:DP:RE:AR:AB:GQ 1/2:10:0.000:0.000:0.260:27.9
3 | g1 34 . G A,T 27.9 PASS . GT:DP:RE:AR:AB:GQ 1/2:10:0.000:0.000:0.000:27.9
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_ac3_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Filtered due to allele count : 39
4 | Remaining records : 3
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Filtered due to quality : 3
4 | Filtered due to genotype quality : 2
5 | Filtered due to ambiguity ratio : 5
6 | Remaining records : 32
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_exp_all.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Remaining records : 42
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest5_rx_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 42
3 | Filtered due to RX : 1
4 | Remaining records : 41
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest6_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 54 . T . . a1000.0 . GT:DP:RE:GQ:RS 0/0:2:1.002:36.0:T,2,1.002
2 | g1 65 . C . . a1000.0 . GT:DP:RE:GQ:RS 0/0:3:1.504:37.0:C,3,1.504
3 | g1 76 . G . . a1000.0 . GT:DP:RE:GQ:RS 0/0:5:2.506:41.0:G,5,2.506
4 | g1 87 . A . . a1000.0 . GT:DP:RE:GQ:RS 0/0:5:2.506:43.0:A,5,2.506
5 | g1 98 . C . . a1000.0 . GT:DP:RE:GQ:RS 0/0:5:2.506:41.0:C,5,2.506
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest6_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to density window : 15
4 | Remaining records : 5
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestASR_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to all samples same as reference : 3
4 | Remaining records : 17
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_AmMu3.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_AmMu4.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_AmMu5.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to not in keep set : 4
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_Avr7.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 8
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 8
4 | Remaining records : 12
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp2.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 11
4 | Remaining records : 9
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp3.vcf:
--------------------------------------------------------------------------------
1 | g1 109 . T . . a1000.0 . GT:DP:RE:GQ:RS:AVR 0/0:5:2.506:43.0:T,5,2.506:0.3 0/0:5:2.506:43.0:T,5,2.506:0.3
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp3.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 19
4 | Remaining records : 1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp4.vcf:
--------------------------------------------------------------------------------
1 | g1 109 . T . . a1000.0 . GT:DP:RE:GQ:RS:AVR 0/0:5:2.506:43.0:T,5,2.506:0.3 0/0:5:2.506:43.0:T,5,2.506:0.3
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp4.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 19
4 | Remaining records : 1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp5.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 19
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp6.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to AVR score : 19
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp7.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestAVR_exp8.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestRCE_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 6
3 | Remaining records : 6
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertestSR_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to same as reference : 3
4 | Remaining records : 17
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_DNP_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 109 . T . . a1000.0 . GT:DP:RE:GQ:DN:DNP:RS 0/0:5:2.506:43.0:.:.:T,5,2.506 0/0:5:0.000:31.0 0/0:5:0.000:31.0:Y:30.0 0/0:5:0.000:31.0:N:0.0
2 | g1 209 . T . . a1000.0 . GT:DP:RE:GQ:DN:DNP:RS 0/0:5:2.506:43.0:.:.:T,5,2.506 0/0:5:0.000:31.0 0/0:5:0.000:31.0:Y:30.0 0/0:5:0.000:31.0:Y:5.0
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_DNP_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 27
3 | Filtered due to de novo score : 25
4 | Remaining records : 2
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_DNP_sample_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 69 . C . . a1000.0 . GT:DP:RE:GQ:RS:DN:DNP 0/0:3:1.504:37.0:C,3,1.504 0/0:5:0.000:31.0 0/0:5:0.000:31.0:.:N:0.0 0/0:5:0.000:31.0:.:Y:6.0
2 | g1 199 . T . . a1000.0 . GT:DP:RE:GQ:DN:DNP:RS 0/0:5:2.506:43.0:.:.:T,5,2.506 0/0:5:0.000:31.0 0/0:5:0.000:31.0:Y:31.0 0/0:5:0.000:31.0:Y:6.0
3 | g1 211 . T . . a1000.0 . GT:DP:RE:GQ:DN:DNP:RS 0/0:5:2.506:43.0:.:.:T,5,2.506 0/0:5:0.000:31.0 0/0:5:0.000:31.0:N 0/0:5:0.000:31.0:Y
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_DNP_sample_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 27
3 | Filtered due to de novo score : 24
4 | Remaining records : 3
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_complex_inc_exc_bed.vcf:
--------------------------------------------------------------------------------
1 | g1 8 . A . . PASS . GT:DP:RE:GQ 0/0:7:0.000:31.0
2 | g1 65 . C . . a1000.0 . GT:DP:RE:GQ:RS 0/0:3:1.504:37.0:C,3,1.504
3 | g1 87 . ATAT . . a1000.0 . GT:DP:RE:GQ:RS 0/0:5:2.506:43.0:A,5,2.506
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_complex_inc_exc_bed.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 9
3 | Filtered due to include file : 3
4 | Filtered due to exclude file : 3
5 | Remaining records : 3
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_complex_inc_exc_vcf.vcf:
--------------------------------------------------------------------------------
1 | g1 8 . A . . PASS . GT:DP:RE:GQ 0/0:7:0.000:31.0
2 | g1 65 . C . . a1000.0 . GT:DP:RE:GQ:RS 0/0:3:1.504:37.0:C,3,1.504
3 | g1 87 . ATAT . . a1000.0 . GT:DP:RE:GQ:RS 0/0:5:2.506:43.0:A,5,2.506
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_complex_inc_exc_vcf.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 9
3 | Filtered due to include file : 3
4 | Filtered due to exclude file : 3
5 | Remaining records : 3
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 1 . A . . PASS . GT:DP:RE:GQ 0/0:5:0.000:31.0
2 | g1 8 . A . . PASS . GT:DP:RE:GQ 0/0:7:0.000:31.0
3 | g1 195 . G . . PASS . GT:DP:RE:GQ 0/0:7:0.000:48.0
4 | g1 205 . G . . PASS . GT:DP:RE:GQ 0/0:7:0.000:48.0
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 4
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/snpfiltertest_exp_clear.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 20
3 | Filtered due to a1000.0 : 16
4 | Remaining records : 20
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcf-sort-tweak-out.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20150807
3 | ##reference=ref
4 | ##contig=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 1 1508257 . T TG,TGG,TGGG . . .
8 | 1 1508257 . TG T . . .
9 | 1 1508257 . TGG T . . .
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcf-sort-tweak.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20150807
3 | ##FORMAT=
4 | ##contig=
5 | ##reference=ref
6 | #CHROM POS ID REF ALT QUAL FILTER INFO
7 | 1 1508257 . TGG T . . .
8 | 1 1508257 . TG T . . .
9 | 1 1508257 . T TG,TGG,TGGG . . .
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfdecompose_out_indels.vcf.txt:
--------------------------------------------------------------------------------
1 | Total records : 16
2 | Number of records decomposed : 11
3 | Remaining records : 32
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfdecompose_out_mnps.vcf.txt:
--------------------------------------------------------------------------------
1 | Total records : 16
2 | Number of records decomposed : 10
3 | Remaining records : 23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfdecompose_out_noref.vcf.txt:
--------------------------------------------------------------------------------
1 | Total records : 16
2 | Number of records decomposed : 9
3 | Remaining records : 22
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfdecompose_out_ref.vcf.txt:
--------------------------------------------------------------------------------
1 | Total records : 16
2 | Number of records decomposed : 9
3 | Remaining records : 22
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcffilterIndDens_exp.vcf:
--------------------------------------------------------------------------------
1 | g1 146 . AA A . a1000.0 . GT:DP:RE:GQ:RS 0/1:1:0.501:33.0:A,1,0.501
2 | g1 146 . A T . a1000.0 . GT:DP:RE:GQ:RS 0/1:1:0.501:33.0:A,1,0.501
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcffilterIndDens_exp.vcf.txt:
--------------------------------------------------------------------------------
1 |
2 | Total records : 2
3 | Remaining records : 2
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcffilterNoGt_exp1.txt:
--------------------------------------------------------------------------------
1 | Error: Specified filters require GT but no such field contained in record:
2 | g1 146 . A T . a1000.0 . DP:RE:GQ:RS 1:0.501:33.0:A,1,0.501
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcffilterNoGt_exp2.txt:
--------------------------------------------------------------------------------
1 | Error: Record does not contain GT field:
2 | g1 146 . A T . a1000.0 . DP:RE:GQ:RS 1:0.501:33.0:A,1,0.501
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge-f1.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##contig=
4 | ##contig=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
7 | chr2 100 . A C . PASS . GT 1/1
8 | chr2 200 . A C . PASS . GT 1/1
9 | chr3 300 . A C . PASS . GT 1/1
10 | chr3 500 . A C . PASS . GT 1/1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge-f2.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##contig=
4 | ##contig=
5 | ##FORMAT=
6 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample2
7 | chr3 200 . A G . PASS . GT 1/1
8 | chr3 500 . A G . PASS . GT 1/1
9 | chr2 100 . A G . PASS . GT 1/1
10 | chr2 900 . A G . PASS . GT 1/1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge-mix-nosample-1.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
3 | ##contig=
4 | #CHROM POS ID REF ALT QUAL FILTER INFO
5 | 1 13372 . G C 608.91 PASS .
6 | 1 13417 . C CGAGA 258189.04 PASS .
7 | 1 13494 . A G 18163.42 PASS .
8 | 1 13504 . G A 6229.58 PASS .
9 | 1 13539 . G C 658.19 PASS .
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge-mix-nosample-2.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##contig=
3 | ##FORMAT=
4 | ##SAMPLE=
5 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
6 | 1 14907 . A G 33635.0 PASS . GT 1|1
7 | 1 14930 . A G 37382.9 PASS . GT 1|1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge_out_mix-nosample.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##reference=[...]
3 | ##CL=[...]
4 | ##contig=
5 | ##FORMAT=
6 | ##SAMPLE=
7 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
8 | 1 13372 . G C 608.91 PASS . GT .
9 | 1 13417 . C CGAGA 258189.04 PASS . GT .
10 | 1 13494 . A G 18163.42 PASS . GT .
11 | 1 13504 . G A 6229.58 PASS . GT .
12 | 1 13539 . G C 658.19 PASS . GT .
13 | 1 14907 . A G 33635.0 PASS . GT 1|1
14 | 1 14930 . A G 37382.9 PASS . GT 1|1
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge_out_simple-rev.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##contig=
8 | ##FORMAT=
9 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample2 sample1
10 | chr2 100 . A G,C . PASS . GT 1/1 2/2
11 | chr2 200 . A C . PASS . GT . 1/1
12 | chr2 900 . A G . PASS . GT 1/1 .
13 | chr3 200 . A G . PASS . GT 1/1 .
14 | chr3 300 . A C . PASS . GT . 1/1
15 | chr3 500 . A G,C . PASS . GT 1/1 2/2
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge_out_simple.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##extraline=foo
3 | ##extraline2=bar
4 | ##CL=[...]
5 | ##contig=
6 | ##contig=
7 | ##contig=
8 | ##FORMAT=
9 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
10 | chr2 100 . A C,G . PASS . GT 1/1 2/2
11 | chr2 200 . A C . PASS . GT 1/1 .
12 | chr2 900 . A G . PASS . GT . 1/1
13 | chr3 200 . A G . PASS . GT . 1/1
14 | chr3 300 . A C . PASS . GT 1/1 .
15 | chr3 500 . A C,G . PASS . GT 1/1 2/2
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfmerge_testSamePos.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##CL=[...]
3 | ##CL=[...]
4 | ##contig=
5 | ##contig=
6 | ##contig=
7 | ##FORMAT=
8 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892
9 | 1 20200602 . C T,G 575.1 PASS XRX GT:DP:RE:GQ 0/1:42:4.891:56 . 0/2:42:4.891:56
10 | 1 20200602 . CA C 575.1 PASS XRX GT:DP:RE:GQ . 0/1:42:4.891:56 .
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/resources/vcfsubset-multi.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##reference=[...]
3 | ##CL=[...]
4 | ##ALT=
5 | ##FILTER=
6 | ##INFO=
7 | ##INFO=