├── .github
└── workflows
│ └── static.yml
├── .gitignore
├── LICENSE.txt
├── README.md
├── build.xml
├── installer
└── resources
│ ├── core
│ ├── RTGOperationsManual.pdf
│ ├── RTGOperationsManual
│ │ ├── _images
│ │ │ ├── ceph-1463.png
│ │ │ ├── chinese-trio.png
│ │ │ ├── math
│ │ │ │ ├── 00b47fa9220275347363dd17597c6ce4efc96fa5.png
│ │ │ │ ├── 0118ce53bf328bf7fa4d2751f727ce6ed1a759fd.png
│ │ │ │ ├── 1dda4b44764a929f5d95a12343b22b3343e7993e.png
│ │ │ │ ├── 23991ec1fa444bd42d05816c69d1ba02c12a264e.png
│ │ │ │ ├── 2895eb405a03db49e2217253743e51b83144c2ac.png
│ │ │ │ ├── 3e33daea0596958aba9bd9cf28865a39b7e48b25.png
│ │ │ │ ├── 4370f8a24787d16b6631cfde4d5e7bc06d8d42c7.png
│ │ │ │ ├── 52ddc0cde6d632f631533173562fe3ca375b1f32.png
│ │ │ │ ├── 57540cfddc027fe046444894db8bb84952eaff1f.png
│ │ │ │ ├── 593c511ee9aeb89e927882c5cb67418a46da3828.png
│ │ │ │ ├── 5a939c5280da7202ca4531f175a7780ad5e1f80a.png
│ │ │ │ ├── 6596b3f1d72eeb3b72dd1cdaaae199a4a3b1a412.png
│ │ │ │ ├── 67e012a427a90dc0c0f8a2d5939a95e5f6ffe591.png
│ │ │ │ ├── 6c754ae3fc49dc56e236eb95ef00cfdcad3df594.png
│ │ │ │ ├── 888f7c323ac0341871e867220ae2d76467d74d6e.png
│ │ │ │ ├── 92ddcd7319ecbea8436f1b18fbebf544a38e4c69.png
│ │ │ │ ├── 9e32cdd0b4d023c3e9b3e724291a03bdbcbee572.png
│ │ │ │ ├── af517d52259b23914a79dc82c765d702ec5cf7b1.png
│ │ │ │ ├── b6f66d1803a9dcb5f12f25c57d4e43fb6584ca7e.png
│ │ │ │ ├── b81c7a12342c0ee157b2c3f1bcfc4f91642187dc.png
│ │ │ │ ├── b988975be41fd13b4d091c10202ba19374643586.png
│ │ │ │ ├── c2aa3dff9bffb099e9dff196fd36aed56ec16baf.png
│ │ │ │ ├── c61adab5a368b41156d78099e64eaef7d3a9fb30.png
│ │ │ │ ├── cefc603e5658facb747581f9567192993f21c7ab.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-family.sh
│ │ ├── sample-clustering
│ │ ├── README.txt
│ │ ├── similarity-kmeans.R
│ │ ├── similarity-simple.R
│ │ └── similarity.pca
│ │ ├── species-abundance
│ │ ├── README.txt
│ │ ├── abundance-graphs-example.xlsm
│ │ └── abundance-graphs-template.xlsm
│ │ └── species-comparison
│ │ ├── README.txt
│ │ └── comparison.R
│ └── models
│ ├── alternate.avr
│ ├── illumina-exome.avr
│ ├── illumina-somatic.avr
│ └── illumina-wgs.avr
├── lib
└── Jama-1.0.3.jar
├── src
├── main
│ ├── java
│ │ └── com
│ │ │ └── rtg
│ │ │ ├── CoreCommand.java
│ │ │ ├── LicensedCommand.java
│ │ │ ├── RtgCore.java
│ │ │ ├── alignment
│ │ │ ├── AlignerMode.java
│ │ │ ├── AlignmentResult.java
│ │ │ ├── BidirectionalEditDistance.java
│ │ │ ├── CgGotohEditDistance.java
│ │ │ ├── EditDistanceFactory.java
│ │ │ ├── HopStepEditDistanceLong.java
│ │ │ ├── LoggingOnlyEditDistance.java
│ │ │ ├── LowerBoundEditDistance.java
│ │ │ ├── LowerBoundEstimator.java
│ │ │ ├── NoIndelsEditDistance.java
│ │ │ ├── ProteinActionsValidator.java
│ │ │ ├── RcCgEditDistance.java
│ │ │ ├── RcEditDistance.java
│ │ │ ├── Seed.java
│ │ │ ├── SeedPositions.java
│ │ │ ├── SeedShifter.java
│ │ │ ├── SeededAligner.java
│ │ │ ├── SingleIndelEditDistance.java
│ │ │ ├── SingleIndelSeededEditDistance.java
│ │ │ ├── SoftClipper.java
│ │ │ ├── UnidirectionalAdaptor.java
│ │ │ ├── UnidirectionalPrioritisedEditDistance.java
│ │ │ └── doc-files
│ │ │ │ ├── singleIndelForwardNegative.jpg
│ │ │ │ ├── singleIndelForwardPositive.jpg
│ │ │ │ ├── singleIndelGeneral.jpg
│ │ │ │ ├── singleIndelReverseNegative.jpg
│ │ │ │ └── singleIndelReversePositive.jpg
│ │ │ ├── assembler
│ │ │ ├── AbstractKDeBruijnGraph.java
│ │ │ ├── AbstractKmer.java
│ │ │ ├── AlignmentChain.java
│ │ │ ├── AlignmentIterator.java
│ │ │ ├── AlignmentSection.java
│ │ │ ├── ApplyReference.java
│ │ │ ├── AssembleCli.java
│ │ │ ├── AssembleParams.java
│ │ │ ├── AssembleTask.java
│ │ │ ├── AsyncKmerIterable.java
│ │ │ ├── AsyncReadPool.java
│ │ │ ├── AsyncReadSource.java
│ │ │ ├── BubbleExplorer.java
│ │ │ ├── ByteKmer.java
│ │ │ ├── Consensus.java
│ │ │ ├── ConstraintCache.java
│ │ │ ├── ConstraintCollector.java
│ │ │ ├── ContigCollector.java
│ │ │ ├── ContigConcatenated.java
│ │ │ ├── ContigPosition.java
│ │ │ ├── CorrectReads.java
│ │ │ ├── CorrectReadsCli.java
│ │ │ ├── CorrectingMutator.java
│ │ │ ├── CountAssemblyEnds.java
│ │ │ ├── DeBruijnAssemblerCli.java
│ │ │ ├── DeBruijnAssemblerTask.java
│ │ │ ├── DeBruijnGraph.java
│ │ │ ├── DeBruijnGraphBuilder.java
│ │ │ ├── DeBruijnParams.java
│ │ │ ├── ExtractPath.java
│ │ │ ├── FilterPaths.java
│ │ │ ├── GraphAligner.java
│ │ │ ├── GraphAlignment.java
│ │ │ ├── GraphCleanup.java
│ │ │ ├── GraphFlowAligner.java
│ │ │ ├── GraphIndex.java
│ │ │ ├── GraphMap.java
│ │ │ ├── GraphMapCli.java
│ │ │ ├── GraphMapParams.java
│ │ │ ├── GraphMapStatistics.java
│ │ │ ├── GraphMapTask.java
│ │ │ ├── GraphSorter.java
│ │ │ ├── GraphToPlot.java
│ │ │ ├── GraphTraversions.java
│ │ │ ├── HashMapDeBruijnGraph.java
│ │ │ ├── Kmer.java
│ │ │ ├── KmerFactory.java
│ │ │ ├── KmerHash.java
│ │ │ ├── KmerHashA.java
│ │ │ ├── KmerIterable.java
│ │ │ ├── KmerIterableFactory.java
│ │ │ ├── KmerIterableFactoryInterface.java
│ │ │ ├── KmerIterator.java
│ │ │ ├── LargeKDeBruijnGraph.java
│ │ │ ├── LowKDeBruijnGraph.java
│ │ │ ├── MergeNodes.java
│ │ │ ├── NullTraversions.java
│ │ │ ├── PacBio.java
│ │ │ ├── PacBioCli.java
│ │ │ ├── PacBioParams.java
│ │ │ ├── PacBioPath.java
│ │ │ ├── PacBioStatistics.java
│ │ │ ├── PairConstraintWriter.java
│ │ │ ├── PairJoiner.java
│ │ │ ├── PalindromeTracker.java
│ │ │ ├── PartialAlignment.java
│ │ │ ├── PathAligner.java
│ │ │ ├── PathTracker.java
│ │ │ ├── PreContig.java
│ │ │ ├── ReadIterator.java
│ │ │ ├── ReadPairSource.java
│ │ │ ├── ReadPairSource454.java
│ │ │ ├── ReadPairSourceMatePair.java
│ │ │ ├── RecoverLinks.java
│ │ │ ├── SequencesReaderIterator.java
│ │ │ ├── StringKmer.java
│ │ │ ├── Traversion.java
│ │ │ └── graph
│ │ │ │ ├── Contig.java
│ │ │ │ ├── ContigByte.java
│ │ │ │ ├── Graph.java
│ │ │ │ ├── GraphFactory.java
│ │ │ │ ├── MutableGraph.java
│ │ │ │ ├── Path.java
│ │ │ │ ├── PathsIterator.java
│ │ │ │ ├── implementation
│ │ │ │ ├── ContigForward.java
│ │ │ │ ├── ContigReverse.java
│ │ │ │ ├── ContigString.java
│ │ │ │ ├── GraphImplementation.java
│ │ │ │ ├── GraphKmerAttribute.java
│ │ │ │ ├── IteratorLocal.java
│ │ │ │ ├── PathArray.java
│ │ │ │ └── PathLocal.java
│ │ │ │ └── io
│ │ │ │ ├── BoundedOutputStream.java
│ │ │ │ ├── BoundedStreams.java
│ │ │ │ ├── GraphReader.java
│ │ │ │ └── GraphWriter.java
│ │ │ ├── blacklist
│ │ │ ├── BinaryMatrix.java
│ │ │ ├── HashCounter.java
│ │ │ ├── HashDist.java
│ │ │ ├── HashDistCli.java
│ │ │ ├── HashDistParams.java
│ │ │ └── HashDistParamsBuilder.java
│ │ │ ├── calibrate
│ │ │ ├── CalibratedPerSequenceExpectedCoverage.java
│ │ │ ├── CalibratingPopulatorFactory.java
│ │ │ ├── CalibratingSamRecordPopulator.java
│ │ │ ├── CalibrationStats.java
│ │ │ ├── Calibrator.java
│ │ │ ├── CalibratorCigarParser.java
│ │ │ ├── ChrStats.java
│ │ │ ├── ChrStatsCli.java
│ │ │ ├── Covariate.java
│ │ │ ├── CovariateArm.java
│ │ │ ├── CovariateBaseQuality.java
│ │ │ ├── CovariateEnum.java
│ │ │ ├── CovariateImpl.java
│ │ │ ├── CovariateMachineCycle.java
│ │ │ ├── CovariateReadGroup.java
│ │ │ ├── CovariateSequence.java
│ │ │ ├── CovariateSequenceFixed.java
│ │ │ ├── CovariateSingleReadGroup.java
│ │ │ ├── CovariateStrings.java
│ │ │ ├── Recalibrate.java
│ │ │ ├── RecalibrateCli.java
│ │ │ ├── SamCalibrationInputs.java
│ │ │ └── StatsProcessor.java
│ │ │ ├── index
│ │ │ ├── AbstractBitVector.java
│ │ │ ├── Add.java
│ │ │ ├── BigBitVector.java
│ │ │ ├── BitVector.java
│ │ │ ├── BlacklistFilterMethod.java
│ │ │ ├── CountingFinder.java
│ │ │ ├── Finder.java
│ │ │ ├── FinderHashValue.java
│ │ │ ├── FinderHashValueExtended.java
│ │ │ ├── FixedRepeatFrequencyFilterMethod.java
│ │ │ ├── HashBitHandle.java
│ │ │ ├── HashBitVector.java
│ │ │ ├── HashBlacklist.java
│ │ │ ├── Index.java
│ │ │ ├── IndexBase.java
│ │ │ ├── IndexCompressed.java
│ │ │ ├── IndexExtended.java
│ │ │ ├── IndexFilterMethod.java
│ │ │ ├── IndexSet.java
│ │ │ ├── IndexSimple.java
│ │ │ ├── IndexUtils.java
│ │ │ ├── IntSet.java
│ │ │ ├── IntSetCaller.java
│ │ │ ├── IntSetSingle.java
│ │ │ ├── IntSetWindow.java
│ │ │ ├── ProportionalRepeatFrequencyFilterMethod.java
│ │ │ ├── ReadIndexCoverageUtils.java
│ │ │ ├── SearchUtils.java
│ │ │ ├── SparseFrequencyHistogram.java
│ │ │ ├── UnfilteredFilterMethod.java
│ │ │ ├── UnionRepeatFrequencyFilterMethod.java
│ │ │ ├── hash
│ │ │ │ ├── ExactHashFunction.java
│ │ │ │ ├── HashFunction.java
│ │ │ │ ├── HashLoop.java
│ │ │ │ ├── InExactHashFunction.java
│ │ │ │ ├── IncrementalHashLoop.java
│ │ │ │ ├── PrimeUtils.java
│ │ │ │ ├── RandomizedExactHashFunction.java
│ │ │ │ ├── ResetHashLoop.java
│ │ │ │ ├── ngs
│ │ │ │ │ ├── CommonHashFunction.java
│ │ │ │ │ ├── FactoryUtil.java
│ │ │ │ │ ├── HashFunctionFactory.java
│ │ │ │ │ ├── ImplementHashFunction.java
│ │ │ │ │ ├── MemScore.java
│ │ │ │ │ ├── NgsHashFunction.java
│ │ │ │ │ ├── NgsHashLoop.java
│ │ │ │ │ ├── NgsHashLoopImpl.java
│ │ │ │ │ ├── OutputProcessor.java
│ │ │ │ │ ├── PcrTemplateCallImplementation.java
│ │ │ │ │ ├── ProteinIncrementalHashLoop.java
│ │ │ │ │ ├── ProteinNgsHashLoop.java
│ │ │ │ │ ├── ProteinReadHashLoop.java
│ │ │ │ │ ├── ProteinTemplateHashLoop.java
│ │ │ │ │ ├── ReadCall.java
│ │ │ │ │ ├── ReadCallImplementation.java
│ │ │ │ │ ├── ReadDecoder.java
│ │ │ │ │ ├── ReadEncoder.java
│ │ │ │ │ ├── ReadHashFunction.java
│ │ │ │ │ ├── TemplateCall.java
│ │ │ │ │ ├── TemplateCallImplementation.java
│ │ │ │ │ ├── TemplateHashFunction.java
│ │ │ │ │ ├── doc-files
│ │ │ │ │ │ └── orientation.jpg
│ │ │ │ │ ├── general
│ │ │ │ │ │ ├── Combinator.java
│ │ │ │ │ │ ├── ExtractAbstract.java
│ │ │ │ │ │ ├── ExtractRead.java
│ │ │ │ │ │ ├── ExtractTemplate.java
│ │ │ │ │ │ ├── Mask.java
│ │ │ │ │ │ ├── SingleMask.java
│ │ │ │ │ │ ├── Skel.java
│ │ │ │ │ │ ├── Skeleton.java
│ │ │ │ │ │ ├── Util.java
│ │ │ │ │ │ └── package.html
│ │ │ │ │ ├── instances
│ │ │ │ │ │ ├── AbstractCG2Mask.java
│ │ │ │ │ │ ├── AbstractCGMask.java
│ │ │ │ │ │ ├── CG2Maska1.java
│ │ │ │ │ │ ├── CG2Maska11.java
│ │ │ │ │ │ ├── CG2Maska15.java
│ │ │ │ │ │ ├── CG2Maskw18.java
│ │ │ │ │ │ ├── CG2Maskw18a1.java
│ │ │ │ │ │ ├── CGMaska0.java
│ │ │ │ │ │ ├── CGMaska15b1.java
│ │ │ │ │ │ ├── CGMaska15b1alt.java
│ │ │ │ │ │ ├── CGMaska1b1.java
│ │ │ │ │ │ ├── CGMaska1b1alt.java
│ │ │ │ │ │ └── doc-files
│ │ │ │ │ │ │ └── CGMaska15.jpg
│ │ │ │ │ ├── package.html
│ │ │ │ │ └── protein
│ │ │ │ │ │ ├── AbstractProteinExtract.java
│ │ │ │ │ │ ├── ProteinExtractRead.java
│ │ │ │ │ │ ├── ProteinExtractTemplate.java
│ │ │ │ │ │ └── ProteinMask.java
│ │ │ │ └── package.html
│ │ │ ├── package.html
│ │ │ ├── params
│ │ │ │ ├── AbstractCreateParamsBuilder.java
│ │ │ │ ├── CountParams.java
│ │ │ │ ├── CreateParams.java
│ │ │ │ ├── ParamsUtils.java
│ │ │ │ └── package.html
│ │ │ ├── queue
│ │ │ │ ├── IndexQueue.java
│ │ │ │ ├── IndexQueues.java
│ │ │ │ └── QueueIterator.java
│ │ │ └── similarity
│ │ │ │ ├── BinaryTree.java
│ │ │ │ ├── IndexSimilarity.java
│ │ │ │ ├── NeighborJoining.java
│ │ │ │ ├── SimilarityMatrix.java
│ │ │ │ ├── SimilaritySorter.java
│ │ │ │ └── package.html
│ │ │ ├── launcher
│ │ │ ├── BuildCommon.java
│ │ │ ├── BuildParams.java
│ │ │ ├── DefaultReaderParams.java
│ │ │ ├── HashingRegion.java
│ │ │ ├── ISequenceParams.java
│ │ │ ├── SequenceParams.java
│ │ │ └── globals
│ │ │ │ └── CoreGlobalFlags.java
│ │ │ ├── metagenomics
│ │ │ ├── AbstractSolver.java
│ │ │ ├── BisectionSolver.java
│ │ │ ├── BlockInfo.java
│ │ │ ├── BlockMapping.java
│ │ │ ├── BlockResult.java
│ │ │ ├── CompositionMetaPipelineCli.java
│ │ │ ├── DefaultIdentifierCreator.java
│ │ │ ├── Frag.java
│ │ │ ├── FunctionalMetaPipelineCli.java
│ │ │ ├── HashingIdentifierCreator.java
│ │ │ ├── IdSet.java
│ │ │ ├── IdentifierCreator.java
│ │ │ ├── LLine.java
│ │ │ ├── Line.java
│ │ │ ├── LineSolver.java
│ │ │ ├── LinearInterpolationSolver.java
│ │ │ ├── LoggingLineSolver.java
│ │ │ ├── MetaPipelineParams.java
│ │ │ ├── MetagenomicsWrapperCli.java
│ │ │ ├── MetagenomicsWrapperTask.java
│ │ │ ├── Minimizer.java
│ │ │ ├── NewtonRaphsonSolver.java
│ │ │ ├── SimpleTerminator.java
│ │ │ ├── Species.java
│ │ │ ├── SpeciesCli.java
│ │ │ ├── SpeciesInfo.java
│ │ │ ├── SpeciesLine.java
│ │ │ ├── SpeciesLineDeriv.java
│ │ │ ├── SpeciesLineLinear.java
│ │ │ ├── SpeciesLineLinearDeriv.java
│ │ │ ├── SpeciesMap.java
│ │ │ ├── SpeciesParams.java
│ │ │ ├── SpeciesResult.java
│ │ │ ├── SpeciesSdfSubset.java
│ │ │ ├── SpeciesStatistics.java
│ │ │ ├── SpeciesTask.java
│ │ │ ├── SubBlockResult.java
│ │ │ ├── TargetTerminator.java
│ │ │ ├── Terminator.java
│ │ │ ├── krona
│ │ │ │ ├── KronaSpeciesNode.java
│ │ │ │ └── KronaSpeciesReportWriter.java
│ │ │ ├── matrix
│ │ │ │ ├── Matrix.java
│ │ │ │ ├── MatrixSimple.java
│ │ │ │ ├── MatrixSymmetric.java
│ │ │ │ ├── MatrixTranspose.java
│ │ │ │ ├── MatrixUtils.java
│ │ │ │ └── Vector.java
│ │ │ └── metasnp
│ │ │ │ ├── AlleleStatReader.java
│ │ │ │ ├── AlphaScore.java
│ │ │ │ ├── AlphaSelector.java
│ │ │ │ ├── ComplicatedBeta.java
│ │ │ │ ├── EmIterate.java
│ │ │ │ ├── Frobenius.java
│ │ │ │ ├── MetaSnpCli.java
│ │ │ │ ├── MetaSnpLine.java
│ │ │ │ ├── MetaSnpReader.java
│ │ │ │ ├── ProbAlpha.java
│ │ │ │ ├── ProbAlphaSimpleBeta.java
│ │ │ │ ├── RandomWalkXiFinder.java
│ │ │ │ ├── VcfMetaSnpReader.java
│ │ │ │ └── XiScore.java
│ │ │ ├── ml
│ │ │ ├── Attribute.java
│ │ │ ├── BaggedClassifier.java
│ │ │ ├── BaggedClassifierBuilder.java
│ │ │ ├── BinarySplitter.java
│ │ │ ├── BinaryTreeClassifier.java
│ │ │ ├── BuildClassifier.java
│ │ │ ├── BuilderFactory.java
│ │ │ ├── Dataset.java
│ │ │ ├── Instance.java
│ │ │ ├── MlDataType.java
│ │ │ ├── MlPredictLoader.java
│ │ │ ├── PredictClassifier.java
│ │ │ ├── RandomTreeBuilder.java
│ │ │ ├── SimpleEvaluation.java
│ │ │ ├── TrainTestSplit.java
│ │ │ ├── ZeroRBuilder.java
│ │ │ └── package.html
│ │ │ ├── mode
│ │ │ └── ProgramMode.java
│ │ │ ├── ngs
│ │ │ ├── AbstractAlignmentWriterThread.java
│ │ │ ├── AbstractMapOutputProcessor.java
│ │ │ ├── AbstractMulticoreFilterConcat.java
│ │ │ ├── AbstractSamResultsFilter.java
│ │ │ ├── AbstractSdfOutputProcessor.java
│ │ │ ├── CgMapCli.java
│ │ │ ├── ClippedOutputProcessor.java
│ │ │ ├── DeduplicatingNStore.java
│ │ │ ├── DefaultOutputProcessor.java
│ │ │ ├── DefaultOutputProcessorSynch.java
│ │ │ ├── FilterConcatIntermediateFiles.java
│ │ │ ├── LongReadMaskParams.java
│ │ │ ├── MapCli.java
│ │ │ ├── MapFCli.java
│ │ │ ├── MapFilterPairedMapStatistics.java
│ │ │ ├── MapFilterSingleEndMapStatistics.java
│ │ │ ├── MapFlags.java
│ │ │ ├── MapParamsHelper.java
│ │ │ ├── MapReportData.java
│ │ │ ├── MapStatistics.java
│ │ │ ├── MapStatisticsField.java
│ │ │ ├── MatchResult.java
│ │ │ ├── MatedSamResultsFilter.java
│ │ │ ├── NameParams.java
│ │ │ ├── NgsFilterParams.java
│ │ │ ├── NgsMaskParams.java
│ │ │ ├── NgsMaskParamsExplicit.java
│ │ │ ├── NgsMaskParamsGeneral.java
│ │ │ ├── NgsMaskParamsProtein.java
│ │ │ ├── NgsOutputParams.java
│ │ │ ├── NgsOutputParamsBuilder.java
│ │ │ ├── NgsParams.java
│ │ │ ├── NgsParamsBuilder.java
│ │ │ ├── NgsResultStreamHandler.java
│ │ │ ├── NgsTask.java
│ │ │ ├── NullOutputProcessor.java
│ │ │ ├── OutputFilter.java
│ │ │ ├── PairedEndMapStatistics.java
│ │ │ ├── PairedEndOutputProcessor.java
│ │ │ ├── PairedTopRandomImplementation.java
│ │ │ ├── PairedTopRandomImplementationSync.java
│ │ │ ├── ReadStatusTracker.java
│ │ │ ├── ReadStatusTrackerSync.java
│ │ │ ├── SamRename.java
│ │ │ ├── SamResultsSansFilter.java
│ │ │ ├── SamSequenceReaderParams.java
│ │ │ ├── SamSingleEndOutputProcessor.java
│ │ │ ├── SansFilterConcat.java
│ │ │ ├── SharedResources.java
│ │ │ ├── SingleEndMapStatistics.java
│ │ │ ├── SingleEndSamResultsFilter.java
│ │ │ ├── SingleEndTopRandomImplementation.java
│ │ │ ├── SingleEndTopRandomImplementationSync.java
│ │ │ ├── TopNImplementation.java
│ │ │ ├── TopNPairedEndOutputProcessorSync.java
│ │ │ ├── UnfilteredPairedEndOutputProcessor.java
│ │ │ ├── UnfilteredSingleEndOutputProcessor.java
│ │ │ ├── UnmappedSamAlignmentWriter.java
│ │ │ ├── UnmappedSamRecordFactory.java
│ │ │ ├── UnmatedSamResultsFilter.java
│ │ │ ├── UptoNStore.java
│ │ │ ├── UptoNStoreSync.java
│ │ │ ├── blocking
│ │ │ │ ├── MapQScoringReadBlocker.java
│ │ │ │ ├── MapQScoringReadBlockerSynch.java
│ │ │ │ ├── ReadBlocker.java
│ │ │ │ └── ReadBlockerSync.java
│ │ │ ├── longread
│ │ │ │ └── LongReadTask.java
│ │ │ ├── package.html
│ │ │ └── tempstage
│ │ │ │ ├── AbstractTempFileWriter.java
│ │ │ │ ├── BinaryTempFileRecord.java
│ │ │ │ ├── PairedTempFileRecordComparator.java
│ │ │ │ ├── PairedTempFileWriter.java
│ │ │ │ ├── PairedTempFileWriterImpl.java
│ │ │ │ ├── SingleEndTempFileWriter.java
│ │ │ │ ├── SmartTempFileWriter.java
│ │ │ │ ├── TempFileRecordComparator.java
│ │ │ │ ├── TempRecordReader.java
│ │ │ │ ├── TempRecordReaderNio.java
│ │ │ │ ├── TempRecordWriter.java
│ │ │ │ ├── TempRecordWriterNio.java
│ │ │ │ └── UnfilteredTempFileWriter.java
│ │ │ ├── package.html
│ │ │ ├── pairedend
│ │ │ ├── AbstractHitInfo.java
│ │ │ ├── AbstractSlidingWindowCollector.java
│ │ │ ├── HitInfo.java
│ │ │ ├── InsertHelper.java
│ │ │ ├── MatedHitInfo.java
│ │ │ ├── ReadStatusListener.java
│ │ │ ├── SlidingWindowCollector.java
│ │ │ ├── UnfilteredHitInfo.java
│ │ │ ├── UnfilteredSlidingWindowCollector.java
│ │ │ └── package.html
│ │ │ ├── position
│ │ │ ├── BuildIncrementalHashLoop.java
│ │ │ ├── BuildResetHashLoop.java
│ │ │ ├── FinderPositionOutput.java
│ │ │ ├── PositionUtils.java
│ │ │ ├── PositionWriterFactory.java
│ │ │ ├── SearchIncrementalHashLoop.java
│ │ │ ├── SearchResetHashLoop.java
│ │ │ ├── output
│ │ │ │ ├── AbstractGappedRegion.java
│ │ │ │ ├── AbstractPositionOutput.java
│ │ │ │ ├── Blosum62.java
│ │ │ │ ├── Blosum62Scores.java
│ │ │ │ ├── GapBuckets.java
│ │ │ │ ├── GapBucketsInfo.java
│ │ │ │ ├── GapProbabilitiesScorer.java
│ │ │ │ ├── GapScorer.java
│ │ │ │ ├── GappedDistribution.java
│ │ │ │ ├── GappedOutput.java
│ │ │ │ ├── GappedRegion.java
│ │ │ │ ├── GappedRegionFactory.java
│ │ │ │ ├── GappedScoreLongRead.java
│ │ │ │ ├── MismatchScores.java
│ │ │ │ ├── NgsWordOutput.java
│ │ │ │ ├── Offset.java
│ │ │ │ ├── OutputFormatType.java
│ │ │ │ ├── OutputProcessorWrapper.java
│ │ │ │ ├── OutputUtils.java
│ │ │ │ ├── PositionDistributionParams.java
│ │ │ │ ├── PositionOutput.java
│ │ │ │ ├── PositionOutputParams.java
│ │ │ │ ├── PositionParams.java
│ │ │ │ ├── PositionWriter.java
│ │ │ │ ├── RawPositionWriter.java
│ │ │ │ ├── Scanner.java
│ │ │ │ ├── Segment.java
│ │ │ │ ├── SegmentCollection.java
│ │ │ │ ├── SegmentCollector.java
│ │ │ │ ├── SegmentOutput.java
│ │ │ │ ├── SegmentWriter.java
│ │ │ │ ├── SurrogateGappedRegion.java
│ │ │ │ ├── SurrogateGappedScoreLongRead.java
│ │ │ │ ├── SurrogateRegion.java
│ │ │ │ ├── Utility.java
│ │ │ │ └── WordOutput.java
│ │ │ └── package.html
│ │ │ ├── protein
│ │ │ ├── AllHitsProteinOutputProcessor.java
│ │ │ ├── GotohProteinEditDistance.java
│ │ │ ├── MapPCli.java
│ │ │ ├── MapProteinCli.java
│ │ │ ├── MapXCli.java
│ │ │ ├── MapXStatistics.java
│ │ │ ├── MapxRename.java
│ │ │ ├── ProteinAlignmentResult.java
│ │ │ ├── ProteinBitScorer.java
│ │ │ ├── ProteinOutputProcessor.java
│ │ │ ├── ProteinReadIndexer.java
│ │ │ ├── ReadLengthHashingState.java
│ │ │ ├── ScoringHelper.java
│ │ │ ├── SequenceLengthBuckets.java
│ │ │ ├── SharedProteinResources.java
│ │ │ ├── SharedStatusCollector.java
│ │ │ ├── TopEqualProteinImplementation.java
│ │ │ ├── TopEqualProteinOutputProcessor.java
│ │ │ ├── TopNProteinImplementation.java
│ │ │ └── TopNProteinOutputProcessor.java
│ │ │ ├── reader
│ │ │ ├── AsyncFastqPairWriter.java
│ │ │ ├── FastqPair.java
│ │ │ ├── FastqPairIterator.java
│ │ │ ├── PairAligner.java
│ │ │ ├── PairAlignmentProcessor.java
│ │ │ ├── PairAlignmentStats.java
│ │ │ ├── PairedEndTrimCli.java
│ │ │ ├── SamToFastq.java
│ │ │ └── SoftClip2Fastq.java
│ │ │ ├── report
│ │ │ ├── CombinedReport.java
│ │ │ ├── MapFSummaryReport.java
│ │ │ ├── MapReport.java
│ │ │ ├── MapReportTemplate.java
│ │ │ ├── MapSummaryReport.java
│ │ │ ├── MapXSummaryReport.java
│ │ │ ├── MetagenomicsReportTemplate.java
│ │ │ ├── Report.java
│ │ │ ├── ReportTemplate.java
│ │ │ ├── ReportType.java
│ │ │ ├── ReportableModule.java
│ │ │ ├── SimilarityReport.java
│ │ │ └── SpeciesReport.java
│ │ │ ├── sam
│ │ │ ├── CigarFormatter.java
│ │ │ ├── CircularBufferMultifileSinglePassReaderWindow.java
│ │ │ ├── CircularBufferMultifileSinglePassReaderWindowSync.java
│ │ │ ├── DedupifyingIterator.java
│ │ │ ├── DedupifyingRecordIterator.java
│ │ │ ├── ExtraSoftClip.java
│ │ │ ├── HomopolymerUtils.java
│ │ │ ├── MinLengthFilter.java
│ │ │ ├── MismatchPositionFormatter.java
│ │ │ ├── MultifileIterator.java
│ │ │ ├── MultifileIteratorRunner.java
│ │ │ ├── PileUp.java
│ │ │ ├── ReferenceSequenceRequiredException.java
│ │ │ ├── Sam2Bam.java
│ │ │ ├── SamIteratorTask.java
│ │ │ ├── SamMergeCli.java
│ │ │ ├── SamMerger.java
│ │ │ ├── SamReaderRecord.java
│ │ │ ├── SamRecordPopulator.java
│ │ │ ├── SamValidator.java
│ │ │ ├── SamValidatorCli.java
│ │ │ ├── SimulatedSuperCigarUnroller.java
│ │ │ ├── SortingSamReader.java
│ │ │ ├── SuperCigar.java
│ │ │ ├── SuperCigarParser.java
│ │ │ ├── SuperCigarValidator.java
│ │ │ ├── ThreadedMultifileIterator.java
│ │ │ ├── ThreadedMultifileIteratorWrapper.java
│ │ │ └── probe
│ │ │ │ ├── DeProbeCli.java
│ │ │ │ ├── NegChecker.java
│ │ │ │ ├── PosChecker.java
│ │ │ │ └── PositionAndStrandChecker.java
│ │ │ ├── scheduler
│ │ │ ├── Dependencies.java
│ │ │ ├── EventList.java
│ │ │ ├── Executor.java
│ │ │ ├── ExecutorRandom.java
│ │ │ ├── ExecutorSequential.java
│ │ │ ├── ExecutorThreaded.java
│ │ │ ├── Job.java
│ │ │ ├── JobFactory.java
│ │ │ ├── JobId.java
│ │ │ ├── JobStatistics.java
│ │ │ ├── LookAhead.java
│ │ │ ├── Result.java
│ │ │ ├── Scheduler.java
│ │ │ ├── SchedulerSynchronized.java
│ │ │ ├── Util.java
│ │ │ └── enumtime
│ │ │ │ ├── EnumTimeId.java
│ │ │ │ └── LocalOrdering.java
│ │ │ ├── segregation
│ │ │ ├── CrossOver.java
│ │ │ ├── FamilyGt.java
│ │ │ ├── GType.java
│ │ │ ├── GTypeMendelian.java
│ │ │ ├── GTypeMendelianFactory.java
│ │ │ ├── InnerAppend.java
│ │ │ ├── Labelling.java
│ │ │ ├── LinkedSet.java
│ │ │ ├── MismatchingPloidyException.java
│ │ │ ├── Pattern.java
│ │ │ ├── PatternArray.java
│ │ │ ├── PatternDiff.java
│ │ │ ├── PatternHolder.java
│ │ │ ├── RegionIterator.java
│ │ │ ├── Search.java
│ │ │ ├── SearchContainer.java
│ │ │ ├── SearchType.java
│ │ │ ├── SegregationBlock.java
│ │ │ ├── SegregationChecker.java
│ │ │ ├── SegregationCheckerCli.java
│ │ │ ├── SegregationVcfSearch.java
│ │ │ └── WhichParent.java
│ │ │ ├── similarity
│ │ │ ├── BuildSearchParams.java
│ │ │ ├── SimilarityCli.java
│ │ │ ├── SimilaritySvd.java
│ │ │ └── package.html
│ │ │ ├── simulation
│ │ │ ├── DwgsimReadNameParser.java
│ │ │ ├── MutatedOffsets.java
│ │ │ ├── MutatedReferenceReadNameParser.java
│ │ │ ├── MutatedSampleOffsets.java
│ │ │ ├── NewReadNameParser.java
│ │ │ ├── NewestReadNameParser.java
│ │ │ ├── OldReadNameParser.java
│ │ │ ├── ReadMappingRoc.java
│ │ │ ├── ReadSimEvalCli.java
│ │ │ ├── ReadSimEvalParams.java
│ │ │ ├── ReadSimEvalStatistics.java
│ │ │ ├── SimulatedReadNameParser.java
│ │ │ ├── SimulatedReadNameParserFactory.java
│ │ │ ├── SoftClipCigarParser.java
│ │ │ └── cnv
│ │ │ │ ├── CnvPriorParams.java
│ │ │ │ ├── CnvRegion.java
│ │ │ │ ├── CnvSimulator.java
│ │ │ │ └── CnvSimulatorCli.java
│ │ │ ├── taxonomy
│ │ │ ├── NcbiTaxDumpReaderCli.java
│ │ │ ├── TaxFilterCli.java
│ │ │ └── TaxStatsCli.java
│ │ │ ├── util
│ │ │ ├── BitPack2IntoLong.java
│ │ │ ├── BitPack3IntoInt.java
│ │ │ ├── BitPack3IntoLong.java
│ │ │ ├── BitPackHelperInt.java
│ │ │ ├── BitPackHelperLong.java
│ │ │ ├── BoundedDouble.java
│ │ │ ├── ComparablePair.java
│ │ │ ├── EthernetAddress.java
│ │ │ ├── FlexArray.java
│ │ │ ├── LongUtils.java
│ │ │ ├── MapSet.java
│ │ │ ├── MaxShiftFactor.java
│ │ │ ├── MaxShiftUtils.java
│ │ │ ├── NormalDistribution.java
│ │ │ ├── Populator.java
│ │ │ ├── PopulatorFactory.java
│ │ │ ├── ResultStreamHandler.java
│ │ │ ├── ReverseDouble.java
│ │ │ ├── Seedable.java
│ │ │ ├── SeparateClassLoader.java
│ │ │ ├── SingletonPopulatorFactory.java
│ │ │ ├── SizeSplit.java
│ │ │ ├── SortedMultiSet.java
│ │ │ ├── Statistics.java
│ │ │ ├── SynchronizedLinkedList.java
│ │ │ ├── ThreadAware.java
│ │ │ ├── TsvUtils.java
│ │ │ ├── memo
│ │ │ │ ├── DoubleFunction.java
│ │ │ │ ├── DoubleMemo.java
│ │ │ │ ├── Function.java
│ │ │ │ ├── IntFunction.java
│ │ │ │ ├── IntMemo.java
│ │ │ │ ├── Memo.java
│ │ │ │ └── package.html
│ │ │ ├── memory
│ │ │ │ └── package.html
│ │ │ ├── package.html
│ │ │ └── store
│ │ │ │ ├── StoreDirProxy.java
│ │ │ │ ├── StoreDirResource.java
│ │ │ │ ├── StoreDirString.java
│ │ │ │ ├── StoreDirectory.java
│ │ │ │ ├── StoreFile.java
│ │ │ │ ├── StoreFileProxy.java
│ │ │ │ ├── StoreFileResource.java
│ │ │ │ └── StoreFileString.java
│ │ │ ├── variant
│ │ │ ├── ArmMachineCyclePhredScaler.java
│ │ │ ├── BaseQualityMachineCyclePhredScaler.java
│ │ │ ├── BaseQualityPhredScaler.java
│ │ │ ├── BaseQualityReadPositionStatsProcessor.java
│ │ │ ├── CalibratedMachineErrorChooser.java
│ │ │ ├── CalibratedMachineErrorParams.java
│ │ │ ├── CalibratedPerSequenceThreshold.java
│ │ │ ├── CovariateIntersectionCycleQualityScaler.java
│ │ │ ├── CoverageThreshold.java
│ │ │ ├── DefaultMachineErrorChooser.java
│ │ │ ├── GenomeConnectivity.java
│ │ │ ├── Interpolate.java
│ │ │ ├── Interpolate2dArray.java
│ │ │ ├── InterpolateArray.java
│ │ │ ├── MachineErrorChooserInterface.java
│ │ │ ├── MapInfo.java
│ │ │ ├── NoQualityException.java
│ │ │ ├── ReadGroupMachineErrorChooser.java
│ │ │ ├── ReadParserInterface.java
│ │ │ ├── SamToMatch.java
│ │ │ ├── SamToMatchCigar.java
│ │ │ ├── SomaticParams.java
│ │ │ ├── SomaticParamsBuilder.java
│ │ │ ├── StaticThreshold.java
│ │ │ ├── ThreadingEnvironment.java
│ │ │ ├── Variant.java
│ │ │ ├── VariantAlignmentRecord.java
│ │ │ ├── VariantAlignmentRecordPopulator.java
│ │ │ ├── VariantLocus.java
│ │ │ ├── VariantOutputLevel.java
│ │ │ ├── VariantOutputOptions.java
│ │ │ ├── VariantParams.java
│ │ │ ├── VariantParamsBuilder.java
│ │ │ ├── VariantSample.java
│ │ │ ├── VariantSampleInfo.java
│ │ │ ├── avr
│ │ │ │ ├── AbstractModelBuilder.java
│ │ │ │ ├── AbstractPredictModel.java
│ │ │ │ ├── Annotation.java
│ │ │ │ ├── AnnotationDataType.java
│ │ │ │ ├── AnnotationLoader.java
│ │ │ │ ├── ArffDatasetWriter.java
│ │ │ │ ├── AttributeExtractor.java
│ │ │ │ ├── AvrStatsCli.java
│ │ │ │ ├── AvrUtils.java
│ │ │ │ ├── BooleanConverter.java
│ │ │ │ ├── BuilderCli.java
│ │ │ │ ├── Converter.java
│ │ │ │ ├── DerivedAnnotation.java
│ │ │ │ ├── DoubleConverter.java
│ │ │ │ ├── FormatAnnotation.java
│ │ │ │ ├── GtQualComplexMultiplierModel.java
│ │ │ │ ├── GtQualComplexMultiplierModelBuilder.java
│ │ │ │ ├── InfoAnnotation.java
│ │ │ │ ├── IntegerConverter.java
│ │ │ │ ├── MlAvrModelBuilder.java
│ │ │ │ ├── MlAvrPredictModel.java
│ │ │ │ ├── ModelFactory.java
│ │ │ │ ├── ModelType.java
│ │ │ │ ├── NullModel.java
│ │ │ │ ├── NullModelBuilder.java
│ │ │ │ ├── PredictCli.java
│ │ │ │ ├── QualAnnotation.java
│ │ │ │ ├── StringConverter.java
│ │ │ │ └── VcfDataset.java
│ │ │ ├── bayes
│ │ │ │ ├── AbstractAlleleBalance.java
│ │ │ │ ├── AbstractFactor.java
│ │ │ │ ├── AbstractGenotypeMeasure.java
│ │ │ │ ├── AlleleBalanceProbability.java
│ │ │ │ ├── AlleleStatistics.java
│ │ │ │ ├── AlleleStatisticsDouble.java
│ │ │ │ ├── AlleleStatisticsInt.java
│ │ │ │ ├── ArrayGenotypeMeasure.java
│ │ │ │ ├── BinaryFactor.java
│ │ │ │ ├── BinomialAlleleBalance.java
│ │ │ │ ├── Code.java
│ │ │ │ ├── CodeDiploid.java
│ │ │ │ ├── CodeHaploid.java
│ │ │ │ ├── CodePowerSet.java
│ │ │ │ ├── DefaultSortedFactor.java
│ │ │ │ ├── Description.java
│ │ │ │ ├── EntropyBinomial.java
│ │ │ │ ├── EntropyRandom.java
│ │ │ │ ├── Evidence.java
│ │ │ │ ├── EvidenceAcceptor.java
│ │ │ │ ├── EvidenceInterface.java
│ │ │ │ ├── Factor.java
│ │ │ │ ├── GenotypeMeasure.java
│ │ │ │ ├── HoeffdingAlleleBalance.java
│ │ │ │ ├── Hypotheses.java
│ │ │ │ ├── HypothesesPowerSet.java
│ │ │ │ ├── Model.java
│ │ │ │ ├── ModelFactory.java
│ │ │ │ ├── ModelInterface.java
│ │ │ │ ├── ModelNone.java
│ │ │ │ ├── NoAlleleBalance.java
│ │ │ │ ├── NoNonIdentityMeasure.java
│ │ │ │ ├── NormalizedFactor.java
│ │ │ │ ├── ReferenceBasedFactory.java
│ │ │ │ ├── SortedFactor.java
│ │ │ │ ├── Statistics.java
│ │ │ │ ├── StatisticsDouble.java
│ │ │ │ ├── StatisticsInt.java
│ │ │ │ ├── UnitFactor.java
│ │ │ │ ├── complex
│ │ │ │ │ ├── AbstractDecomposer.java
│ │ │ │ │ ├── AligningDecomposer.java
│ │ │ │ │ ├── ComplexTemplate.java
│ │ │ │ │ ├── Decomposer.java
│ │ │ │ │ ├── DenovoChecker.java
│ │ │ │ │ ├── DescriptionComplex.java
│ │ │ │ │ ├── DoNothingDecomposer.java
│ │ │ │ │ ├── EvidenceComplex.java
│ │ │ │ │ ├── HypothesesComplex.java
│ │ │ │ │ ├── IndelUtils.java
│ │ │ │ │ ├── IonTorrentCallFilter.java
│ │ │ │ │ ├── LineageDenovoChecker.java
│ │ │ │ │ ├── MatchMultiSet.java
│ │ │ │ │ ├── MaxShiftCigarParser.java
│ │ │ │ │ ├── MendelianDenovoChecker.java
│ │ │ │ │ ├── ScoreInterfaceMemo.java
│ │ │ │ │ ├── ScoreInterfaceMemoInterface.java
│ │ │ │ │ ├── ScoreInterfaceMemoIonT.java
│ │ │ │ │ ├── SimpleDecomposer.java
│ │ │ │ │ ├── SingleCounts.java
│ │ │ │ │ ├── StatisticsComplex.java
│ │ │ │ │ └── Trimmer.java
│ │ │ │ ├── doc-files
│ │ │ │ │ ├── diagrams.pptx
│ │ │ │ │ └── diagrams
│ │ │ │ │ │ ├── Slide1.jpg
│ │ │ │ │ │ ├── Slide2.jpg
│ │ │ │ │ │ ├── trimmed1.jpg
│ │ │ │ │ │ └── trimmed2.jpg
│ │ │ │ ├── multisample
│ │ │ │ │ ├── AbstractJointCallerConfiguration.java
│ │ │ │ │ ├── AbstractMultisampleCaller.java
│ │ │ │ │ ├── AbstractMultisampleCli.java
│ │ │ │ │ ├── AlignmentRecordMatcher.java
│ │ │ │ │ ├── AlleleBalanceFactor.java
│ │ │ │ │ ├── BedComplexitiesWriter.java
│ │ │ │ │ ├── ChunkInfo.java
│ │ │ │ │ ├── ComplexCaller.java
│ │ │ │ │ ├── ComplexRegion.java
│ │ │ │ │ ├── Complexities.java
│ │ │ │ │ ├── DecomposerType.java
│ │ │ │ │ ├── HaploidDiploidHypotheses.java
│ │ │ │ │ ├── HypothesisScore.java
│ │ │ │ │ ├── HypothesisScores.java
│ │ │ │ │ ├── IndividualSampleFactory.java
│ │ │ │ │ ├── IndividualSampleProcessor.java
│ │ │ │ │ ├── JointCallerConfigurator.java
│ │ │ │ │ ├── MultisampleJointCaller.java
│ │ │ │ │ ├── MultisampleJointScorer.java
│ │ │ │ │ ├── MultisampleTask.java
│ │ │ │ │ ├── MultisampleUtils.java
│ │ │ │ │ ├── OutputUtils.java
│ │ │ │ │ ├── PriorContainer.java
│ │ │ │ │ ├── RepeatAntiMeasurer.java
│ │ │ │ │ ├── RepeatMeasurer.java
│ │ │ │ │ ├── SingleNMerRepeatMeasurer.java
│ │ │ │ │ ├── Utils.java
│ │ │ │ │ ├── VariantAlleleTrigger.java
│ │ │ │ │ ├── VcfEquivalentFilter.java
│ │ │ │ │ ├── cancer
│ │ │ │ │ │ ├── AbstractSomaticCaller.java
│ │ │ │ │ │ ├── AbstractSomaticPosterior.java
│ │ │ │ │ │ ├── AlleleSomaticCaller.java
│ │ │ │ │ │ ├── AlleleSomaticPriorsFactory.java
│ │ │ │ │ │ ├── CachedDefaultSomaticPriorsFactory.java
│ │ │ │ │ │ ├── CodeCross.java
│ │ │ │ │ │ ├── ContaminatedSomaticCaller.java
│ │ │ │ │ │ ├── DefaultSomaticPriorsFactory.java
│ │ │ │ │ │ ├── HypothesesCancer.java
│ │ │ │ │ │ ├── ModelCancerAllele.java
│ │ │ │ │ │ ├── ModelCancerAlleleFactory.java
│ │ │ │ │ │ ├── ModelCancerContamination.java
│ │ │ │ │ │ ├── ModelCancerFactory.java
│ │ │ │ │ │ ├── PriorBedRangeLoader.java
│ │ │ │ │ │ ├── PureSomaticCaller.java
│ │ │ │ │ │ ├── Scorer.java
│ │ │ │ │ │ ├── SomaticCallerConfiguration.java
│ │ │ │ │ │ ├── SomaticCli.java
│ │ │ │ │ │ ├── SomaticFilter.java
│ │ │ │ │ │ ├── SomaticPosteriorAllele.java
│ │ │ │ │ │ ├── SomaticPosteriorContaminated.java
│ │ │ │ │ │ ├── SomaticPosteriorPure.java
│ │ │ │ │ │ ├── SomaticPriors.java
│ │ │ │ │ │ ├── SomaticPriorsAllele.java
│ │ │ │ │ │ ├── SomaticPriorsFactory.java
│ │ │ │ │ │ ├── SomaticRecordUtils.java
│ │ │ │ │ │ ├── SomaticStatistics.java
│ │ │ │ │ │ ├── TopScorer.java
│ │ │ │ │ │ ├── TotalScorer.java
│ │ │ │ │ │ ├── TumorOnlyCli.java
│ │ │ │ │ │ └── doc-files
│ │ │ │ │ │ │ └── makeInitialPriors.jpg
│ │ │ │ │ ├── family
│ │ │ │ │ │ ├── AbstractFamilyPosterior.java
│ │ │ │ │ │ ├── AbstractSegregationHaploid.java
│ │ │ │ │ │ ├── AlleleProbability.java
│ │ │ │ │ │ ├── AlleleProbabilityHH.java
│ │ │ │ │ │ ├── AlleleProbabilityHN.java
│ │ │ │ │ │ ├── AlleleSetProbabilityDiploid.java
│ │ │ │ │ │ ├── AlleleSetProbabilityHaploid.java
│ │ │ │ │ │ ├── BinomialSpecial.java
│ │ │ │ │ │ ├── BitSet.java
│ │ │ │ │ │ ├── DefaultWeightedLattice.java
│ │ │ │ │ │ ├── DescriptionDisease.java
│ │ │ │ │ │ ├── Disease.java
│ │ │ │ │ │ ├── DiseasedFamilyCaller.java
│ │ │ │ │ │ ├── DiseasedFamilyCallerConfiguration.java
│ │ │ │ │ │ ├── DiseasedFamilyPosterior.java
│ │ │ │ │ │ ├── FamilyCaller.java
│ │ │ │ │ │ ├── FamilyCallerConfiguration.java
│ │ │ │ │ │ ├── FamilyCli.java
│ │ │ │ │ │ ├── FamilyPosterior.java
│ │ │ │ │ │ ├── FastDiseasedFamilyPosterior.java
│ │ │ │ │ │ ├── FastFamilyPosterior.java
│ │ │ │ │ │ ├── HypothesesDisease.java
│ │ │ │ │ │ ├── ISegregationScore.java
│ │ │ │ │ │ ├── MendelianAlleleProbability.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityCombiner.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityDiploid.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityDiploidDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityFactory.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHDD.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHDDDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHDH.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHDHDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHHD.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHHDDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHHH.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityHHHDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityNHH.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityNHHDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityNHN.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityNHNDeNovo.java
│ │ │ │ │ │ ├── MendelianAlleleProbabilityNormal.java
│ │ │ │ │ │ ├── SFunction.java
│ │ │ │ │ │ ├── SegregationScore.java
│ │ │ │ │ │ ├── SegregationTrivial.java
│ │ │ │ │ │ ├── SegregationVcfAnnotator.java
│ │ │ │ │ │ ├── UniqueId.java
│ │ │ │ │ │ └── WeightedLattice.java
│ │ │ │ │ ├── forwardbackward
│ │ │ │ │ │ ├── BContainer.java
│ │ │ │ │ │ ├── CommonFormulas.java
│ │ │ │ │ │ ├── FamilyCallerFB.java
│ │ │ │ │ │ ├── FamilyPosteriorFB.java
│ │ │ │ │ │ └── MutableFactor.java
│ │ │ │ │ ├── lineage
│ │ │ │ │ │ ├── AbstractFactor.java
│ │ │ │ │ │ ├── DefaultFactor.java
│ │ │ │ │ │ ├── Factor.java
│ │ │ │ │ │ ├── ForwardBackwardLineage.java
│ │ │ │ │ │ ├── Lineage.java
│ │ │ │ │ │ ├── LineageCallerConfiguration.java
│ │ │ │ │ │ ├── LineageCli.java
│ │ │ │ │ │ ├── MendelianLineageFactor.java
│ │ │ │ │ │ ├── ModelFactor.java
│ │ │ │ │ │ ├── ToDefaultFactor.java
│ │ │ │ │ │ └── Variable.java
│ │ │ │ │ ├── multithread
│ │ │ │ │ │ ├── DependenciesMultiSample.java
│ │ │ │ │ │ ├── EventListMultiSample.java
│ │ │ │ │ │ ├── JobIdMultisample.java
│ │ │ │ │ │ ├── JobType.java
│ │ │ │ │ │ └── MultisampleStatistics.java
│ │ │ │ │ ├── package.html
│ │ │ │ │ ├── population
│ │ │ │ │ │ ├── AlleleCounts.java
│ │ │ │ │ │ ├── AlleleCountsFileReader.java
│ │ │ │ │ │ ├── DescriptionCounts.java
│ │ │ │ │ │ ├── EmAlgorithm.java
│ │ │ │ │ │ ├── EmResult.java
│ │ │ │ │ │ ├── Estimator.java
│ │ │ │ │ │ ├── HwEstimator.java
│ │ │ │ │ │ ├── NullEstimator.java
│ │ │ │ │ │ ├── NullJointScorer.java
│ │ │ │ │ │ ├── PopulationCaller.java
│ │ │ │ │ │ ├── PopulationCallerConfiguration.java
│ │ │ │ │ │ ├── PopulationCli.java
│ │ │ │ │ │ ├── PopulationHwHypothesesCreator.java
│ │ │ │ │ │ └── SiteSpecificPriors.java
│ │ │ │ │ ├── singleton
│ │ │ │ │ │ ├── SingletonCaller.java
│ │ │ │ │ │ ├── SingletonCallerConfiguration.java
│ │ │ │ │ │ └── SingletonCli.java
│ │ │ │ │ └── statistics
│ │ │ │ │ │ ├── AlleleBalanceTable.java
│ │ │ │ │ │ ├── VstatsCaller.java
│ │ │ │ │ │ ├── VstatsCallerConfiguration.java
│ │ │ │ │ │ └── VstatsCli.java
│ │ │ │ └── snp
│ │ │ │ │ ├── CachedEvidenceFactory.java
│ │ │ │ │ ├── CigarParserModel.java
│ │ │ │ │ ├── DescriptionCommon.java
│ │ │ │ │ ├── DescriptionNone.java
│ │ │ │ │ ├── DescriptionSnp.java
│ │ │ │ │ ├── EvidenceIndel.java
│ │ │ │ │ ├── EvidenceIndelFactory.java
│ │ │ │ │ ├── EvidenceMatcher.java
│ │ │ │ │ ├── EvidenceQ.java
│ │ │ │ │ ├── EvidenceQFactory.java
│ │ │ │ │ ├── HypothesesCommon.java
│ │ │ │ │ ├── HypothesesNone.java
│ │ │ │ │ ├── HypothesesPrior.java
│ │ │ │ │ ├── HypothesesSnp.java
│ │ │ │ │ ├── IndelDetector.java
│ │ │ │ │ ├── IndelDetectorFactory.java
│ │ │ │ │ ├── IndelIgnorer.java
│ │ │ │ │ ├── IndelIgnorerFactory.java
│ │ │ │ │ ├── IndelMatcher.java
│ │ │ │ │ ├── MatcherInterface.java
│ │ │ │ │ ├── ModelCommonFactory.java
│ │ │ │ │ ├── ModelNoneFactory.java
│ │ │ │ │ ├── ModelSnpFactory.java
│ │ │ │ │ ├── ReferenceBasedBuffer.java
│ │ │ │ │ ├── StatisticsSnp.java
│ │ │ │ │ └── SwitchingReferenceBasedBuffer.java
│ │ │ ├── cnv
│ │ │ │ ├── CnvCli.java
│ │ │ │ ├── CnvProductParams.java
│ │ │ │ ├── CnvProductTask.java
│ │ │ │ ├── CnvRatio.java
│ │ │ │ ├── GnuOutput.java
│ │ │ │ ├── LeastSquaresModel.java
│ │ │ │ ├── LsmOutput.java
│ │ │ │ ├── NBlockDetector.java
│ │ │ │ ├── SimpleOutput.java
│ │ │ │ ├── preprocess
│ │ │ │ │ ├── AddGc.java
│ │ │ │ │ ├── AddLength.java
│ │ │ │ │ ├── AddLog.java
│ │ │ │ │ ├── AddRatio.java
│ │ │ │ │ ├── Column.java
│ │ │ │ │ ├── DatasetProcessor.java
│ │ │ │ │ ├── GcNormalize.java
│ │ │ │ │ ├── IntColumn.java
│ │ │ │ │ ├── IntersectJoin.java
│ │ │ │ │ ├── MeanNormalize.java
│ │ │ │ │ ├── MedianNormalize.java
│ │ │ │ │ ├── NumericColumn.java
│ │ │ │ │ ├── ObjectColumn.java
│ │ │ │ │ ├── RegionColumn.java
│ │ │ │ │ ├── RegionDataset.java
│ │ │ │ │ ├── RegionPredicate.java
│ │ │ │ │ ├── SimpleJoin.java
│ │ │ │ │ ├── StringColumn.java
│ │ │ │ │ ├── UnionJoin.java
│ │ │ │ │ ├── WeightedMeanNormalize.java
│ │ │ │ │ └── WeightedMedianNormalize.java
│ │ │ │ ├── region
│ │ │ │ │ ├── AbstractCnvRegion.java
│ │ │ │ │ ├── ComplexCnvRegion.java
│ │ │ │ │ ├── EmptyRegion.java
│ │ │ │ │ ├── Region.java
│ │ │ │ │ ├── RegionUtils.java
│ │ │ │ │ └── SimpleCnvRegion.java
│ │ │ │ └── segment
│ │ │ │ │ ├── AdjacentSegments.java
│ │ │ │ │ ├── CnvPonBuildCli.java
│ │ │ │ │ ├── CnvSummaryCli.java
│ │ │ │ │ ├── CnvSummaryReport.java
│ │ │ │ │ ├── EnergySegmentScorer.java
│ │ │ │ │ ├── Segment.java
│ │ │ │ │ ├── SegmentChain.java
│ │ │ │ │ ├── SegmentCli.java
│ │ │ │ │ ├── SegmentParams.java
│ │ │ │ │ ├── SegmentScorer.java
│ │ │ │ │ ├── SegmentTask.java
│ │ │ │ │ └── SegmentVcfOutputFormatter.java
│ │ │ ├── coverage
│ │ │ │ ├── AbstractMateInfoReaderRecord.java
│ │ │ │ ├── CoverageBedWriter.java
│ │ │ │ ├── CoverageCli.java
│ │ │ │ ├── CoverageParams.java
│ │ │ │ ├── CoverageProcessor.java
│ │ │ │ ├── CoverageReaderRecord.java
│ │ │ │ ├── CoverageStatistics.java
│ │ │ │ ├── CoverageTask.java
│ │ │ │ └── CoverageTsvWriter.java
│ │ │ ├── format
│ │ │ │ ├── GenotypeLikelihoodUtils.java
│ │ │ │ ├── VariantOutputVcfFormatter.java
│ │ │ │ ├── VcfFilterField.java
│ │ │ │ ├── VcfFormatField.java
│ │ │ │ └── VcfInfoField.java
│ │ │ ├── match
│ │ │ │ ├── AlignmentMatch.java
│ │ │ │ ├── AlleleAsReadMatch.java
│ │ │ │ ├── Match.java
│ │ │ │ └── OrdinalMatchComparator.java
│ │ │ ├── package.html
│ │ │ ├── realign
│ │ │ │ ├── AbstractAlignmentEnvironment.java
│ │ │ │ ├── AbstractAllPaths.java
│ │ │ │ ├── AbstractAllPathsFastUnderflow.java
│ │ │ │ ├── AlignmentEnvironment.java
│ │ │ │ ├── AlignmentEnvironmentCG.java
│ │ │ │ ├── AlignmentEnvironmentGenome.java
│ │ │ │ ├── AlignmentEnvironmentGenomeSubstitution.java
│ │ │ │ ├── AlignmentEnvironmentRead.java
│ │ │ │ ├── AllPaths.java
│ │ │ │ ├── ByteArrayAdaptor.java
│ │ │ │ ├── Delta.java
│ │ │ │ ├── DeltaImplementation.java
│ │ │ │ ├── DeltaInterface.java
│ │ │ │ ├── DeltaSlowly.java
│ │ │ │ ├── Environment.java
│ │ │ │ ├── EnvironmentCombined.java
│ │ │ │ ├── EnvironmentDecorator.java
│ │ │ │ ├── EnvironmentHomopolymer.java
│ │ │ │ ├── EnvironmentImplementation.java
│ │ │ │ ├── EnvironmentSNP.java
│ │ │ │ ├── EnvironmentSubread.java
│ │ │ │ ├── HomoPolymerParams.java
│ │ │ │ ├── HomopolymerMatrix.java
│ │ │ │ ├── HomopolymerRepeats.java
│ │ │ │ ├── InvertCgTemplateEnvironment.java
│ │ │ │ ├── InvertedEnvironment.java
│ │ │ │ ├── RealignParams.java
│ │ │ │ ├── RealignParamsGenome.java
│ │ │ │ ├── RealignParamsImplementation.java
│ │ │ │ ├── ScoreFastUnderflow.java
│ │ │ │ ├── ScoreFastUnderflowCG.java
│ │ │ │ ├── ScoreFastUnderflowHomopolymer.java
│ │ │ │ ├── ScoreMatrix.java
│ │ │ │ ├── ScoreMatrixCG.java
│ │ │ │ ├── ScoreMatrixCGReverse.java
│ │ │ │ ├── ScoreMatrixReverse.java
│ │ │ │ └── treealign
│ │ │ │ │ ├── ReadTrie.java
│ │ │ │ │ ├── SubTrie.java
│ │ │ │ │ └── Trie.java
│ │ │ ├── sv
│ │ │ │ ├── AllCounts.java
│ │ │ │ ├── BayesianSignal.java
│ │ │ │ ├── BreakpointBayesianSignal.java
│ │ │ │ ├── Corrections.java
│ │ │ │ ├── CumulativeSamCounts.java
│ │ │ │ ├── DeleteBoundaryBayesianSignal.java
│ │ │ │ ├── Distribution.java
│ │ │ │ ├── DistributionArray.java
│ │ │ │ ├── DistributionConstant.java
│ │ │ │ ├── DistributionStep.java
│ │ │ │ ├── DistributionUtils.java
│ │ │ │ ├── DuplicateDonorBayesianSignal.java
│ │ │ │ ├── FusionFilter.java
│ │ │ │ ├── HeterozygousBayesianSignal.java
│ │ │ │ ├── NormalBayesianSignal.java
│ │ │ │ ├── NovelInsertionBayesianSignal.java
│ │ │ │ ├── ReadGroupState.java
│ │ │ │ ├── ReadGroupStats.java
│ │ │ │ ├── ReadGroupStatsCalculator.java
│ │ │ │ ├── SamArray.java
│ │ │ │ ├── SamCounts.java
│ │ │ │ ├── Signal.java
│ │ │ │ ├── SignalConstantLn.java
│ │ │ │ ├── SignalCount.java
│ │ │ │ ├── SignalDistributionLn.java
│ │ │ │ ├── SignalSum.java
│ │ │ │ ├── SvCliUtils.java
│ │ │ │ ├── SvInterestingRegionExtractor.java
│ │ │ │ ├── SvParams.java
│ │ │ │ ├── SvToolCli.java
│ │ │ │ ├── SvToolParams.java
│ │ │ │ ├── SvToolTask.java
│ │ │ │ ├── UnmatedAugmenter.java
│ │ │ │ ├── UnmatedAugmenterCli.java
│ │ │ │ ├── discord
│ │ │ │ │ ├── BedDiscordantOutputFormatter.java
│ │ │ │ │ ├── BreakpointConstraint.java
│ │ │ │ │ ├── BreakpointPosition.java
│ │ │ │ │ ├── DebugComparator.java
│ │ │ │ │ ├── DebugDiscordantOutputFormatter.java
│ │ │ │ │ ├── DiscordBedRecord.java
│ │ │ │ │ ├── DiscordantOutputFormatter.java
│ │ │ │ │ ├── DiscordantReadSet.java
│ │ │ │ │ ├── DiscordantTool.java
│ │ │ │ │ ├── DiscordantToolCli.java
│ │ │ │ │ ├── DiscordantToolParams.java
│ │ │ │ │ ├── DiscordantToolStatistics.java
│ │ │ │ │ ├── ReorderingDebugOutput.java
│ │ │ │ │ ├── SmartBedWriter.java
│ │ │ │ │ ├── VcfDiscordantOutputFormatter.java
│ │ │ │ │ ├── doc-files
│ │ │ │ │ │ ├── BreakpointDiagrams.ppt
│ │ │ │ │ │ └── BreakpointDiagrams
│ │ │ │ │ │ │ ├── Slide1.jpg
│ │ │ │ │ │ │ ├── Slide2.jpg
│ │ │ │ │ │ │ ├── Slide3.jpg
│ │ │ │ │ │ │ ├── Slide4.jpg
│ │ │ │ │ │ │ ├── Slide5.jpg
│ │ │ │ │ │ │ ├── Slide6.jpg
│ │ │ │ │ │ │ └── Slide7.jpg
│ │ │ │ │ └── pattern
│ │ │ │ │ │ ├── BreakpointPatternParams.java
│ │ │ │ │ │ ├── BreakpointStore.java
│ │ │ │ │ │ ├── DeletionOverlapFilter.java
│ │ │ │ │ │ ├── SvPatternsCli.java
│ │ │ │ │ │ ├── SvPatternsTask.java
│ │ │ │ │ │ └── VcfBreakpoint.java
│ │ │ │ └── doc-files
│ │ │ │ │ ├── SignalDiagramsHomo.ppt
│ │ │ │ │ └── notch.jpg
│ │ │ └── util
│ │ │ │ ├── CgUnroller.java
│ │ │ │ ├── SuperCigarUnroller.java
│ │ │ │ ├── VariantUtils.java
│ │ │ │ └── arithmetic
│ │ │ │ ├── LogApproximatePossibility.java
│ │ │ │ ├── LogPossibility.java
│ │ │ │ ├── PossibilityArithmetic.java
│ │ │ │ └── SimplePossibility.java
│ │ │ ├── vcf
│ │ │ └── validator
│ │ │ │ ├── NumericRuleSet.java
│ │ │ │ ├── RuleSet.java
│ │ │ │ ├── RuleValidationException.java
│ │ │ │ └── VcfValidatorCli.java
│ │ │ ├── visualization
│ │ │ ├── Aview.java
│ │ │ ├── AviewModel.java
│ │ │ ├── AviewParams.java
│ │ │ ├── AviewParamsBuilder.java
│ │ │ ├── AviewVariant.java
│ │ │ ├── CigarHelper.java
│ │ │ ├── SamAssistance.java
│ │ │ ├── SamAssistanceCg.java
│ │ │ ├── SamAssistanceCgLegacy.java
│ │ │ ├── SamAssistanceSimple.java
│ │ │ ├── SamHelper.java
│ │ │ ├── SuperCigarUnroller.java
│ │ │ ├── UnrolledRead.java
│ │ │ └── VariantHelper.java
│ │ │ └── zooma
│ │ │ ├── NativeZooma.java
│ │ │ ├── ZoomaNativeBuildIndexCli.java
│ │ │ └── ZoomaNativeMapReadsCli.java
│ └── resources
│ │ └── com
│ │ └── rtg
│ │ ├── alignment
│ │ └── penalties
│ │ │ ├── affine.properties
│ │ │ └── alignertable.properties
│ │ ├── metagenomics
│ │ └── krona
│ │ │ └── resources
│ │ │ ├── hidden.png
│ │ │ ├── krona-2.0.js
│ │ │ └── loading.gif
│ │ ├── report
│ │ └── resources
│ │ │ ├── coverage.vm
│ │ │ ├── format_summary.html
│ │ │ ├── map_report.html
│ │ │ ├── mapf_report.html
│ │ │ ├── mapx_report.html
│ │ │ ├── mapx_wrapper.html
│ │ │ ├── metagenomics_report.html
│ │ │ ├── species_report.html
│ │ │ ├── species_wrapper.html
│ │ │ ├── svd.html
│ │ │ ├── variant.vm
│ │ │ └── wol.html
│ │ └── vcf
│ │ └── validator
│ │ └── rules.properties
└── test
│ ├── java
│ └── com
│ │ └── rtg
│ │ ├── BlatantlyLeaveFileOpenTest.java
│ │ ├── CoreCommandTest.java
│ │ ├── HelpCommandTest.java
│ │ ├── LicenseCommandTest.java
│ │ ├── LicensedCommandTest.java
│ │ ├── RtgCoreTest.java
│ │ ├── alignment
│ │ ├── AbstractEditDistanceTest.java
│ │ ├── AlignerModeTest.java
│ │ ├── AlignmentResultTest.java
│ │ ├── CgGotohEditDistanceTest.java
│ │ ├── EditDistanceChainAnalyzer.java
│ │ ├── EditDistanceChainTest.java
│ │ ├── EditDistanceFactoryTest.java
│ │ ├── HopStepEditDistanceLongTest.java
│ │ ├── LoggingOnlyEditDistanceTest.java
│ │ ├── LowerBoundEditDistanceTest.java
│ │ ├── LowerBoundEstimatorTest.java
│ │ ├── NoIndelsEditDistanceTest.java
│ │ ├── ProteinActionsValidatorTest.java
│ │ ├── RcCgEditDistanceTest.java
│ │ ├── RcEditDistanceTest.java
│ │ ├── SeedPositionsTest.java
│ │ ├── SeedShifterTest.java
│ │ ├── SeedTest.java
│ │ ├── SeededAlignerTest.java
│ │ ├── SingleIndelEditDistancePropsFileTest.java
│ │ ├── SingleIndelEditDistanceTest.java
│ │ ├── SingleIndelSeededEditDistanceTest.java
│ │ ├── SoftClipperTest.java
│ │ ├── UnidirectionalAdaptorTest.java
│ │ └── UnidirectionalPrioritisedEditDistanceTest.java
│ │ ├── assembler
│ │ ├── AbstractDeBruijnGraphTest.java
│ │ ├── AbstractKmerTest.java
│ │ ├── AlignmentChainTest.java
│ │ ├── AlignmentIteratorTest.java
│ │ ├── AlignmentSectionTest.java
│ │ ├── ApplyReferenceTest.java
│ │ ├── AssembleCliTest.java
│ │ ├── AssembleParamsTest.java
│ │ ├── AssembleTaskTest.java
│ │ ├── AsyncKmerIterableTest.java
│ │ ├── AsyncReadPoolTest.java
│ │ ├── AsyncReadSourceTest.java
│ │ ├── BubbleExplorerTest.java
│ │ ├── ByteKmerTest.java
│ │ ├── ConsensusTest.java
│ │ ├── ConstraintCacheTest.java
│ │ ├── ConstraintCollectorTest.java
│ │ ├── ContigCollectorTest.java
│ │ ├── ContigConcatenatedTest.java
│ │ ├── ContigPositionTest.java
│ │ ├── CorrectReadsCliTest.java
│ │ ├── CorrectReadsTest.java
│ │ ├── CorrectingMutatorTest.java
│ │ ├── CountAssemblyEndsTest.java
│ │ ├── DeBruijnAssemblerCliTest.java
│ │ ├── DeBruijnAssemblerTaskTest.java
│ │ ├── DeBruijnGraphBuilderTest.java
│ │ ├── DeBruijnParamsTest.java
│ │ ├── ExtractPathTest.java
│ │ ├── FilterPathsTest.java
│ │ ├── GraphAlignerTest.java
│ │ ├── GraphAlignmentTest.java
│ │ ├── GraphCleanupTest.java
│ │ ├── GraphFlowAlignerTest.java
│ │ ├── GraphIndexTest.java
│ │ ├── GraphMapCliTest.java
│ │ ├── GraphMapParamsTest.java
│ │ ├── GraphMapStatisticsTest.java
│ │ ├── GraphMapTaskTest.java
│ │ ├── GraphMapTest.java
│ │ ├── GraphSorterTest.java
│ │ ├── GraphToPlotTest.java
│ │ ├── GraphTraversionsTest.java
│ │ ├── HashMapDeBruijnGraphTest.java
│ │ ├── KmerHashATest.java
│ │ ├── KmerHashTest.java
│ │ ├── KmerIterableFactoryTest.java
│ │ ├── KmerIteratorTest.java
│ │ ├── LargeKDeBruijnGraphTest.java
│ │ ├── LowKDeBruijnGraphTest.java
│ │ ├── MergeNodesTest.java
│ │ ├── NullTraversionsTest.java
│ │ ├── PacBioCliTest.java
│ │ ├── PacBioParamsTest.java
│ │ ├── PacBioPathTest.java
│ │ ├── PacBioStatisticsTest.java
│ │ ├── PacBioTest.java
│ │ ├── PairConstraintWriterTest.java
│ │ ├── PairJoinerTest.java
│ │ ├── PalindromeTrackerTest.java
│ │ ├── PartialAlignmentTest.java
│ │ ├── PathAlignerTest.java
│ │ ├── PathTrackerTest.java
│ │ ├── PreContigTest.java
│ │ ├── ReadIteratorTest.java
│ │ ├── ReadPairSource454Test.java
│ │ ├── ReadPairSourceMatePairTest.java
│ │ ├── ReadPairSourceTest.java
│ │ ├── RecoverLinksTest.java
│ │ ├── SequencesReaderIteratorTest.java
│ │ ├── StringKmerTest.java
│ │ ├── TraversionTest.java
│ │ └── graph
│ │ │ ├── ContigByteTest.java
│ │ │ ├── implementation
│ │ │ ├── ContigStringTest.java
│ │ │ ├── GraphImplementationTest.java
│ │ │ ├── GraphKmerAttributeTest.java
│ │ │ ├── IteratorLocalTest.java
│ │ │ └── PathArrayTest.java
│ │ │ └── io
│ │ │ ├── BoundedOutputStreamTest.java
│ │ │ ├── CommonIOTest.java
│ │ │ ├── GraphReaderTest.java
│ │ │ ├── GraphWriterTest.java
│ │ │ ├── StoreDirMutator.java
│ │ │ └── StoreDirMutatorTest.java
│ │ ├── blacklist
│ │ ├── BinaryMatrixTest.java
│ │ ├── HashCounterTest.java
│ │ ├── HashDistCliTest.java
│ │ ├── HashDistParamsTest.java
│ │ └── HashDistTest.java
│ │ ├── calibrate
│ │ ├── CalibratingPopulatorFactoryTest.java
│ │ ├── CalibratingSamRecordPopulatorTest.java
│ │ ├── CalibrationStatsTest.java
│ │ ├── CalibratorTest.java
│ │ ├── ChrStatsCliTest.java
│ │ ├── ChrStatsTest.java
│ │ ├── CovariateArmTest.java
│ │ ├── CovariateBaseQualityTest.java
│ │ ├── CovariateEnumTest.java
│ │ ├── CovariateMachineCycleTest.java
│ │ ├── CovariateReadGroupTest.java
│ │ ├── CovariateSequenceFixedTest.java
│ │ ├── CovariateSequenceTest.java
│ │ ├── CovariateSingleReadGroupTest.java
│ │ ├── RecalibrateCliTest.java
│ │ └── SamCalibrationInputsTest.java
│ │ ├── index
│ │ ├── AbstractBitVectorTest.java
│ │ ├── AbstractIndexTest.java
│ │ ├── BigBitVectorTest.java
│ │ ├── BitVectorTest.java
│ │ ├── BlacklistFilterMethodTest.java
│ │ ├── CountingFinderTest.java
│ │ ├── FinderTest.java
│ │ ├── FixedRepeatFrequencyFilterMethodTest.java
│ │ ├── HashBitHandleTest.java
│ │ ├── HashBitVectorTest.java
│ │ ├── HashBlacklistTest.java
│ │ ├── IndexBaseTest.java
│ │ ├── IndexCompressedExtendedTest.java
│ │ ├── IndexCompressedTest.java
│ │ ├── IndexSetTest.java
│ │ ├── IndexSimpleTest.java
│ │ ├── IndexUtilsTest.java
│ │ ├── IntSetSingleTest.java
│ │ ├── IntSetTest.java
│ │ ├── IntSetWindowTest.java
│ │ ├── ProportionalRepeatFrequencyFilterMethodTest.java
│ │ ├── ReadIndexCoverageUtilsTest.java
│ │ ├── SearchUtilsTest.java
│ │ ├── SparseFrequencyHistogramTest.java
│ │ ├── UnfilteredFilterMethodTest.java
│ │ ├── UnionRepeatFrequencyFilterMethodTest.java
│ │ ├── hash
│ │ │ ├── AbstractHashFunctionTest.java
│ │ │ ├── AbstractHashLoopTest.java
│ │ │ ├── AbstractIncrementalHashLoopTest.java
│ │ │ ├── ExactHashFunctionTest.java
│ │ │ ├── HashLoopTest.java
│ │ │ ├── InExactHashFunctionTest.java
│ │ │ ├── IncrementalHashLoopTest.java
│ │ │ ├── PrimeUtilsTest.java
│ │ │ ├── RandomizedExactHashFunctionTest.java
│ │ │ ├── ResetHashLoopTest.java
│ │ │ └── ngs
│ │ │ │ ├── FactoryUtilTest.java
│ │ │ │ ├── FakeProteinMask.java
│ │ │ │ ├── ImplementHashFunctionCloneTest.java
│ │ │ │ ├── ImplementHashFunctionTest.java
│ │ │ │ ├── IndexMock.java
│ │ │ │ ├── MemScoreTest.java
│ │ │ │ ├── NgsHashLoopImplTest.java
│ │ │ │ ├── PcrTemplateCallImplementationTest.java
│ │ │ │ ├── ProteinIncrementalHashLoopTest.java
│ │ │ │ ├── ProteinNgsHashLoopTest.java
│ │ │ │ ├── ProteinReadHashLoopTest.java
│ │ │ │ ├── ProteinTemplateHashLoopTest.java
│ │ │ │ ├── ReadCallImplementationTest.java
│ │ │ │ ├── ReadDecoderTest.java
│ │ │ │ ├── ReadEncoderTest.java
│ │ │ │ ├── TemplateCallImplementationTest.java
│ │ │ │ ├── general
│ │ │ │ ├── CombinatorTest.java
│ │ │ │ ├── ExtractAbstractTest.java
│ │ │ │ ├── ExtractReadTest.java
│ │ │ │ ├── ExtractTemplateTest.java
│ │ │ │ ├── MaskTest.java
│ │ │ │ ├── SingleMaskTest.java
│ │ │ │ ├── SkelTest.java
│ │ │ │ ├── SkeletonTest.java
│ │ │ │ └── UtilTest.java
│ │ │ │ ├── instances
│ │ │ │ ├── AbstractSplitTest.java
│ │ │ │ ├── CG2Maska11Test.java
│ │ │ │ ├── CG2Maska15Test.java
│ │ │ │ ├── CG2Maska1Test.java
│ │ │ │ ├── CG2Maskw18Test.java
│ │ │ │ ├── CG2Maskw18a1Test.java
│ │ │ │ ├── CGMaska0Test.java
│ │ │ │ ├── CGMaska15b1Test.java
│ │ │ │ ├── CGMaska15b1altTest.java
│ │ │ │ ├── CGMaska1b1Test.java
│ │ │ │ ├── CGMaska1b1altTest.java
│ │ │ │ ├── CheckMask.java
│ │ │ │ ├── DummyCG2MaskTest.java
│ │ │ │ ├── DummyCGMaskTest.java
│ │ │ │ ├── SplitL4w2s1e1.java
│ │ │ │ ├── Substitute.java
│ │ │ │ ├── SubstituteCG.java
│ │ │ │ ├── SubstituteIndel.java
│ │ │ │ ├── SubstituteIndelTest.java
│ │ │ │ ├── SubstituteProtein.java
│ │ │ │ └── SubstituteTest.java
│ │ │ │ └── protein
│ │ │ │ ├── DummyProteinExtractTest.java
│ │ │ │ ├── ProteinExtractReadTest.java
│ │ │ │ ├── ProteinExtractTemplateTest.java
│ │ │ │ └── ProteinMaskTest.java
│ │ ├── params
│ │ │ ├── CountParamsTest.java
│ │ │ ├── CreateParamsTest.java
│ │ │ └── ParamsUtilsTest.java
│ │ ├── queue
│ │ │ ├── IndexIteratorQueueTest.java
│ │ │ ├── IndexQueueTest.java
│ │ │ ├── IndexQueuesTest.java
│ │ │ └── QueueIteratorTest.java
│ │ └── similarity
│ │ │ ├── IndexSimilarityTest.java
│ │ │ ├── NeighborJoiningTest.java
│ │ │ ├── SimilarityMatrixTest.java
│ │ │ └── SimilaritySorterTest.java
│ │ ├── launcher
│ │ ├── AbstractParamsCliTest.java
│ │ ├── BuildCommonTest.java
│ │ ├── BuildParamsTest.java
│ │ ├── DefaultReaderParamsTest.java
│ │ ├── HashingRegionTest.java
│ │ ├── MockSequenceParams.java
│ │ ├── SequenceLengthMessageBuildSearchParams.java
│ │ ├── SequenceParamsTest.java
│ │ └── StreamUtil.java
│ │ ├── metagenomics
│ │ ├── AbstractSolverTest.java
│ │ ├── BisectionSolverTest.java
│ │ ├── BlockMappingTest.java
│ │ ├── CompositionMetaPipelineCliTest.java
│ │ ├── DefaultIdentifierCreatorTest.java
│ │ ├── DummySolverTest.java
│ │ ├── FragTest.java
│ │ ├── FunctionalMetaPipelineCliTest.java
│ │ ├── HashingIdentifierCreatorTest.java
│ │ ├── IdSetTest.java
│ │ ├── LLineTest.java
│ │ ├── LineTest.java
│ │ ├── LinearInterpolationSolverTest.java
│ │ ├── LoggingLineSolverTest.java
│ │ ├── MetaPipelineParamsTest.java
│ │ ├── MetagenomicsWrapperCliTest.java
│ │ ├── MetagenomicsWrapperTaskTest.java
│ │ ├── MinimizerTest.java
│ │ ├── NewtonRaphsonSolverTest.java
│ │ ├── SimpleTerminatorTest.java
│ │ ├── SpeciesCliTest.java
│ │ ├── SpeciesInfoTest.java
│ │ ├── SpeciesLineDerivTest.java
│ │ ├── SpeciesLineLinearDerivTest.java
│ │ ├── SpeciesLineLinearTest.java
│ │ ├── SpeciesLineTest.java
│ │ ├── SpeciesMapTest.java
│ │ ├── SpeciesParamsTest.java
│ │ ├── SpeciesResultTest.java
│ │ ├── SpeciesSdfSubsetTest.java
│ │ ├── SpeciesStatisticsTest.java
│ │ ├── SpeciesTest.java
│ │ ├── SubBlockResultTest.java
│ │ ├── TargetTerminatorTest.java
│ │ ├── krona
│ │ │ ├── KronaSpeciesNodeTest.java
│ │ │ └── KronaSpeciesReportWriterTest.java
│ │ ├── matrix
│ │ │ ├── MatrixSimpleTest.java
│ │ │ ├── MatrixSymmetricTest.java
│ │ │ ├── MatrixTransposeTest.java
│ │ │ ├── MatrixUtilsTest.java
│ │ │ └── VectorTest.java
│ │ └── metasnp
│ │ │ ├── AlleleStatReaderTest.java
│ │ │ ├── AlphaScoreTest.java
│ │ │ ├── AlphaSelectorTest.java
│ │ │ ├── ComplicatedBetaTest.java
│ │ │ ├── EmIterateTest.java
│ │ │ ├── FrobeniusTest.java
│ │ │ ├── MetaSnpCliTest.java
│ │ │ ├── MetaSnpLineTest.java
│ │ │ ├── ProbAlphaSimpleBetaTest.java
│ │ │ ├── RandomWalkXiFinderTest.java
│ │ │ ├── VcfMetaSnpReaderTest.java
│ │ │ └── XiScoreTest.java
│ │ ├── misc
│ │ └── JvmCrashTest.java
│ │ ├── ml
│ │ ├── AbstractBuildClassifierTest.java
│ │ ├── AttributeTest.java
│ │ ├── BaggedClassifierBuilderTest.java
│ │ ├── BinarySplitterTest.java
│ │ ├── BinaryTreeClassifierTest.java
│ │ ├── DatasetTest.java
│ │ ├── InstanceTest.java
│ │ ├── MlDataTypeTest.java
│ │ ├── MlPredictLoaderTest.java
│ │ ├── RandomTreeBuilderTest.java
│ │ ├── SimpleEvaluationTest.java
│ │ ├── TrainTestSplitTest.java
│ │ └── ZeroRBuilderTest.java
│ │ ├── mode
│ │ └── ProgramModeTest.java
│ │ ├── ngs
│ │ ├── AbstractPairedEndOutputProcessorSyncTest.java
│ │ ├── AbstractPairedEndOutputProcessorTest.java
│ │ ├── CgMapCliTest.java
│ │ ├── CgMapFlagsValidatorTest.java
│ │ ├── ClippedOutputProcessorTest.java
│ │ ├── DeduplicatingNStoreTest.java
│ │ ├── DefaultOutputProcessorSynchTest.java
│ │ ├── DefaultOutputProcessorTest.java
│ │ ├── DummyAlignmentWriterThreadTest.java
│ │ ├── DummyMapOutputProcessorTest.java
│ │ ├── DummySamResultsFilterTest.java
│ │ ├── DummySdfOutputProcessorTest.java
│ │ ├── FilterConcatIntermediateFilesTest.java
│ │ ├── LongReadMaskParamsTest.java
│ │ ├── MapCliTest.java
│ │ ├── MapFCliTest.java
│ │ ├── MapFilterPairedMapStatisticsTest.java
│ │ ├── MapFilterSingleEndMapStatisticsTest.java
│ │ ├── MapFlagsTest.java
│ │ ├── MapParamsHelperTest.java
│ │ ├── MapReportDataTest.java
│ │ ├── MapStatisticsFieldTest.java
│ │ ├── MatchResultTest.java
│ │ ├── MatedSamResultsFilterTest.java
│ │ ├── NgsCgTest.java
│ │ ├── NgsFilterParamsTest.java
│ │ ├── NgsLongTest.java
│ │ ├── NgsLongThreadsTest.java
│ │ ├── NgsMaskParamsExplicitTest.java
│ │ ├── NgsMaskParamsGeneralTest.java
│ │ ├── NgsMaskParamsProteinTest.java
│ │ ├── NgsOutputParamsTest.java
│ │ ├── NgsPairedEndTest.java
│ │ ├── NgsParamsTest.java
│ │ ├── NgsResultStreamHandlerTest.java
│ │ ├── NgsTaskFunctionalTest.java
│ │ ├── NgsTaskTest.java
│ │ ├── NgsTestUtils.java
│ │ ├── NgsThreadTest.java
│ │ ├── NullOutputProcessorTest.java
│ │ ├── OutputFilterTest.java
│ │ ├── PairedEndMapStatisticsTest.java
│ │ ├── PairedEndOutputProcessorTest.java
│ │ ├── PairedTopRandomImplementationSyncTest.java
│ │ ├── PairedTopRandomImplementationTest.java
│ │ ├── RamMapFunctionalTest.java
│ │ ├── ReadStatusTrackerSyncTest.java
│ │ ├── ReadStatusTrackerTest.java
│ │ ├── SamRenameTest.java
│ │ ├── SamResultsSansFilterTest.java
│ │ ├── SamSequenceReaderParamsTest.java
│ │ ├── SamSingleEndOutputProcessorTest.java
│ │ ├── SharedResourcesTest.java
│ │ ├── SingleEndMapStatisticsTest.java
│ │ ├── SingleEndSamResultsFilterTest.java
│ │ ├── SingleEndTopRandomImplementationSyncTest.java
│ │ ├── SingleEndTopRandomImplementationTest.java
│ │ ├── TestSamOutput.java
│ │ ├── TopNImplementationTest.java
│ │ ├── TopNPairedEndOutputProcessorSyncTest.java
│ │ ├── UnfilteredPairedEndOutputProcessorTest.java
│ │ ├── UnfilteredSingleEndOutputProcessorTest.java
│ │ ├── UnmappedSamAlignmentWriterTest.java
│ │ ├── UnmatedSamResultsFilterTest.java
│ │ ├── UptoNStoreSyncTest.java
│ │ ├── blocking
│ │ │ ├── MapQScoringReadBlockerSynchTest.java
│ │ │ ├── MapQScoringReadBlockerTest.java
│ │ │ ├── ReadBlockerSyncTest.java
│ │ │ └── ReadBlockerTest.java
│ │ ├── longread
│ │ │ └── LongReadTaskTest.java
│ │ └── tempstage
│ │ │ ├── AbstractTempRecordReadWriteTest.java
│ │ │ ├── BinaryTempFileRecordTest.java
│ │ │ ├── CgBinaryTempFileRecordTest.java
│ │ │ ├── PairedBinaryTempFileRecordTest.java
│ │ │ ├── PairedTempFileRecordComparatorTest.java
│ │ │ ├── PairedTempFileWriterImplTest.java
│ │ │ ├── SingleEndTempFileWriterTest.java
│ │ │ ├── SmartTempFileWriterTest.java
│ │ │ ├── TempFileRecordComparatorTest.java
│ │ │ ├── TempRecordNioTest.java
│ │ │ ├── TestThroughput.java
│ │ │ ├── UnfilteredBinaryTempFileRecordTest.java
│ │ │ └── UnfilteredTempFileWriterTest.java
│ │ ├── pairedend
│ │ ├── InsertHelperTest.java
│ │ ├── MatedHitInfoTest.java
│ │ ├── SlidingWindowCollectorTest.java
│ │ ├── UnfilteredHitInfoTest.java
│ │ └── UnfilteredSlidingWindowCollectorTest.java
│ │ ├── position
│ │ ├── AbstractPositionHashLoopTest.java
│ │ ├── BuildIncrementalHashLoopTest.java
│ │ ├── BuildResetHashLoopTest.java
│ │ ├── FinderPositionOutputTest.java
│ │ ├── MockIndex.java
│ │ ├── MockPositionOutput.java
│ │ ├── PositionUtilsTest.java
│ │ ├── PositionWriterFactoryTest.java
│ │ ├── SearchIncrementalHashLoopTest.java
│ │ ├── SearchResetHashLoopTest.java
│ │ └── output
│ │ │ ├── AbstractGappedRegionTest.java
│ │ │ ├── AbstractPositionWriterTest.java
│ │ │ ├── Blosum62ScoresTest.java
│ │ │ ├── Blosum62Test.java
│ │ │ ├── DummyPositionOutputTest.java
│ │ │ ├── GapBucketsInfoTest.java
│ │ │ ├── GapBucketsTest.java
│ │ │ ├── GapProbabilitiesScorerTest.java
│ │ │ ├── GappedDistributionTest.java
│ │ │ ├── GappedOutputTest.java
│ │ │ ├── GappedRegionTest.java
│ │ │ ├── MismatchScoresTest.java
│ │ │ ├── MockSegmentWriter.java
│ │ │ ├── NgsWordOutputTest.java
│ │ │ ├── OffsetTest.java
│ │ │ ├── OutputFormatTypeTest.java
│ │ │ ├── OutputUtilsTest.java
│ │ │ ├── PositionDistributionParamsTest.java
│ │ │ ├── PositionOutputParamsTest.java
│ │ │ ├── PositionOutputTest.java
│ │ │ ├── PositionParamsTest.java
│ │ │ ├── RawPositionWriterTest.java
│ │ │ ├── ScannerTest.java
│ │ │ ├── SegmentCollectionTest.java
│ │ │ ├── SegmentCollectorTest.java
│ │ │ ├── SegmentOutputTest.java
│ │ │ ├── SegmentTest.java
│ │ │ ├── SurrogateGappedRegionTest.java
│ │ │ ├── UtilityTest.java
│ │ │ └── WordOutputTest.java
│ │ ├── protein
│ │ ├── GotohProteinEditDistanceTest.java
│ │ ├── MapPCliTest.java
│ │ ├── MapXCliTest.java
│ │ ├── MapXFunctionalTest.java
│ │ ├── MapXStatisticsTest.java
│ │ ├── MapXValidatorTest.java
│ │ ├── MapxRenameTest.java
│ │ ├── ProteinAlignmentResultTest.java
│ │ ├── ProteinBitScorerTest.java
│ │ ├── ProteinOutputProcessorTest.java
│ │ ├── ProteinReadIndexerTest.java
│ │ ├── ReadLengthHashingStateTest.java
│ │ ├── ScoringHelperTest.java
│ │ ├── SequenceLengthBucketsTest.java
│ │ ├── SharedProteinResourcesTest.java
│ │ ├── SharedStatusCollectorTest.java
│ │ ├── TopEqualProteinImplementationTest.java
│ │ ├── TopEqualProteinOutputProcessorTest.java
│ │ └── TopNProteinOutputProcessorTest.java
│ │ ├── reader
│ │ ├── AsyncFastqPairWriterTest.java
│ │ ├── FastqPairIteratorTest.java
│ │ ├── FastqPairTest.java
│ │ ├── PairAlignerTest.java
│ │ ├── PairAlignmentProcessorTest.java
│ │ ├── PairAlignmentStatsTest.java
│ │ ├── PairedEndTrimCliTest.java
│ │ ├── SamToFastqTest.java
│ │ └── SoftClip2FastqTest.java
│ │ ├── report
│ │ ├── AbstractReportTest.java
│ │ ├── CombinedReportTest.java
│ │ ├── MapFSummaryReportTest.java
│ │ ├── MapReportTemplateTest.java
│ │ ├── MapReportTest.java
│ │ ├── MapXSummaryReportTest.java
│ │ ├── MetagenomicsReportTemplateTest.java
│ │ ├── ReportTemplateTest.java
│ │ ├── ReportTypeTest.java
│ │ ├── ReportableModuleTest.java
│ │ ├── SimilarityReportTest.java
│ │ └── SpeciesReportTest.java
│ │ ├── sam
│ │ ├── CigarFormatterTest.java
│ │ ├── CigarSubsequenceTest.java
│ │ ├── CircularBufferMultifileSinglePassReaderWindowSyncTest.java
│ │ ├── CircularBufferMultifileSinglePassReaderWindowTest.java
│ │ ├── DedupifyingIteratorTest.java
│ │ ├── DedupifyingRecordIteratorTest.java
│ │ ├── ExtraSoftClipTest.java
│ │ ├── HomopolymerUtilsTest.java
│ │ ├── MinLengthFilterTest.java
│ │ ├── MismatchPositionFormatterTest.java
│ │ ├── MultifileIteratorTest.java
│ │ ├── PileUpTest.java
│ │ ├── RandomArrayList.java
│ │ ├── RandomArrayListTest.java
│ │ ├── Sam2BamTest.java
│ │ ├── SamExceptionChecker.java
│ │ ├── SamIteratorTaskTest.java
│ │ ├── SamMergeCliTest.java
│ │ ├── SamPicardTest.java
│ │ ├── SamReaderRecordTest.java
│ │ ├── SamRecordPopulatorTest.java
│ │ ├── SamValidatorCliTest.java
│ │ ├── SamValidatorTest.java
│ │ ├── SimulatedSuperCigarUnrollerTest.java
│ │ ├── SortingSamReaderTest.java
│ │ ├── SuperCigarParserTest.java
│ │ ├── SuperCigarTest.java
│ │ ├── SuperCigarValidatorTest.java
│ │ ├── ThreadedMultifileIteratorTest.java
│ │ ├── ThreadedMultifileIteratorWrapperTest.java
│ │ └── probe
│ │ │ ├── DeProbeCliTest.java
│ │ │ ├── NegCheckerTest.java
│ │ │ ├── PosCheckerTest.java
│ │ │ └── PositionAndStrandCheckerTest.java
│ │ ├── scheduler
│ │ ├── AbstractDependenciesTest.java
│ │ ├── ExecutorRandomTest.java
│ │ ├── ExecutorSequentialTest.java
│ │ ├── ExecutorThreadedTest.java
│ │ ├── JobTest.java
│ │ ├── LookAheadTest.java
│ │ ├── ResultTest.java
│ │ ├── SchedulerSynchronizedTest.java
│ │ ├── UtilTest.java
│ │ ├── enumtime
│ │ │ ├── EnumTimeIdTest.java
│ │ │ └── LocalOrderingTest.java
│ │ └── example
│ │ │ ├── DependenciesExample.java
│ │ │ ├── DependenciesExampleTest.java
│ │ │ ├── ExampleJobId.java
│ │ │ ├── JobFactoryExample.java
│ │ │ ├── JobFactoryExampleTest.java
│ │ │ ├── JobType.java
│ │ │ ├── JobTypeTest.java
│ │ │ ├── MockJob.java
│ │ │ └── MockResult.java
│ │ ├── segregation
│ │ ├── CrossOverTest.java
│ │ ├── FamilyGtTest.java
│ │ ├── GTypeMendelianFactoryTest.java
│ │ ├── GTypeTest.java
│ │ ├── InnerAppendTest.java
│ │ ├── LabellingTest.java
│ │ ├── LinkedSetTest.java
│ │ ├── MismatchingPloidyExceptionTest.java
│ │ ├── PatternArrayTest.java
│ │ ├── PatternDiffTest.java
│ │ ├── PatternHolderTest.java
│ │ ├── PatternTest.java
│ │ ├── SearchContainerTest.java
│ │ ├── SearchTypeTest.java
│ │ ├── SegregationBlockTest.java
│ │ ├── SegregationCheckerCliTest.java
│ │ ├── SegregationVcfSearchTest.java
│ │ └── WhichParentTest.java
│ │ ├── similarity
│ │ ├── BuildSearchParamsTest.java
│ │ ├── SimilarityCliTest.java
│ │ ├── SimilarityFlagsValidatorTest.java
│ │ └── SimilaritySvdTest.java
│ │ ├── simulation
│ │ ├── AbstractSimulatedReadNameParserTest.java
│ │ ├── CnvFileChecker.java
│ │ ├── DwgsimReadNameParserTest.java
│ │ ├── MutatedOffsetsTest.java
│ │ ├── MutatedReferenceReadNameParserTest.java
│ │ ├── NewReadNameParserTest.java
│ │ ├── NewestReadNameParserTest.java
│ │ ├── OldReadNameParserTest.java
│ │ ├── ReadMappingRocTest.java
│ │ ├── ReadSimEvalCliTest.java
│ │ ├── ReadSimEvalParamsTest.java
│ │ ├── ReadSimEvalStatisticsTest.java
│ │ ├── SimulatedReadNameParserFactoryTest.java
│ │ ├── SoftClipCigarParserTest.java
│ │ └── cnv
│ │ │ ├── CnvPriorParamsTest.java
│ │ │ ├── CnvRegionTest.java
│ │ │ ├── CnvSimulatorCliTest.java
│ │ │ └── CnvSimulatorTest.java
│ │ ├── taxonomy
│ │ ├── NcbiTaxDumpReaderCliTest.java
│ │ ├── TaxFilterCliTest.java
│ │ └── TaxStatsCliTest.java
│ │ ├── util
│ │ ├── BitPack2IntoLongTest.java
│ │ ├── BitPack3IntoIntTest.java
│ │ ├── BitPack3IntoLongTest.java
│ │ ├── BitPackHelperIntTest.java
│ │ ├── BitPackHelperLongTest.java
│ │ ├── BoundedDoubleTest.java
│ │ ├── ComparablePairTest.java
│ │ ├── EthernetAddressTest.java
│ │ ├── FlexArrayTest.java
│ │ ├── LongUtilsTest.java
│ │ ├── MapSetTest.java
│ │ ├── MaxShiftFactorTest.java
│ │ ├── MaxShiftUtilsTest.java
│ │ ├── MockAppendable.java
│ │ ├── NormalDistributionTest.java
│ │ ├── ResultStreamHandlerTest.java
│ │ ├── ReverseDoubleTest.java
│ │ ├── SeparateClassLoaderTest.java
│ │ ├── SingletonPopulatorFactoryTest.java
│ │ ├── SizeSplitTest.java
│ │ ├── SortedMultiSetTest.java
│ │ ├── StatisticsTest.java
│ │ ├── SynchronizedLinkedListTest.java
│ │ ├── TsvUtilsTest.java
│ │ ├── array
│ │ │ ├── ArrayTiming.java
│ │ │ ├── NativeArrayTiming.java
│ │ │ ├── bitindex
│ │ │ │ └── BitIndexRegression.java
│ │ │ ├── byteindex
│ │ │ │ ├── ByteChunksRegression.java
│ │ │ │ └── SmallChunksTest.java
│ │ │ ├── intindex
│ │ │ │ ├── IntChunksRegression.java
│ │ │ │ └── SmallChunksTest.java
│ │ │ └── packedindex
│ │ │ │ └── PackedIndexRegression.java
│ │ ├── memo
│ │ │ ├── DoubleMemoTest.java
│ │ │ ├── IntMemoTest.java
│ │ │ └── MemoTest.java
│ │ ├── store
│ │ │ ├── AbstractStoreDirTest.java
│ │ │ ├── AbstractStoreTest.java
│ │ │ ├── StoreDirProxyTest.java
│ │ │ ├── StoreDirResourceTest.java
│ │ │ ├── StoreDirStringTest.java
│ │ │ ├── StoreFileProxyTest.java
│ │ │ ├── StoreFileResourceTest.java
│ │ │ └── StoreFileStringTest.java
│ │ └── test
│ │ │ └── params
│ │ │ └── AllTestParamsSuite.java
│ │ ├── variant
│ │ ├── AlleleCountsFileConverter.java
│ │ ├── ArmMachineCyclePhredScalerTest.java
│ │ ├── BaseQualityMachineCyclePhredScalerTest.java
│ │ ├── BaseQualityPhredScalerTest.java
│ │ ├── CalibratedMachineErrorChooserTest.java
│ │ ├── CalibratedMachineErrorParamsTest.java
│ │ ├── CalibratedPerSequenceThresholdTest.java
│ │ ├── CovariateIntersectionCycleQualityScalerTest.java
│ │ ├── DefaultMachineErrorChooserTest.java
│ │ ├── GenomeConnectivityTest.java
│ │ ├── Interpolate2dArrayTest.java
│ │ ├── InterpolateArrayTest.java
│ │ ├── NoQualityExceptionTest.java
│ │ ├── ReadGroupMachineErrorChooserTest.java
│ │ ├── SamToMatchCigarTest.java
│ │ ├── SomaticParamsTest.java
│ │ ├── StaticThresholdTest.java
│ │ ├── ThreadingEnvironmentTest.java
│ │ ├── VariantAlignmentRecordPopulatorTest.java
│ │ ├── VariantAlignmentRecordTest.java
│ │ ├── VariantLocusTest.java
│ │ ├── VariantNanoTest.java
│ │ ├── VariantOutputLevelTest.java
│ │ ├── VariantParamsTest.java
│ │ ├── VariantSampleInfoTest.java
│ │ ├── VariantSampleTest.java
│ │ ├── VariantTest.java
│ │ ├── VariantTestUtils.java
│ │ ├── avr
│ │ │ ├── AbstractModelBuilderTest.java
│ │ │ ├── AbstractPredictModelTest.java
│ │ │ ├── AnnotationDataTypeTest.java
│ │ │ ├── AnnotationLoaderTest.java
│ │ │ ├── ArffDatasetWriterTest.java
│ │ │ ├── AttributeExtractorTest.java
│ │ │ ├── AvrStatsCliTest.java
│ │ │ ├── AvrUtilsTest.java
│ │ │ ├── BooleanConverterTest.java
│ │ │ ├── BuilderCliTest.java
│ │ │ ├── DerivedAnnotationTest.java
│ │ │ ├── DoubleConverterTest.java
│ │ │ ├── DummyModelBuilderTest.java
│ │ │ ├── DummyPredictModelTest.java
│ │ │ ├── FormatAnnotationTest.java
│ │ │ ├── GtQualComplexMultiplierModelBuilderTest.java
│ │ │ ├── GtQualComplexMultiplierModelTest.java
│ │ │ ├── InfoAnnotationTest.java
│ │ │ ├── IntegerConverterTest.java
│ │ │ ├── MlAvrModelBuilderTest.java
│ │ │ ├── MlAvrPredictModelTest.java
│ │ │ ├── ModelFactoryTest.java
│ │ │ ├── ModelTypeTest.java
│ │ │ ├── NullModelBuilderTest.java
│ │ │ ├── NullModelTest.java
│ │ │ ├── PredictCliTest.java
│ │ │ ├── QualAnnotationTest.java
│ │ │ ├── StringConverterTest.java
│ │ │ └── VcfDatasetTest.java
│ │ ├── bayes
│ │ │ ├── AbstractAlleleBalanceTest.java
│ │ │ ├── AbstractAlleleStatisticsTest.java
│ │ │ ├── AbstractStatisticsTest.java
│ │ │ ├── AlleleStatisticsDoubleTest.java
│ │ │ ├── AlleleStatisticsIntTest.java
│ │ │ ├── ArrayGenotypeMeasureTest.java
│ │ │ ├── BinaryFactorTest.java
│ │ │ ├── BinomialAlleleBalanceTest.java
│ │ │ ├── CodeDiploidTest.java
│ │ │ ├── CodeHaploidTest.java
│ │ │ ├── CodePowerSetTest.java
│ │ │ ├── DefaultSortedFactorTest.java
│ │ │ ├── EntropyBinomialTest.java
│ │ │ ├── EntropyRandomTest.java
│ │ │ ├── EvidenceTest.java
│ │ │ ├── HoeffdingAlleleBalanceTest.java
│ │ │ ├── HypothesesPowerSetTest.java
│ │ │ ├── HypothesesTest.java
│ │ │ ├── MockEvidence.java
│ │ │ ├── MockGenotypeMeasure.java
│ │ │ ├── MockHypotheses.java
│ │ │ ├── MockModel.java
│ │ │ ├── ModelNoneTest.java
│ │ │ ├── ModelTest.java
│ │ │ ├── NoAlleleBalanceTest.java
│ │ │ ├── NoNonIdentityMeasureTest.java
│ │ │ ├── NormalizedFactorTest.java
│ │ │ ├── StatisticsDoubleTest.java
│ │ │ ├── StatisticsIntTest.java
│ │ │ ├── UnitFactorTest.java
│ │ │ ├── complex
│ │ │ │ ├── AbstractDecomposerTest.java
│ │ │ │ ├── AligningDecomposerTest.java
│ │ │ │ ├── ComplexTemplateTest.java
│ │ │ │ ├── DescriptionComplexTest.java
│ │ │ │ ├── DoNothingDecomposerTest.java
│ │ │ │ ├── DummyDecomposerTest.java
│ │ │ │ ├── EvidenceComplexTest.java
│ │ │ │ ├── HypothesesComplexTest.java
│ │ │ │ ├── IndelUtilsTest.java
│ │ │ │ ├── IonTorrentCallFilterTest.java
│ │ │ │ ├── LineageDenovoCheckerTest.java
│ │ │ │ ├── MatchMultiSetTest.java
│ │ │ │ ├── MaxShiftCigarParserTest.java
│ │ │ │ ├── MendelianDenovoCheckerTest.java
│ │ │ │ ├── ScoreInterfaceMemoIonTTest.java
│ │ │ │ ├── ScoreInterfaceMemoTest.java
│ │ │ │ ├── SimpleDecomposerTest.java
│ │ │ │ ├── SingleCountsTest.java
│ │ │ │ ├── StatisticsComplexTest.java
│ │ │ │ └── TrimmerTest.java
│ │ │ ├── multisample
│ │ │ │ ├── AbstractCallerCliTest.java
│ │ │ │ ├── AlignmentRecordMatcherTest.java
│ │ │ │ ├── AlleleBalanceFactorTest.java
│ │ │ │ ├── BedComplexitiesWriterTest.java
│ │ │ │ ├── ChunkInfoTest.java
│ │ │ │ ├── ComplexCallerTest.java
│ │ │ │ ├── ComplexRegionTest.java
│ │ │ │ ├── ComplexitiesTest.java
│ │ │ │ ├── DecomposerTypeTest.java
│ │ │ │ ├── HaploidDiploidHypothesesTest.java
│ │ │ │ ├── HypothesisScoreTest.java
│ │ │ │ ├── HypothesisScoresTest.java
│ │ │ │ ├── IndividualSampleFactoryTest.java
│ │ │ │ ├── IndividualSampleProcessorTest.java
│ │ │ │ ├── MultisampleTaskSequentialTest.java
│ │ │ │ ├── MultisampleTaskT1Test.java
│ │ │ │ ├── MultisampleTaskT4Test.java
│ │ │ │ ├── MultisampleTaskTest.java
│ │ │ │ ├── MultisampleUtilsTest.java
│ │ │ │ ├── OutputUtilsTest.java
│ │ │ │ ├── PriorContainerTest.java
│ │ │ │ ├── RepeatAntiMeasurerTest.java
│ │ │ │ ├── SingleNMerRepeatMeasurerTest.java
│ │ │ │ ├── TestUtils.java
│ │ │ │ ├── UtilsTest.java
│ │ │ │ ├── VariantAlleleTriggerTest.java
│ │ │ │ ├── VcfEquivalentFilterTest.java
│ │ │ │ ├── cancer
│ │ │ │ │ ├── AbstractSomaticCallerTest.java
│ │ │ │ │ ├── AlleleSomaticCallerTest.java
│ │ │ │ │ ├── AlleleSomaticPriorsFactoryTest.java
│ │ │ │ │ ├── CachedDefaultSomaticPriorsFactoryTest.java
│ │ │ │ │ ├── CancerConvergenceTest.java
│ │ │ │ │ ├── CodeCrossTest.java
│ │ │ │ │ ├── ContaminatedSomaticCallerTest.java
│ │ │ │ │ ├── DefaultSomaticPriorsFactoryTest.java
│ │ │ │ │ ├── EvidenceWrapper.java
│ │ │ │ │ ├── HypothesesCancerTest.java
│ │ │ │ │ ├── ModelCancerAlleleFactoryTest.java
│ │ │ │ │ ├── ModelCancerAlleleTest.java
│ │ │ │ │ ├── ModelCancerContaminationTest.java
│ │ │ │ │ ├── ModelCancerFactoryTest.java
│ │ │ │ │ ├── ModelIncrementer.java
│ │ │ │ │ ├── PriorBedRangeLoaderTest.java
│ │ │ │ │ ├── PureSomaticCallerTest.java
│ │ │ │ │ ├── SomaticCallerConfigurationTest.java
│ │ │ │ │ ├── SomaticCliTest.java
│ │ │ │ │ ├── SomaticFilterTest.java
│ │ │ │ │ ├── SomaticNanoTest.java
│ │ │ │ │ ├── SomaticPosteriorAlleleTest.java
│ │ │ │ │ ├── SomaticPosteriorContaminatedTest.java
│ │ │ │ │ ├── SomaticPosteriorPureTest.java
│ │ │ │ │ ├── SomaticPriorsAlleleTest.java
│ │ │ │ │ ├── SomaticPriorsTest.java
│ │ │ │ │ ├── SomaticRecordUtilsTest.java
│ │ │ │ │ ├── SomaticStatisticsTest.java
│ │ │ │ │ ├── TopScorerTest.java
│ │ │ │ │ ├── TotalScorerTest.java
│ │ │ │ │ └── TumorOnlyCliTest.java
│ │ │ │ ├── family
│ │ │ │ │ ├── AbstractFamilyPosteriorTest.java
│ │ │ │ │ ├── AlleleProbabilityHHTest.java
│ │ │ │ │ ├── AlleleProbabilityHNTest.java
│ │ │ │ │ ├── AlleleSetProbabilityDiploidTest.java
│ │ │ │ │ ├── AlleleSetProbabilityHaploidTest.java
│ │ │ │ │ ├── BinomialSpecialTest.java
│ │ │ │ │ ├── BitSetTest.java
│ │ │ │ │ ├── DefaultWeightedLatticeTest.java
│ │ │ │ │ ├── DescriptionDiseaseTest.java
│ │ │ │ │ ├── DiseaseTest.java
│ │ │ │ │ ├── DiseasedFamilyCallerConfigurationTest.java
│ │ │ │ │ ├── DiseasedFamilyCallerTest.java
│ │ │ │ │ ├── DiseasedFamilyPosteriorTest.java
│ │ │ │ │ ├── DummySegregationHaploidTest.java
│ │ │ │ │ ├── FamilyCallerConfigurationTest.java
│ │ │ │ │ ├── FamilyCallerTest.java
│ │ │ │ │ ├── FamilyCliTest.java
│ │ │ │ │ ├── FamilyNanoTest.java
│ │ │ │ │ ├── FamilyPosteriorTest.java
│ │ │ │ │ ├── FastDiseasedFamilyPosteriorTest.java
│ │ │ │ │ ├── FastFamilyPosteriorTest.java
│ │ │ │ │ ├── HypothesesDiseaseTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityCombinerTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityDiploidDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityDiploidTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHDDDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHDDTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHDHDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHDHTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHHDDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHHDTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHHHDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityHHHTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityNHHDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityNHHTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityNHNDeNovoTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityNHNTest.java
│ │ │ │ │ ├── MendelianAlleleProbabilityNormalTest.java
│ │ │ │ │ ├── SFunctionTest.java
│ │ │ │ │ ├── SegregationScoreTest.java
│ │ │ │ │ ├── SegregationTrivialTest.java
│ │ │ │ │ ├── SegregationVcfAnnotatorTest.java
│ │ │ │ │ └── UniqueIdTest.java
│ │ │ │ ├── forwardbackward
│ │ │ │ │ ├── BContainerTest.java
│ │ │ │ │ ├── CommonFormulasTest.java
│ │ │ │ │ ├── FamilyCallerFBTest.java
│ │ │ │ │ ├── FamilyPosteriorFBTest.java
│ │ │ │ │ └── MutableFactorTest.java
│ │ │ │ ├── lineage
│ │ │ │ │ ├── DefaultFactorTest.java
│ │ │ │ │ ├── ForwardBackwardLineageTest.java
│ │ │ │ │ ├── LineageCallerConfigurationTest.java
│ │ │ │ │ ├── LineageCliTest.java
│ │ │ │ │ ├── LineageTest.java
│ │ │ │ │ ├── MendelianLineageFactorTest.java
│ │ │ │ │ ├── ModelFactorTest.java
│ │ │ │ │ └── VariableTest.java
│ │ │ │ ├── multithread
│ │ │ │ │ ├── DependenciesMultiSampleTest.java
│ │ │ │ │ ├── EventListMultiSampleTest.java
│ │ │ │ │ ├── JobIdMultisampleTest.java
│ │ │ │ │ ├── JobTypeTest.java
│ │ │ │ │ └── MultisampleStatisticsTest.java
│ │ │ │ ├── population
│ │ │ │ │ ├── AbstractEstimatorTest.java
│ │ │ │ │ ├── AlleleCountsFileReaderTest.java
│ │ │ │ │ ├── AlleleCountsTest.java
│ │ │ │ │ ├── ChrType.java
│ │ │ │ │ ├── Convergence.java
│ │ │ │ │ ├── ConvergencePlot.java
│ │ │ │ │ ├── ConvergencePlotTest.java
│ │ │ │ │ ├── ConvergenceTest.java
│ │ │ │ │ ├── ConvergenceXY.java
│ │ │ │ │ ├── ConvergenceXYZ.java
│ │ │ │ │ ├── ConvergenceYZ.java
│ │ │ │ │ ├── DescriptionCountsTest.java
│ │ │ │ │ ├── EmAlgorithmTest.java
│ │ │ │ │ ├── EmResultTest.java
│ │ │ │ │ ├── HwEstimatorTest.java
│ │ │ │ │ ├── NullEstimatorTest.java
│ │ │ │ │ ├── PopulationCallerConfigurationTest.java
│ │ │ │ │ ├── PopulationCallerTest.java
│ │ │ │ │ ├── PopulationCliTest.java
│ │ │ │ │ ├── PopulationHwHypothesesCreatorTest.java
│ │ │ │ │ └── PopulationNanoTest.java
│ │ │ │ ├── singleton
│ │ │ │ │ ├── SingletonCallerConfigurationTest.java
│ │ │ │ │ ├── SingletonCallerTest.java
│ │ │ │ │ ├── SingletonCliTest.java
│ │ │ │ │ └── SingletonValidatorTest.java
│ │ │ │ └── statistics
│ │ │ │ │ ├── AlleleBalanceTableTest.java
│ │ │ │ │ ├── VstatsCallerConfigurationTest.java
│ │ │ │ │ ├── VstatsCallerTest.java
│ │ │ │ │ └── VstatsCliTest.java
│ │ │ └── snp
│ │ │ │ ├── CigarParserModelTest.java
│ │ │ │ ├── DescriptionCommonTest.java
│ │ │ │ ├── DescriptionNoneTest.java
│ │ │ │ ├── DescriptionSnpTest.java
│ │ │ │ ├── EvidenceIndelFactoryTest.java
│ │ │ │ ├── EvidenceIndelTest.java
│ │ │ │ ├── EvidenceMatcherTest.java
│ │ │ │ ├── EvidenceQFactoryTest.java
│ │ │ │ ├── EvidenceQTest.java
│ │ │ │ ├── HypothesesMock.java
│ │ │ │ ├── HypothesesNoneTest.java
│ │ │ │ ├── HypothesesPriorTest.java
│ │ │ │ ├── HypothesesSnpTest.java
│ │ │ │ ├── IndelDetectorFactoryTest.java
│ │ │ │ ├── IndelDetectorTest.java
│ │ │ │ ├── IndelIgnorerFactoryTest.java
│ │ │ │ ├── IndelIgnorerTest.java
│ │ │ │ ├── IndelMatcherTest.java
│ │ │ │ ├── ModelNoneFactoryTest.java
│ │ │ │ ├── ModelSnpFactoryTest.java
│ │ │ │ ├── ReferenceBasedBufferTest.java
│ │ │ │ ├── StatisticsSnpTest.java
│ │ │ │ └── SwitchingReferenceBasedBufferTest.java
│ │ ├── cnv
│ │ │ ├── CnvCliTest.java
│ │ │ ├── CnvProductParamsTest.java
│ │ │ ├── CnvProductTaskTest.java
│ │ │ ├── CnvRatioTest.java
│ │ │ ├── GnuOutputTest.java
│ │ │ ├── LeastSquaresModelTest.java
│ │ │ ├── NBlockDetectorTest.java
│ │ │ ├── SimpleOutputTest.java
│ │ │ ├── preprocess
│ │ │ │ ├── AddGcTest.java
│ │ │ │ ├── AddLengthTest.java
│ │ │ │ ├── AddLogTest.java
│ │ │ │ ├── AddRatioTest.java
│ │ │ │ ├── GcNormalizeTest.java
│ │ │ │ ├── IntColumnTest.java
│ │ │ │ ├── IntersectJoinTest.java
│ │ │ │ ├── MeanNormalizeTest.java
│ │ │ │ ├── MedianNormalizeTest.java
│ │ │ │ ├── RegionColumnTest.java
│ │ │ │ ├── RegionDatasetTest.java
│ │ │ │ ├── SimpleJoinTest.java
│ │ │ │ ├── StringColumnTest.java
│ │ │ │ ├── UnionJoinTest.java
│ │ │ │ ├── WeightedMeanNormalizeTest.java
│ │ │ │ └── WeightedMedianNormalizeTest.java
│ │ │ ├── region
│ │ │ │ ├── ComplexCnvRegionTest.java
│ │ │ │ ├── DummyCnvRegionTest.java
│ │ │ │ ├── EmptyRegionTest.java
│ │ │ │ ├── RegionUtilsTest.java
│ │ │ │ └── SimpleCnvRegionTest.java
│ │ │ └── segment
│ │ │ │ ├── AdjacentSegmentsTest.java
│ │ │ │ ├── CnvPonBuildCliTest.java
│ │ │ │ ├── CnvSummaryCliTest.java
│ │ │ │ ├── CnvSummaryReportTest.java
│ │ │ │ ├── EnergySegmentScorerTest.java
│ │ │ │ ├── SegmentChainTest.java
│ │ │ │ ├── SegmentCliTest.java
│ │ │ │ ├── SegmentParamsTest.java
│ │ │ │ ├── SegmentTest.java
│ │ │ │ └── SegmentVcfOutputFormatterTest.java
│ │ ├── coverage
│ │ │ ├── CoverageBedWriterTest.java
│ │ │ ├── CoverageCliTest.java
│ │ │ ├── CoverageParamsTest.java
│ │ │ ├── CoverageReaderRecordTest.java
│ │ │ ├── CoverageStatisticsTest.java
│ │ │ ├── CoverageTaskTest.java
│ │ │ ├── CoverageTsvWriterTest.java
│ │ │ └── DummyMateInfoReaderRecordTest.java
│ │ ├── format
│ │ │ ├── GenotypeLikelihoodUtilsTest.java
│ │ │ ├── VariantOutputVcfFormatterTest.java
│ │ │ ├── VcfFilterFieldTest.java
│ │ │ ├── VcfFormatFieldTest.java
│ │ │ └── VcfInfoFieldTest.java
│ │ ├── match
│ │ │ ├── AlignmentMatchTest.java
│ │ │ ├── AlleleAsReadMatchTest.java
│ │ │ ├── MatchTest.java
│ │ │ └── OrdinalMatchComparatorTest.java
│ │ ├── realign
│ │ │ ├── AbstractRealignTest.java
│ │ │ ├── AbstractScoreMatrixCGReverseTest.java
│ │ │ ├── AbstractScoreMatrixCGTest.java
│ │ │ ├── AbstractScoreMatrixReverseTest.java
│ │ │ ├── AlignmentEnvironmentCGTest.java
│ │ │ ├── AlignmentEnvironmentGenomeSubstitutionTest.java
│ │ │ ├── AlignmentEnvironmentGenomeTest.java
│ │ │ ├── AlignmentEnvironmentReadTest.java
│ │ │ ├── ByteArrayAdaptorTest.java
│ │ │ ├── CgRealignTest.java
│ │ │ ├── DeltaImplementationSimpleTest.java
│ │ │ ├── DeltaImplementationTest.java
│ │ │ ├── DeltaSlowlyTest.java
│ │ │ ├── EnvironmentCombinedTest.java
│ │ │ ├── EnvironmentDecoratorTest.java
│ │ │ ├── EnvironmentHomopolymerTest.java
│ │ │ ├── EnvironmentImplementationTest.java
│ │ │ ├── EnvironmentSNPTest.java
│ │ │ ├── EnvironmentSubreadTest.java
│ │ │ ├── HomoPolymerParamsTest.java
│ │ │ ├── HomopolymerMatrixTest.java
│ │ │ ├── HomopolymerRepeatsTest.java
│ │ │ ├── InvertCgTemplateEnvironmentTest.java
│ │ │ ├── InvertedEnvironmentTest.java
│ │ │ ├── ProbabilityArray.java
│ │ │ ├── RealignParamsGenomeTest.java
│ │ │ ├── RealignParamsImplementationTest.java
│ │ │ ├── ScoreFastUnderflowCGTest.java
│ │ │ ├── ScoreFastUnderflowHomopolymerTest.java
│ │ │ ├── ScoreFastUnderflowTest.java
│ │ │ ├── ScoreMatrixCGReverseTestSuite.java
│ │ │ ├── ScoreMatrixCGTestSuite.java
│ │ │ ├── ScoreMatrixReverseTestSuite.java
│ │ │ ├── ScoreMatrixTest.java
│ │ │ └── treealign
│ │ │ │ ├── ReadTrieTest.java
│ │ │ │ ├── SubTrieTest.java
│ │ │ │ └── TrieTest.java
│ │ ├── sv
│ │ │ ├── AbstractBayesianSignalTest.java
│ │ │ ├── AbstractSamCountsTest.java
│ │ │ ├── AllCountsTest.java
│ │ │ ├── BayesianSignalTest.java
│ │ │ ├── BreakpointBayesianSignalTest.java
│ │ │ ├── CorrectionsTest.java
│ │ │ ├── CumulativeSamCountsTest.java
│ │ │ ├── DeleteBoundaryBayesianSignalTest.java
│ │ │ ├── DistributionArrayTest.java
│ │ │ ├── DistributionConstantTest.java
│ │ │ ├── DistributionStepTest.java
│ │ │ ├── DistributionTestUtils.java
│ │ │ ├── DistributionUtilsTest.java
│ │ │ ├── DuplicateDonorBayesianSignalTest.java
│ │ │ ├── FusionFilterTest.java
│ │ │ ├── HeterozygousBayesianSignalTest.java
│ │ │ ├── NormalBayesianSignalTest.java
│ │ │ ├── NovelInsertionBayesianSignalTest.java
│ │ │ ├── ReadGroupStateTest.java
│ │ │ ├── ReadGroupStatsCalculatorTest.java
│ │ │ ├── ReadGroupStatsTest.java
│ │ │ ├── SamArrayTest.java
│ │ │ ├── SignalConstantLnTest.java
│ │ │ ├── SignalCountTest.java
│ │ │ ├── SignalDistributionLnTest.java
│ │ │ ├── SignalSumTest.java
│ │ │ ├── SvCliUtilsTest.java
│ │ │ ├── SvInterestingRegionExtractorTest.java
│ │ │ ├── SvParamsTest.java
│ │ │ ├── SvToolCliTest.java
│ │ │ ├── SvToolParamsTest.java
│ │ │ ├── SvToolTaskTest.java
│ │ │ ├── UnmatedAugmenterCliTest.java
│ │ │ ├── UnmatedAugmenterTest.java
│ │ │ └── discord
│ │ │ │ ├── BedDiscordantOutputFormatterTest.java
│ │ │ │ ├── BreakpointConstraintTest.java
│ │ │ │ ├── BreakpointPositionTest.java
│ │ │ │ ├── DebugComparatorTest.java
│ │ │ │ ├── DebugDiscordantOutputFormatterTest.java
│ │ │ │ ├── DiscordantReadSetTest.java
│ │ │ │ ├── DiscordantToolCliTest.java
│ │ │ │ ├── DiscordantToolParamsTest.java
│ │ │ │ ├── DiscordantToolStatisticsTest.java
│ │ │ │ ├── DiscordantToolTest.java
│ │ │ │ ├── FlipTest.java
│ │ │ │ ├── MockSam.java
│ │ │ │ ├── ReorderingDebugOutputTest.java
│ │ │ │ ├── SmartBedWriterTest.java
│ │ │ │ ├── VcfDiscordantOutputFormatterTest.java
│ │ │ │ └── pattern
│ │ │ │ ├── BreakpointPatternParamsTest.java
│ │ │ │ ├── BreakpointStoreTest.java
│ │ │ │ ├── DeletionOverlapFilterTest.java
│ │ │ │ ├── SvPatternsCliTest.java
│ │ │ │ ├── SvPatternsTaskTest.java
│ │ │ │ └── VcfBreakpointTest.java
│ │ └── util
│ │ │ ├── CgUnrollerTest.java
│ │ │ ├── SuperCigarUnrollerTest.java
│ │ │ ├── VariantUtilsTest.java
│ │ │ └── arithmetic
│ │ │ ├── AbstractPossibilityTest.java
│ │ │ ├── LogApproximatePossibilityTest.java
│ │ │ ├── LogPossibilityTest.java
│ │ │ ├── SimplePossibilityTest.java
│ │ │ └── Timing.java
│ │ ├── vcf
│ │ └── validator
│ │ │ ├── NumericRuleSetTest.java
│ │ │ ├── RuleSetTest.java
│ │ │ ├── RuleValidationExceptionTest.java
│ │ │ └── VcfValidatorCliTest.java
│ │ ├── visualization
│ │ ├── AviewModelTest.java
│ │ ├── AviewParamsBuilderTest.java
│ │ ├── AviewParamsTest.java
│ │ ├── AviewTest.java
│ │ ├── AviewVariantTest.java
│ │ ├── CigarHelperTest.java
│ │ ├── SamAssistanceCgLegacyTest.java
│ │ ├── SamAssistanceCgTest.java
│ │ ├── SamAssistanceSimpleTest.java
│ │ ├── SamHelperTest.java
│ │ ├── SamTestHelper.java
│ │ ├── SuperCigarUnrollerTest.java
│ │ ├── UnrolledReadTest.java
│ │ └── VariantHelperTest.java
│ │ └── zooma
│ │ ├── NativeZoomaTest.java
│ │ ├── ZoomaNativeBuildIndexCliTest.java
│ │ └── ZoomaNativeMapReadsCliTest.java
│ └── resources
│ └── com
│ └── rtg
│ ├── alignment
│ └── resources
│ │ ├── cg-gotoh-edit-distance-spreadsheet-left.txt
│ │ ├── cg-gotoh-edit-distance-spreadsheet-right.txt
│ │ ├── cg-gotoh-edit-distance-spreadsheet-strip.txt
│ │ └── read1000a.txt
│ ├── assembler
│ ├── graph
│ │ └── io
│ │ │ └── resources
│ │ │ ├── contig1
│ │ │ ├── contigLong
│ │ │ ├── header1
│ │ │ ├── header2
│ │ │ ├── headerLong
│ │ │ ├── manifest
│ │ │ ├── paths1
│ │ │ └── pathsLong
│ ├── planning
│ │ └── resources
│ │ │ ├── contig.1.fa
│ │ │ ├── contig.2.fa
│ │ │ ├── header.txt
│ │ │ ├── manifest.txt
│ │ │ └── path.1.txt
│ └── resources
│ │ ├── graph-to-plot-cross.txt
│ │ ├── graph-to-plot-dot.txt
│ │ └── graph-to-plot-palindrome.txt
│ ├── blacklist
│ └── resources
│ │ ├── blacklist.txt
│ │ └── histogram.txt
│ ├── calibrate
│ └── resources
│ │ ├── reference.txt
│ │ └── test.calibration
│ ├── index
│ ├── hash
│ │ └── ngs
│ │ │ └── instances
│ │ │ └── resources
│ │ │ ├── cg2maska1-empty.txt
│ │ │ ├── cg2maska1-overlap3.txt
│ │ │ ├── cg2maska1-overlap4.txt
│ │ │ ├── cg2maska1-test2.txt
│ │ │ ├── cg2maska1-test3.txt
│ │ │ ├── cg2maska11-empty.txt
│ │ │ ├── cg2maska11-overlap3.txt
│ │ │ ├── cg2maska11-overlap4.txt
│ │ │ ├── cg2maska11-test2.txt
│ │ │ ├── cg2maska11-test3.txt
│ │ │ ├── cg2maska15-empty.txt
│ │ │ ├── cg2maska15-overlap3.txt
│ │ │ ├── cg2maska15-overlap4.txt
│ │ │ ├── cg2maska15-overlap5.txt
│ │ │ ├── cg2maska15-test2.txt
│ │ │ ├── cg2maska15-test3.txt
│ │ │ ├── cg2maskw18-empty.txt
│ │ │ ├── cg2maskw18-overlap3.txt
│ │ │ ├── cg2maskw18-overlap4.txt
│ │ │ ├── cg2maskw18-test2.txt
│ │ │ ├── cg2maskw18-test3.txt
│ │ │ ├── cg2maskw18a1-empty.txt
│ │ │ ├── cg2maskw18a1-overlap3.txt
│ │ │ ├── cg2maskw18a1-overlap4.txt
│ │ │ ├── cg2maskw18a1-test2.txt
│ │ │ ├── cg2maskw18a1-test3.txt
│ │ │ ├── cgmaska15alttest1.txt
│ │ │ ├── cgmaska15test1.txt
│ │ │ ├── cgmaska15test2.txt
│ │ │ ├── cgmaska15test3.txt
│ │ │ └── cgmaska15testEmpty.txt
│ └── resources
│ │ ├── Size1ToStringfalse
│ │ ├── Size1ToStringtrue
│ │ ├── ToStringEmpty1false
│ │ ├── ToStringEmpty1true
│ │ ├── ToStringEmpty2false
│ │ ├── ToStringEmpty2true
│ │ ├── indexcompressedtest_Long.txt
│ │ └── indexcompressedtest_Overflow2.txt
│ ├── metagenomics
│ └── resources
│ │ ├── constructacomplicated2
│ │ ├── empty
│ │ ├── fragstats
│ │ ├── sequences.fasta
│ │ ├── sequences_reduced.fasta
│ │ ├── speciescli-krona.out
│ │ ├── taxonomy.tsv
│ │ ├── taxonomy_lookup.tsv
│ │ ├── taxonomy_lookup_reduced.tsv
│ │ └── taxonomy_remove.tsv
│ ├── ml
│ └── resources
│ │ ├── testBaggedVersion_1
│ │ ├── testBinarySplitterVersion_1
│ │ ├── testBinarySplitterVersion_2
│ │ ├── testBinaryTreeVersion_1
│ │ ├── testZeroRVersion_1
│ │ └── testZeroRVersion_2
│ ├── ngs
│ ├── longread
│ │ └── resources
│ │ │ ├── longreadtask-testsingleend.txt
│ │ │ ├── longreadtask-testsingleendmtrev.txt
│ │ │ ├── testOffEdge.txt
│ │ │ ├── testOffEdge2.txt
│ │ │ └── testOffEdge2paired.txt
│ └── resources
│ │ ├── 1_46877260_xxx.sam
│ │ ├── dawtt-unmapped
│ │ ├── dawtt-unmated
│ │ ├── mapFlagsExtended.txt
│ │ ├── mapf-endtoend-alignments
│ │ ├── mapf-endtoend-unmapped
│ │ ├── matesamepos.sam
│ │ ├── ngscg.txt
│ │ ├── ngscg_0.txt
│ │ ├── ngscg_1.txt
│ │ ├── ngscg_2.txt
│ │ ├── ngscg_rev.txt
│ │ ├── ngscg_side.txt
│ │ ├── ngsparams_testInitExtendedFlags.txt
│ │ ├── ngspe.txt
│ │ ├── ngspe_ns.txt
│ │ ├── ngspe_rev.txt
│ │ ├── ngspe_side.txt
│ │ ├── no-sex-ref.sam
│ │ ├── peops_tc.txt
│ │ ├── proteinalignresults.txt
│ │ ├── proteinalignresults_one_sub.txt
│ │ ├── rammap.txt
│ │ ├── ref_1_46877260.fasta
│ │ ├── srsf-unmated
│ │ ├── svprep-expected-names.txt
│ │ ├── svprep-expected.txt
│ │ ├── svprep-left.fasta
│ │ ├── svprep-right.fasta
│ │ ├── svprep-template.fasta
│ │ ├── tnpeop_un.txt
│ │ ├── tnpeop_unmapped.txt
│ │ ├── tnpeops_pe_unfiltered.txt
│ │ ├── tnpeops_pe_unfiltered_sortedAppend.txt
│ │ ├── tnpeops_sortedAppend.txt
│ │ ├── tnpeops_tc.txt
│ │ ├── topnpeops-checkunmated-unmapped
│ │ ├── topnpeops-checkunmated-unmated
│ │ ├── topnpeops-checkunmated-unmated-cal
│ │ ├── topnpeops-checkunmated-unmated-region-cal
│ │ ├── topnpeops-checkunmatedaugment-unmapped
│ │ ├── topnpeops-checkunmatedaugment-unmated
│ │ ├── upeops-endtoend-alignments
│ │ ├── upeops-endtoend-unmapped
│ │ ├── upeops-unmapped
│ │ ├── upeops-unmated
│ │ └── usrf-unmated
│ ├── protein
│ └── resources
│ │ ├── 250.txt
│ │ ├── mapped.tsv
│ │ ├── mapped_rename.tsv
│ │ ├── mapxtestresults.txt
│ │ ├── mapxtestresults_one_sub.txt
│ │ ├── mapxtestresults_partial.txt
│ │ ├── mcProt.fa
│ │ ├── mcReads.fa
│ │ ├── mcResults
│ │ ├── pop-exp-unmapped.tsv
│ │ ├── pop-exp1-alignments.tsv
│ │ ├── pop-exp2-alignments.tsv
│ │ ├── pop-no-prot-alignments.tsv
│ │ ├── pop-no-prot-unmapped.tsv
│ │ ├── pop-prot-alignments.tsv
│ │ ├── pop-prot-unmapped.tsv
│ │ ├── test-topn.txt
│ │ ├── test-topn250.txt
│ │ ├── unmapped.tsv
│ │ └── unmapped_rename.tsv
│ ├── reader
│ └── resources
│ │ ├── expected_1.fastq
│ │ ├── expected_2.fastq
│ │ ├── input.sam
│ │ ├── pair-aligner-zero-phred-del.fq
│ │ ├── pair-aligner-zero-phred-ins.fq
│ │ ├── petrim-e2e-drop-pairs.fastq
│ │ ├── petrim-e2e-drop-reads.fastq
│ │ ├── petrim-e2e-min-length.fastq
│ │ ├── petrim-e2e-probes.fastq
│ │ ├── petrim-e2e-probes.fragment-lengths.tsv
│ │ ├── petrim-e2e-probes.left-read-lengths.tsv
│ │ ├── petrim-e2e-probes.overlap-lengths.tsv
│ │ ├── petrim-e2e-probes.right-read-lengths.tsv
│ │ ├── petrim-e2e-probes.summary.txt
│ │ ├── softclip2fastq.fq
│ │ ├── softclip2fastq_1.fq
│ │ ├── softclip2fastq_2.fq
│ │ └── softclip2fastq_rf.fq
│ ├── report
│ └── resources
│ │ ├── mapx.log.txt
│ │ └── test.html
│ ├── sam
│ ├── probe
│ │ └── resources
│ │ │ ├── alignments.sam
│ │ │ ├── expected.cigar_ops.tsv
│ │ │ ├── expected.on_target.tsv
│ │ │ ├── expected.out.txt
│ │ │ ├── expected.probes.tsv
│ │ │ ├── expected.stripped.sam
│ │ │ ├── expected.summary.tsv
│ │ │ ├── negative_strand_probe_counts.bed
│ │ │ ├── positive_strand_probe_counts.bed
│ │ │ └── probes.bed
│ └── resources
│ │ ├── badReadBase.sam
│ │ ├── readerWindowInsert.sam
│ │ ├── sfm-rmdup
│ │ ├── sfm-rmdup-stdout
│ │ ├── simplestdout
│ │ └── simplestdout-newheader
│ ├── segregation
│ └── resources
│ │ ├── Xchromosome.vcf
│ │ ├── crossover.vcf
│ │ ├── crossovers_annotated.vcf
│ │ ├── crossovers_annotated_repaired.vcf
│ │ ├── regions.bed
│ │ └── test.vcf
│ ├── similarity
│ └── resources
│ │ ├── phylogeny_testFlags.txt
│ │ ├── similarity.tsv
│ │ └── svd.tsv
│ ├── simulation
│ ├── resources
│ │ ├── mutations.vcf
│ │ ├── overlapdels.vcf
│ │ ├── readsimsam.txt
│ │ └── readsimsambad.txt
│ └── sv
│ │ └── resources
│ │ ├── del1.fasta
│ │ ├── del2.fasta
│ │ ├── doubledelmerged.vcf
│ │ ├── dup1.fasta
│ │ ├── dup2.fasta
│ │ ├── inv1.fasta
│ │ ├── inv2.fasta
│ │ ├── merge.vcf
│ │ ├── merge2.vcf
│ │ ├── mergeXchr-exp.vcf
│ │ ├── mergeXchr.vcf
│ │ ├── mergeXchrcnv.vcf
│ │ ├── mergecnv.vcf
│ │ ├── mergedoubledelcnv.vcf
│ │ ├── mergetripledelcnv-exp.vcf
│ │ ├── mergetripledelcnv.vcf
│ │ ├── shorty.fasta
│ │ ├── simplemerged.vcf
│ │ └── simplemerged2.vcf
│ ├── taxonomy
│ └── resources
│ │ ├── citations.dmp
│ │ ├── delnodes.dmp
│ │ ├── division.dmp
│ │ ├── gencode.dmp
│ │ ├── ids_remove.txt
│ │ ├── ids_remove_all_seqs.txt
│ │ ├── ids_remove_seqs.txt
│ │ ├── ids_subset.txt
│ │ ├── ids_subtree.txt
│ │ ├── merged.dmp
│ │ ├── names.dmp
│ │ ├── no_rank_rename.txt
│ │ ├── nodes.dmp
│ │ ├── taxVerifyDire2Err
│ │ ├── taxVerifyDireErr
│ │ ├── taxVerifyErr
│ │ ├── taxVerifyOut
│ │ ├── taxonomy.tsv
│ │ ├── taxonomy_norank_rename.tsv
│ │ ├── taxonomy_remove.tsv
│ │ ├── taxonomy_remove_all_sequences.tsv
│ │ ├── taxonomy_remove_all_sequences_lookup.tsv
│ │ ├── taxonomy_remove_lookup.tsv
│ │ ├── taxonomy_remove_sequences.tsv
│ │ ├── taxonomy_remove_sequences_lookup.tsv
│ │ ├── taxonomy_subset.tsv
│ │ ├── taxonomy_subset_lookup.tsv
│ │ ├── taxonomy_subtree.tsv
│ │ └── taxonomy_subtree_lookup.tsv
│ ├── util
│ └── testFile
│ ├── variant
│ ├── avr
│ │ └── resources
│ │ │ ├── arff-dataset.arff
│ │ │ ├── avrstats.txt
│ │ │ ├── default.avr
│ │ │ ├── gtcomplex.props
│ │ │ ├── gtqualcomplexmodel.avr
│ │ │ ├── mlmodel.avr
│ │ │ ├── multisample.vcf
│ │ │ ├── negatives.vcf
│ │ │ ├── null.avr
│ │ │ ├── posandneg.vcf
│ │ │ ├── positives.vcf
│ │ │ ├── predict.vcf
│ │ │ ├── predictSample.vcf
│ │ │ └── testMlAvrPredictModelVersion_1
│ ├── bayes
│ │ ├── complex
│ │ │ └── resources
│ │ │ │ ├── HypothesesComplex-AddingN
│ │ │ │ ├── HypothesesComplex-AmbiguousRead
│ │ │ │ ├── HypothesesComplex-CloneConstructor
│ │ │ │ ├── HypothesesComplex-CloneConstructor2
│ │ │ │ ├── HypothesesComplex-EmptyMatches
│ │ │ │ ├── HypothesesComplex-EmptyMatchesAll
│ │ │ │ ├── HypothesesComplex-FromConvergence
│ │ │ │ ├── HypothesesComplex-FromConvergence2
│ │ │ │ ├── HypothesesComplex-MatchesAllWithSecondOutput
│ │ │ │ ├── HypothesesComplex-NonDefaultEventRates
│ │ │ │ ├── HypothesesComplex-ObviousSingleNtInsertionMatchesHeteroCall
│ │ │ │ ├── HypothesesComplex-ObviousSingleNtInsertionMatchesHomoCall
│ │ │ │ ├── HypothesesComplex-PriorsBug
│ │ │ │ ├── insertionpriortest0.txt
│ │ │ │ ├── kappamemotest0.txt
│ │ │ │ └── kappatest0.txt
│ │ └── multisample
│ │ │ ├── cancer
│ │ │ └── resources
│ │ │ │ ├── contaminationbug.calibration
│ │ │ │ ├── contaminationbug.ref
│ │ │ │ ├── contaminationbug.sam
│ │ │ │ ├── somaticnanotest.vcf
│ │ │ │ ├── somaticnanotest1.vcf
│ │ │ │ ├── somaticnanotest2.vcf
│ │ │ │ ├── somaticnanotest3.vcf
│ │ │ │ ├── somaticnanotest4.vcf
│ │ │ │ ├── somaticnanotest5.vcf
│ │ │ │ ├── somaticnanotest5b.vcf
│ │ │ │ ├── somaticnanotest6.vcf
│ │ │ │ ├── somaticnanotestLoh.vcf
│ │ │ │ ├── somaticnanotestLohDiploid.vcf
│ │ │ │ ├── somaticnanotestLohDiploid1.vcf
│ │ │ │ ├── somaticnanotestLongInsert.vcf
│ │ │ │ ├── somaticnanotestLongInsertNoN.vcf
│ │ │ │ ├── somaticnanotestcontaminationbugtest.vcf
│ │ │ │ ├── test1_cancer.sam
│ │ │ │ ├── test1_normal.sam
│ │ │ │ ├── test2_cancer.sam
│ │ │ │ ├── test2_normal.sam
│ │ │ │ ├── test3_cancer.sam
│ │ │ │ ├── test3_normal.sam
│ │ │ │ ├── test5_cancer.sam
│ │ │ │ ├── test5_normal.sam
│ │ │ │ ├── test6_cancer.sam
│ │ │ │ ├── test6_normal.sam
│ │ │ │ ├── testLohDiploid_cancer.sam
│ │ │ │ ├── testLohDiploid_normal.sam
│ │ │ │ ├── testLoh_cancer.sam
│ │ │ │ ├── testLoh_normal.sam
│ │ │ │ ├── testLongInsertNoN_cancer.sam
│ │ │ │ ├── testLongInsertNoN_normal.sam
│ │ │ │ ├── testLongInsert_cancer.sam
│ │ │ │ └── testLongInsert_normal.sam
│ │ │ ├── family
│ │ │ └── resources
│ │ │ │ ├── WMD.ped
│ │ │ │ ├── family_denovo.sam
│ │ │ │ ├── familycaller-allOutput
│ │ │ │ ├── familycaller-comparison.vcf
│ │ │ │ ├── familycaller-comparison2
│ │ │ │ ├── familycaller-comparison3
│ │ │ │ ├── familycaller-comparison4
│ │ │ │ ├── familycaller-comparison5
│ │ │ │ ├── familycaller-comparison6
│ │ │ │ ├── familycaller-comparisonPloidy
│ │ │ │ ├── familynanotest-denovo.vcf
│ │ │ │ ├── familynanotest-denovo_hom.vcf
│ │ │ │ ├── familynanotest-nodenovo.vcf
│ │ │ │ ├── input.bam
│ │ │ │ ├── input.bam.bai
│ │ │ │ ├── input.bam.calibration
│ │ │ │ └── subset_template.fasta
│ │ │ ├── forwardbackward
│ │ │ └── resources
│ │ │ │ ├── familycallerfb-allOutput
│ │ │ │ ├── familycallerfb-comparison.vcf
│ │ │ │ ├── familycallerfb-comparison2
│ │ │ │ ├── familycallerfb-comparison3
│ │ │ │ ├── familycallerfb-comparison4
│ │ │ │ ├── familycallerfb-comparison5
│ │ │ │ ├── familycallerfb-comparison6
│ │ │ │ └── familycallerfb-comparisonPloidy
│ │ │ ├── lineage
│ │ │ └── resources
│ │ │ │ ├── ref.fasta
│ │ │ │ ├── threeSample.ped
│ │ │ │ ├── threeSample.sam
│ │ │ │ ├── threeSample_expected.txt
│ │ │ │ ├── twoSample.ped
│ │ │ │ ├── twoSample.sam
│ │ │ │ ├── twoSampleDisconnected.ped
│ │ │ │ ├── twoSampleDisconnected.sam
│ │ │ │ ├── twoSampleDisconnected_expected.txt
│ │ │ │ └── twoSample_expected.txt
│ │ │ ├── population
│ │ │ └── resources
│ │ │ │ ├── it_diploid_lge
│ │ │ │ ├── it_diploid_med
│ │ │ │ ├── it_diploid_small
│ │ │ │ ├── it_haploid_lge
│ │ │ │ ├── it_haploid_med
│ │ │ │ ├── it_haploid_small
│ │ │ │ ├── it_null_lge
│ │ │ │ ├── it_null_med
│ │ │ │ ├── it_null_small
│ │ │ │ ├── pophwhypcomplex
│ │ │ │ ├── pophwhypcomplexpruning
│ │ │ │ ├── pophwhyptest
│ │ │ │ ├── pophwnovelty
│ │ │ │ ├── poppathological
│ │ │ │ ├── populationnanotest-denovo.vcf
│ │ │ │ ├── populationnanotest-denovo_hom.vcf
│ │ │ │ ├── populationnanotest-denovo_mixed.vcf
│ │ │ │ ├── populationnanotest-denovo_prop.vcf
│ │ │ │ ├── populationnanotest-nodenovo.vcf
│ │ │ │ ├── populationnanotest-nodenovo_prop.vcf
│ │ │ │ ├── vc_diploid_lge
│ │ │ │ ├── vc_diploid_med
│ │ │ │ ├── vc_diploid_small
│ │ │ │ ├── vc_haploid_lge
│ │ │ │ ├── vc_haploid_med
│ │ │ │ ├── vc_haploid_small
│ │ │ │ ├── vc_null_lge
│ │ │ │ ├── vc_null_med
│ │ │ │ └── vc_null_small
│ │ │ └── resources
│ │ │ ├── bed_region_template.fasta
│ │ │ ├── indel_triggering_deletion.sam
│ │ │ ├── indel_triggering_deletion_reverse.sam
│ │ │ ├── indel_triggering_fraction.sam
│ │ │ ├── indel_triggering_on2_same.sam
│ │ │ ├── indel_triggering_on2_split.sam
│ │ │ ├── populationnanotest-indel_triggering_deletion.bed
│ │ │ ├── populationnanotest-indel_triggering_deletion.vcf
│ │ │ ├── populationnanotest-indel_triggering_deletion_reverse.bed
│ │ │ ├── populationnanotest-indel_triggering_deletion_reverse.vcf
│ │ │ ├── populationnanotest-indel_triggering_fraction.bed
│ │ │ ├── populationnanotest-indel_triggering_fraction.vcf
│ │ │ ├── populationnanotest-indel_triggering_on2_same.bed
│ │ │ ├── populationnanotest-indel_triggering_on2_same.vcf
│ │ │ ├── populationnanotest-indel_triggering_on2_split.bed
│ │ │ ├── populationnanotest-indel_triggering_on2_split.vcf
│ │ │ ├── populationnanotest-startOfReferenceN.vcf
│ │ │ ├── populationnanotest-testBedRegion.vcf
│ │ │ ├── populationnanotest-testBedRegionPlusRegion.vcf
│ │ │ ├── startOfReferenceN.sam
│ │ │ ├── testBedRegion.bed
│ │ │ └── testBedRegion.sam
│ ├── cnv
│ │ ├── resources
│ │ │ ├── babySam.sam
│ │ │ ├── babySamTarget.sam
│ │ │ ├── cnv.cnv
│ │ │ ├── cnv.ratio
│ │ │ ├── cnv1.cnv
│ │ │ ├── cnv1.ratio
│ │ │ ├── otherDict.sam
│ │ │ ├── testFilter.bam
│ │ │ ├── testFilter.bam.bai
│ │ │ └── testFilter.sam
│ │ └── segment
│ │ │ └── resources
│ │ │ ├── case.bed
│ │ │ ├── control.bed
│ │ │ ├── coverage.bed
│ │ │ ├── expected.out-gc.txt
│ │ │ ├── expected.out-panel.txt
│ │ │ ├── expected.out.txt
│ │ │ ├── expected.panel.bed
│ │ │ ├── expected.segments-gc.vcf
│ │ │ ├── expected.segments-panel.vcf
│ │ │ ├── expected.segments.vcf
│ │ │ ├── expected.sum-out.txt
│ │ │ ├── expected.summary-gc.txt
│ │ │ ├── expected.summary-panel.txt
│ │ │ ├── expected.summary.bed
│ │ │ ├── expected.summary.txt
│ │ │ ├── expected.unsegmented-gc.bed
│ │ │ ├── expected.unsegmented-panel.bed
│ │ │ ├── expected.unsegmented.bed
│ │ │ ├── my.vcf
│ │ │ ├── panel.bed
│ │ │ ├── ref.fa
│ │ │ ├── regions.bed
│ │ │ ├── singleRecord.vcf
│ │ │ ├── singleRecordOutput.txt
│ │ │ └── svof-example.txt
│ ├── coverage
│ │ └── resources
│ │ │ ├── covBedRegion.bed
│ │ │ ├── covBedRegion.tsv
│ │ │ ├── covBedRegionNoTemplate.txt
│ │ │ ├── covBedRegionPerRegion.bed
│ │ │ ├── coveragetasktest-out.txt
│ │ │ ├── coveragetasktest1-smooth1.txt
│ │ │ ├── coveragetasktest1.txt
│ │ │ ├── coveragetasktest2-smooth1.txt
│ │ │ ├── coveragetasktest2-smooth2.txt
│ │ │ ├── coveragetasktest2.txt
│ │ │ ├── coveragetasktest3.txt
│ │ │ ├── coveragetasktest3region.txt
│ │ │ ├── coveragetasktest5.txt
│ │ │ ├── coveragetasktest5IHfraction.txt
│ │ │ ├── coveragetasktestErrorRates.txt
│ │ │ ├── coveragetasktestGapStatsOut.txt
│ │ │ ├── coveragetasktestLevelsStatsOut.txt
│ │ │ ├── coveragetasktestStats.txt
│ │ │ ├── coveragetasktestStatsOut.txt
│ │ │ ├── coveragetasktest_clipping.bed
│ │ │ ├── coveragetasktest_clipping.tsv
│ │ │ ├── coveragetasktestadditional.txt
│ │ │ ├── coveragetasktestadditionalRC.txt
│ │ │ ├── coveragetasktestih1nh2.txt
│ │ │ ├── coveragetasktestperbase.txt
│ │ │ ├── covstats-add-median.txt
│ │ │ ├── covstats-levels.tsv
│ │ │ ├── covstats-stats.tsv
│ │ │ └── covstats-summary.txt
│ ├── format
│ │ └── resources
│ │ │ ├── vcfformatfield-headers.vcf
│ │ │ ├── vcfinfofield-header.txt
│ │ │ ├── vovf-disease-header1.vcf
│ │ │ ├── vovf-multi-header1.vcf
│ │ │ ├── vovf-single-header1.vcf
│ │ │ └── vovf-test-several.vcf
│ ├── realign
│ │ └── resources
│ │ │ ├── homopolymermatrix-short-circuit.txt
│ │ │ ├── homopolymermatrix-test.txt
│ │ │ ├── scorematrix-homopolymer.txt
│ │ │ ├── scorematrix-re-use1.txt
│ │ │ ├── scorematrix-re-use2.txt
│ │ │ ├── scorematrix-reverse-typical.txt
│ │ │ ├── scorematrix-small.txt
│ │ │ ├── scorematrix-typical.txt
│ │ │ ├── scorematrixcg-reverse-tostring.txt
│ │ │ ├── scorematrixcg-reverse-v2-tostring.txt
│ │ │ ├── scorematrixcg-tostring.txt
│ │ │ └── scorematrixcg-v2-tostring.txt
│ ├── resources
│ │ ├── bug1508_reads.sam.gz
│ │ ├── bug1508_ref.fasta
│ │ ├── bug1524.fasta
│ │ ├── bug1524.sam.gz
│ │ ├── bug1524.txt
│ │ ├── bug1524.vcf
│ │ ├── bug1675_reads.sam.gz
│ │ ├── bug1675_ref.fasta
│ │ ├── calibration_global_sample.calibration
│ │ ├── calibration_sample.calibration
│ │ ├── cg.txt
│ │ ├── complexambigsuppression.sam
│ │ ├── complexambigsuppressiontemplate.fa
│ │ ├── complexhypercomplex.sam
│ │ ├── complexhypercomplextemplate.fa
│ │ ├── complexreadorder.sam.gz
│ │ ├── complexreadorder.sam.gz.tbi
│ │ ├── complexssp.fa
│ │ ├── complexssp2.sam
│ │ ├── complexssp_pop.vcf
│ │ ├── coverage_mated.sam
│ │ ├── coverage_mated.sam.gz
│ │ ├── coverage_mated.sam.gz.calibration
│ │ ├── coverage_unmated.sam.gz
│ │ ├── coverage_unmated.sam.gz.calibration
│ │ ├── genome1_mated.sam.gz.calibration
│ │ ├── genome1_unmated.sam.gz.calibration
│ │ ├── genome2_mated.sam.gz.calibration
│ │ ├── genome2_unmated.sam.gz.calibration
│ │ ├── genome3_mated.sam.gz.calibration
│ │ ├── genome3_unmated.sam.gz.calibration
│ │ ├── hyper_oldcli.vcf
│ │ ├── hypersam.sam
│ │ ├── hypertemplate.fa
│ │ ├── ident-insert2-genome.fa
│ │ ├── ident-insert2.sam
│ │ ├── longindelmessy.sam
│ │ ├── n-mappings.sam
│ │ ├── n2-mappings.sam
│ │ ├── n2-mappings2.sam
│ │ ├── out.rtg.txt
│ │ ├── pop58.vcf
│ │ ├── sam11.sam.gz
│ │ ├── sam11.sam.gz.tbi
│ │ ├── test.calibration
│ │ ├── test2.calibration
│ │ ├── test3.calibration
│ │ ├── test4.calibration
│ │ ├── variantnano_tabix.vcf
│ │ ├── variantnano_tabix2.vcf
│ │ ├── variantnanotest-complexambsuppression.vcf
│ │ ├── variantnanotest-identityinsert.vcf
│ │ ├── variantnanotest1.vcf
│ │ ├── variantnanotest10.vcf
│ │ ├── variantnanotest11.vcf
│ │ ├── variantnanotest12.vcf
│ │ ├── variantnanotest13.vcf
│ │ ├── variantnanotest14.vcf
│ │ ├── variantnanotest15.vcf
│ │ ├── variantnanotest16.vcf
│ │ ├── variantnanotest17.vcf
│ │ ├── variantnanotest18.vcf
│ │ ├── variantnanotest19.vcf
│ │ ├── variantnanotest2.vcf
│ │ ├── variantnanotest20.vcf
│ │ ├── variantnanotest21.vcf
│ │ ├── variantnanotest22.vcf
│ │ ├── variantnanotest23.vcf
│ │ ├── variantnanotest25.vcf
│ │ ├── variantnanotest26.vcf
│ │ ├── variantnanotest27.vcf
│ │ ├── variantnanotest28.vcf
│ │ ├── variantnanotest29.vcf
│ │ ├── variantnanotest3.vcf
│ │ ├── variantnanotest30.vcf
│ │ ├── variantnanotest31.vcf
│ │ ├── variantnanotest32.vcf
│ │ ├── variantnanotest33.vcf
│ │ ├── variantnanotest34.vcf
│ │ ├── variantnanotest35.vcf
│ │ ├── variantnanotest36.vcf
│ │ ├── variantnanotest37.vcf
│ │ ├── variantnanotest38.vcf
│ │ ├── variantnanotest39.vcf
│ │ ├── variantnanotest4.vcf
│ │ ├── variantnanotest40.vcf
│ │ ├── variantnanotest41.vcf
│ │ ├── variantnanotest42.vcf
│ │ ├── variantnanotest43.vcf
│ │ ├── variantnanotest44.vcf
│ │ ├── variantnanotest45.vcf
│ │ ├── variantnanotest46.vcf
│ │ ├── variantnanotest47.vcf
│ │ ├── variantnanotest48.vcf
│ │ ├── variantnanotest49.vcf
│ │ ├── variantnanotest5.vcf
│ │ ├── variantnanotest50.vcf
│ │ ├── variantnanotest51.vcf
│ │ ├── variantnanotest52.vcf
│ │ ├── variantnanotest53.vcf
│ │ ├── variantnanotest54.vcf
│ │ ├── variantnanotest55.vcf
│ │ ├── variantnanotest56.vcf
│ │ ├── variantnanotest57.vcf
│ │ ├── variantnanotest58.vcf
│ │ ├── variantnanotest59.vcf
│ │ ├── variantnanotest6.vcf
│ │ ├── variantnanotest60.vcf
│ │ ├── variantnanotest62.vcf
│ │ ├── variantnanotest63.vcf
│ │ ├── variantnanotest64.vcf
│ │ ├── variantnanotest65.vcf
│ │ ├── variantnanotest66.vcf
│ │ ├── variantnanotest67.vcf
│ │ ├── variantnanotest68.vcf
│ │ ├── variantnanotest69.vcf
│ │ ├── variantnanotest7.vcf
│ │ ├── variantnanotest70.vcf
│ │ ├── variantnanotest71.vcf
│ │ ├── variantnanotest72.vcf
│ │ ├── variantnanotest8.vcf
│ │ ├── variantnanotest9.vcf
│ │ ├── vcf_to_rtg_NA00001.txt
│ │ ├── vcf_to_rtg_NA00002.txt
│ │ ├── vcfcomplexsoftcliptest.sam
│ │ ├── vcfdiff1a.vcf
│ │ ├── vcfdiff1b.vcf
│ │ ├── vcfdiff2a.vcf
│ │ ├── vcfdiff2b.vcf
│ │ ├── vcfdiff3a.vcf
│ │ ├── vcfdiff3b.vcf
│ │ ├── vcfsnpsoftcliptest.sam
│ │ ├── vcftest.sam
│ │ └── vcftesttmpl.fa
│ └── sv
│ │ ├── discord
│ │ ├── pattern
│ │ │ └── resources
│ │ │ │ ├── discordant_pairs.vcf.gz
│ │ │ │ ├── sv_load.txt
│ │ │ │ └── sv_patterns.bed
│ │ └── resources
│ │ │ ├── depth-2.txt
│ │ │ ├── discordantstats
│ │ │ ├── end-to-end.txt
│ │ │ ├── null-intersection-false.txt
│ │ │ └── null-intersection-true.txt
│ │ └── resources
│ │ ├── augmented.sam
│ │ ├── fusion_in.vcf
│ │ ├── fusion_in_acceptor.bed
│ │ ├── fusion_in_donor.bed
│ │ ├── fusion_in_score.tsv
│ │ ├── fusion_out_filtered.vcf
│ │ ├── gcCounts.sam.gz
│ │ ├── gcInvestigation.sam
│ │ ├── mergecombined-aug.sam
│ │ ├── mergeunmapped-aug.sam
│ │ ├── rgstats.txt
│ │ ├── small_sv_bayes.bed
│ │ ├── small_sv_interesting.bed
│ │ ├── small_sv_simple.txt
│ │ ├── smallsvMappings.sam.gz
│ │ ├── smallsvMappings.sam.gz.tbi
│ │ ├── smallsvTemplate.dwa
│ │ ├── sv_int_region.txt
│ │ ├── svtasktest1.txt
│ │ ├── svtasktest1_bayes.txt
│ │ ├── svtasktest4.txt
│ │ ├── svtasktest4_bayes.txt
│ │ └── testTemplate.dwa
│ ├── vcf
│ └── validator
│ │ └── resources
│ │ ├── badHeaders.txt
│ │ ├── badHeaders.vcf
│ │ ├── boringNormal.vcf
│ │ ├── fullOfBad.txt
│ │ ├── fullOfBad.vcf
│ │ └── fullOfBad_verbose.txt
│ ├── visualization
│ └── resources
│ │ ├── aview-basecolor.txt
│ │ ├── aview-color.txt
│ │ ├── aview-delete-exp.txt
│ │ ├── aview-deletes.txt
│ │ ├── aview-inserts.txt
│ │ ├── aview-nocolor.txt
│ │ ├── aview-rg.txt
│ │ ├── aview-testinputlist.txt
│ │ ├── aview-toomuchtemplate.txt
│ │ ├── expected2.txt
│ │ ├── extracted.sam
│ │ ├── extracted2.sam
│ │ ├── extracted3.sam
│ │ └── genome.fa
│ └── zooma
│ └── resources
│ └── testzmap.sam
└── test
├── bedRegions.bed
└── bedRegions.bed.gz
/.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 | /.idea
34 | /target
35 | *.iml
36 |
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/installer/resources/core/RTGOperationsManual/_sources/index.rst.txt:
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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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1 | const DOCUMENTATION_OPTIONS = {
2 | VERSION: '3.13',
3 | LANGUAGE: 'en',
4 | COLLAPSE_INDEX: false,
5 | BUILDER: 'html',
6 | FILE_SUFFIX: '.html',
7 | LINK_SUFFIX: '.html',
8 | HAS_SOURCE: true,
9 | SOURCELINK_SUFFIX: '.txt',
10 | NAVIGATION_WITH_KEYS: false,
11 | SHOW_SEARCH_SUMMARY: true,
12 | ENABLE_SEARCH_SHORTCUTS: true,
13 | };
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1 | RTG Example Script For Visualizing Similarity Output
2 | ====================================================
3 |
4 | Example R scripts to provide a simple interactive visualization of the
5 | similarity of samples, based on the principal component analysis
6 | output of the RTG similarity module.
7 |
8 | These scripts are provided as an example intended to be modified to
9 | suit your specific pipeline needs. Further instructions are contained
10 | within each of the scripts.
11 |
12 | similarity-simple.R Visualize RTG similarity PCA output using sample labelling
13 | similarity-kmeans.R Visualize RTG similarity PCA using k-means clustering
14 | similarity.pca Example principal component analysis output from RTG similarity
15 |
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/installer/resources/core/scripts/species-abundance/README.txt:
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1 | Example Excel Files
===================
This folder contains example worksheets showing how you might plot abundance
graphs from the RTG species tool output. These Excel files are provided as
examples intended to be modified to suit your specific needs.
abundance-graphs-example.xlsm An example of generating abundance graphs from RTG species output, with example data
abundance-graphs-template.xlsm An example of generating abundance graphs from RTG species output, without example data
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/installer/resources/core/scripts/species-comparison/README.txt:
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1 | RTG Example Script For Comparison Of Species Runs
2 | =================================================
3 |
4 | Example R script to provide a visual comparison between the output of two
5 | runs of the RTG species module.
6 |
7 | This script is provided as an example intended to be modified to suit your
8 | specific pipeline needs.
9 |
10 | comparison.R Compare RTG species outputs
11 |
12 |
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/installer/resources/models/alternate.avr:
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/src/main/java/com/rtg/index/hash/ngs/general/package.html:
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1 |
2 | All the pieces necessary to implement general masks for short reads.
3 |
4 |
5 |
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/src/main/java/com/rtg/index/hash/ngs/package.html:
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1 |
2 | Hashing functions for index building when processing short reads.
3 |
4 | Dealing with Complete Genomics data
5 |
6 | Complete genomics data is tricky because the right side reads need to be
7 | reverse complemented when they are read in to get the buffers set up correctly
8 | so the masking is aligned correctly.
9 |
10 | This diagram has a go at illustrating this.
11 |
12 |
13 |
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/src/main/java/com/rtg/index/hash/package.html:
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1 |
2 | Hashing functions for index building.
3 |
4 |
5 |
--------------------------------------------------------------------------------
/src/main/java/com/rtg/index/package.html:
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1 |
2 | Classes associated with the building and searching of SLIM indexes.
3 |
4 |
5 |
--------------------------------------------------------------------------------
/src/main/java/com/rtg/index/params/package.html:
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1 |
2 | Indexing and searching parameters.
3 |
4 |
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/src/main/java/com/rtg/index/similarity/package.html:
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1 |
2 | Classes associated with computing similarity between genomes.
3 |
4 |
5 |
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/src/main/java/com/rtg/ml/package.html:
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1 |
2 |
3 | Machine learning.
4 |
5 |
6 |
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/src/main/java/com/rtg/ngs/package.html:
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1 |
2 | Processing to take SLIM 1.3 parser friendly output and write as a scored map from reads to templates..
3 |
4 | Score has the main to be run and there is a script in exec.sh.
5 |
6 |
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/src/main/java/com/rtg/package.html:
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1 |
2 | All the core code associated with SLIM search. Consists primarily of
3 | those components developed by Reel Two. See package build to main classes to
4 | be called to run SLIM.
5 |
6 |
7 |
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/src/main/java/com/rtg/pairedend/package.html:
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1 |
2 | Provides interfaces and classes for performing paired-end read matching and alignment output directly from the output of the index matching module.
3 |
4 |
--------------------------------------------------------------------------------
/src/main/java/com/rtg/position/package.html:
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1 |
2 | Classes for implementing position.
3 |
4 |
5 |
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/src/main/java/com/rtg/similarity/package.html:
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1 |
2 |
3 | This is phylogeny. I don't know what this is, but here it is.
4 |
5 |
6 |
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/src/main/java/com/rtg/util/memo/package.html:
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1 |
2 | Memo utilities for remembering the values of expensive to compute functions.
3 |
4 |
5 |
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/src/main/java/com/rtg/util/memory/package.html:
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1 |
2 | Memory utilities.
3 |
4 |
5 |
--------------------------------------------------------------------------------
/src/main/java/com/rtg/util/package.html:
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1 |
2 |
3 | Utility classes for general use in project
4 |
5 |
6 |
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/src/main/java/com/rtg/variant/bayes/multisample/package.html:
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1 |
2 | Code supporting simultaneous variant calling on multiple genomes. More information regarding the scheduler design
3 |
4 |
5 |
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/src/main/java/com/rtg/variant/package.html:
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1 |
2 | All code associated with finding variance in a set of mapped reads against a reference genome.
3 |
4 |
5 |
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/src/main/resources/com/rtg/report/resources/format_summary.html:
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1 |
2 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
13 |
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/src/main/resources/com/rtg/report/resources/map_report.html:
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1 | __PARAMETER_SUMMARY__
2 | __SUMMARY_FILE_TITLE__
3 | __SUMMARY_FILE__
4 | __FULL_NAME__
5 |
6 |
--------------------------------------------------------------------------------
/src/main/resources/com/rtg/report/resources/mapf_report.html:
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1 |
2 | Sample: __SAMPLE__
3 | DataBase: __DATABASE__
4 | Results Directory: __DIRECTORY__
5 |
6 |
7 |
8 | Sensitivity settings: __SENSITIVITY_SETTINGS__
9 | Reporting (SAM/BAM records): __REPORTING_SETTINGS__
10 | Command line arguments: __COMMAND_LINE__
11 |
12 |
13 | __MAPF_SUMMARY__
14 |
15 |
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/src/main/resources/com/rtg/report/resources/mapx_report.html:
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1 |
2 | Sample: __SAMPLE__
3 | DataBase: __DATABASE__
4 | Command line: __COMMAND_LINE__
5 | Results Directory: __DIRECTORY__
6 |
7 |
8 | __MAPX_SUMMARY__
9 |
10 |
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/src/main/resources/com/rtg/report/resources/mapx_wrapper.html:
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1 | Metabolic Pathway Analysis
2 | A. Translated search summary
3 |
--------------------------------------------------------------------------------
/src/main/resources/com/rtg/report/resources/metagenomics_report.html:
--------------------------------------------------------------------------------
1 | RTG Analytics
2 | Version: __VERSION__
3 |
4 | Data QC and Formatting
5 |
6 | - RTG mapf (contaminant removal- e.g. human reads in microbiome samples)
7 |
8 |
9 | Metagenomic Community Profiling
10 |
11 | - RTG map (reference alignment to nucleotide sequences)
12 | - RTG species (produce abundance estimates, genome coverage statistics, and diversity
13 | metrics)
14 |
15 | Metabolic Pathway Analysis
16 |
17 | - RTG mapx (translated nucleotide search) together with HMP's HUMAnN software (gene and
18 | pathway abundance and coverage estimates)
19 |
20 | __MAPF_REPORT__
21 | __SPECIES_REPORT__
22 | __MAPX_REPORT__
23 |
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/src/main/resources/com/rtg/report/resources/species_report.html:
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1 | __SUMMARY__
2 |
3 | __SUMMARY_FILE__
4 |
5 | __FULL_NAME__
6 |
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/src/main/resources/com/rtg/report/resources/species_wrapper.html:
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1 | Metagenomic Community Profiling
2 |
3 | RTG processes whole genome 'shotgun' metagenomic data by aligning reads to reference genomes
4 | and uses RTG algorithms to compute genome coverage, species abundance, and community
5 | composition. Three abundance estimates are reported:
6 |
7 |
8 | - Abundance of an individual genome/organism among the identified genomes. Provides a
9 | relative 'count' on a per microbe basis.
10 | - Abundance of a particular genome or species normalized by DNA sequence size.
11 | - Abundance of a particular genome or species in a sample, taking into account both mapped
12 | and unmapped reads.
13 |
14 | A. Reference Alignment Summary
15 | __MAP_REPORT__
16 | B. Species Data Summary
17 | __SPECIES_REPORT__
18 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/contig1:
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1 | >1 foo=val1 bar=bar1
2 | ACGT
3 | >2 foo=val2
4 | CGTA
5 | >3
6 | GTAC
7 | >4
8 | TACG
9 | >5
10 | AA
11 | >6
12 | CC
13 | >7
14 | GG
15 | >8
16 | TT
17 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/contigLong:
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1 | >1
2 | ACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAA
3 | ACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAAACTGGGTTAA
4 | >2
5 | AAAA
6 | >3
7 | CCCC
8 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/header1:
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1 | version 0.0
2 | command test
3 | contigOverlap 0
4 | contig foo foo comment
5 | contig bar bar comment
6 | path boo comment boo
7 | path oob comment oob
8 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/header2:
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1 | version 0.0
2 | date 2012/05/15 16:03:00
3 | command test
4 | guid 00000000-0000-002a-0000-000000000065
5 | contigOverlap 0
6 | inputguid 00000000-0000-0001-0000-000000000001
7 | inputguid 00000000-0000-0015-0000-000000000067
8 | contig con1 comment1
9 | contig con2 comment2
10 | contig deleted true if this contig has been deleted
11 | path deleted true if this path has been deleted
12 | path path1 pcomment1
13 | path path2 pcomment2
14 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/headerLong:
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1 | version 0.0
2 | command test
3 | contigOverlap 0
4 | contig deleted true if this contig has been deleted
5 | path deleted true if this path has been deleted
6 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/manifest:
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1 | b0bd9730e6ec25b3ca59f6553dbc6051 contig.1.fa
2 | c7b340681e25ece8b53dd5f34aca1bb1 path.1.txt
3 |
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/src/test/resources/com/rtg/assembler/graph/io/resources/paths1:
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1 | path 1
2 | contigs 1 -2
3 | path 2
4 | contigs 2 -3 4
5 | path 3 boo=p3
6 | contigs -3 5 6
7 | path 4
8 | contigs 3 7
9 |
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/src/test/resources/com/rtg/assembler/planning/resources/contig.1.fa:
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1 | >1 cov=42
2 | ACGTN
3 | NNNNN
4 | >2 cov=1 tip=12.34
5 | AAAAAAAAAAAAAAA
6 |
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/src/test/resources/com/rtg/assembler/planning/resources/contig.2.fa:
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1 | >3 cov=42 tip=1.9
2 | ACGTN
3 | NNNNN
4 | >4 cov=1
5 | AAAAAAAAAAAAAAA
6 | >5
7 | TTTT
8 |
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/src/test/resources/com/rtg/assembler/planning/resources/header.txt:
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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 |
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/src/test/resources/com/rtg/assembler/planning/resources/manifest.txt:
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1 | 679af26cc6be203716b233059553d3db contig.1.fa
2 | 13fe7baff6414685a6f20f65e11dc879 contig.2.fa
3 | 762b36734794180251a4a46aefde8a68 header.txt
4 | d9189dc58dccd27b0b26d1fda7dbd114 path.1.txt
5 |
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/src/test/resources/com/rtg/assembler/planning/resources/path.1.txt:
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1 | #An example of a path file
2 | path 1 min=3
3 | contigs +2 -1 -4
4 | path 2
5 | contigs +1 -2
6 |
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/src/test/resources/com/rtg/assembler/resources/graph-to-plot-cross.txt:
--------------------------------------------------------------------------------
1 | digraph contigGraph {
2 | graph [rankdir=LR, ratio=fill]
3 | node0 [label="+1\n3 0", color=red, shape=box];
4 | node1 [label="+2\n3 0"];
5 | node2 [label="+3\n3 0"];
6 | node3 [label="+4\n3 0"];
7 | node4 [label="+5\n3 0"];
8 | node0 -> node1[label="2"];
9 | node1 -> node3[label="2"];
10 | node1 -> node4[];
11 | node2 -> node1[];
12 | }
13 |
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/src/test/resources/com/rtg/assembler/resources/graph-to-plot-dot.txt:
--------------------------------------------------------------------------------
1 | digraph contigGraph {
2 | graph [rankdir=LR, ratio=fill]
3 | node0 [label="-2\n5 3"];
4 | node1 [label="+1\n4 2"];
5 | node2 [label="+3\n6 4", color=red, shape=box];
6 | node3 [label="+4\n7 5"];
7 | node4 [label="+5\n8 6"];
8 | node5 [label="+6\n9 7"];
9 | node6 [label="+7\n10 8", style=dashed];
10 | node7 [label="+9\n12 10", style=dashed];
11 | node0 -> node2[];
12 | node0 -> node4[];
13 | node1 -> node0[label="2"];
14 | node2 -> node4[];
15 | node2 -> node5[];
16 | node3 -> node2[];
17 | node4 -> node7[];
18 | node5 -> node7[];
19 | node6 -> node5[];
20 | }
21 |
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/src/test/resources/com/rtg/assembler/resources/graph-to-plot-palindrome.txt:
--------------------------------------------------------------------------------
1 | digraph contigGraph {
2 | graph [rankdir=LR, ratio=fill]
3 | node0 [label="-2\n5 3"];
4 | node1 [label="+1\n4 2", color=red, shape=box];
5 | node2 [label="+3\n6 4"];
6 | node0 -> node1[color=red];
7 | node0 -> node2[color=red];
8 | node1 -> node0[color=red];
9 | node2 -> node0[color=red];
10 | }
11 |
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/src/test/resources/com/rtg/blacklist/resources/blacklist.txt:
--------------------------------------------------------------------------------
1 | A 5
2 | C 3
3 | G 2
4 | T 3
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/blacklist/resources/histogram.txt:
--------------------------------------------------------------------------------
1 | 2 1
2 | 3 2
3 | 5 1
4 |
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/src/test/resources/com/rtg/calibrate/resources/reference.txt:
--------------------------------------------------------------------------------
1 | #
2 | version 1
3 |
4 | # Unless otherwise specified, assume diploid linear. Well-formed chromosomes should be explicitly listed
5 | # separately so this applies primarily to unplaced contigs and decoy sequences
6 | either def diploid linear
7 |
8 | # List the autosomal chromosomes explicitly. These are used to help determine "normal" coverage levels
9 | # during mapping and variant calling
10 | either seq seq1 diploid linear
11 | either seq seq2 diploid linear
12 | either seq seq5 diploid linear
13 | either seq seq6 diploid linear
14 | either seq seq7 diploid linear
15 | either seq seq8 diploid linear
16 |
17 | # Define how the male and female get the X and Y chromosomes
18 | male seq seq3 haploid linear seq4
19 | male seq seq4 haploid linear seq3
20 | female seq seq3 diploid linear
21 | female seq seq4 none linear
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/calibrate/resources/test.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build c27615f (2011-10-27), calibrate v3.0
2 | @del:some_reads 0 49 0 1
3 | @ins:some_reads 0 64 3 0 0 0 1
4 | @mnp:some_reads 0 6782 452 65 15 2 1
5 | @nh:some_reads 0 7978
6 | @sequence 1000 seq0
7 | @sequence 1000 seq1
8 | @sequence 1100 seq2
9 | @sequence 1010 seq3
10 | @sequence 1001 seq4
11 | @sequence 1010 seq5
12 | @sequence 1011 seq6
13 | @sequence 1110 seq7
14 | @sequence 1010 seq8
15 | @covar readgroup basequality sequence equal diff ins del
16 | some_reads 20 seq0 310001 3011 15 24
17 | some_reads 20 seq1 320010 3021 15 24
18 | some_reads 20 seq2 290100 3011 15 24
19 | some_reads 20 seq3 151000 1521 7 12
20 | some_reads 20 seq4 150002 1521 6 12
21 | some_reads 20 seq5 295020 3021 15 24
22 | some_reads 20 seq6 300200 3011 15 24
23 | some_reads 20 seq7 300100 3021 15 24
24 | some_reads 20 seq8 310083 3011 15 24
25 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska1-empty.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=2
3 | set name=1234 length=23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska1-overlap3.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=2
3 | set name=1234 length=23
4 | readCall index=0 id=5
5 | hash=00000000:00000000:00000000:00000000:00110011:00111001:11010101:01001010
6 | readCall index=1 id=5
7 | hash=00000000:00000000:00000000:00000000:00011001:10011001:01010101:01010100
8 | templateCall position=10 index=1
9 | hash=00000000:00000000:00000000:00000000:00011001:10011001:01010101:01010100
10 | templateCall position=10 index=0
11 | hash=00000000:00000000:00000000:00000000:00110011:00111001:11010101:01001010
12 | templateCall position=10 index=0
13 | hash=00000000:00000000:00000000:00000000:00100110:01101001:10101010:10101010
14 | templateCall position=10 index=0
15 | hash=00000000:00000000:00000000:00000000:00001100:11001001:11010101:01001010
16 | done
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska1-overlap4.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=2
3 | set name=1234 length=23
4 | readCall index=0 id=5
5 | hash=00000000:00000000:00000000:00000000:00110011:00111100:11010101:01010101
6 | readCall index=1 id=5
7 | hash=00000000:00000000:00000000:00000000:00001100:11001100:10101010:10101000
8 | templateCall position=10 index=1
9 | hash=00000000:00000000:00000000:00000000:00001100:11001100:10101010:10101000
10 | templateCall position=10 index=0
11 | hash=00000000:00000000:00000000:00000000:00111001:10011100:11101010:10110101
12 | templateCall position=10 index=0
13 | hash=00000000:00000000:00000000:00000000:00110011:00111100:11010101:01010101
14 | templateCall position=10 index=0
15 | hash=00000000:00000000:00000000:00000000:00100110:01101100:10101010:10110101
16 | done
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska1-test2.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=2
3 | set name=1234 length=23
4 | readCall index=0 id=5
5 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111111
6 | readCall index=1 id=5
7 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111100
8 | templateCall position=10 index=1
9 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111100
10 | templateCall position=10 index=0
11 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111111
12 | templateCall position=10 index=0
13 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111111
14 | templateCall position=10 index=0
15 | hash=00000000:00000000:00000000:00000000:00111111:11111111:11111111:11111111
16 | done
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska1-test3.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=2
3 | set name=1234 length=23
4 | readCall index=0 id=5
5 | hash=00000000:00000000:00000000:00000000:00111111:11111111:10000000:00000000
6 | readCall index=1 id=5
7 | hash=00000000:00000000:00000000:00000000:00111111:11111111:00000000:00000000
8 | templateCall position=10 index=1
9 | hash=00000000:00000000:00000000:00000000:00111111:11111111:00000000:00000000
10 | templateCall position=10 index=0
11 | hash=00000000:00000000:00000000:00000000:00111111:11111111:10000000:00000000
12 | templateCall position=10 index=0
13 | hash=00000000:00000000:00000000:00000000:00111111:11111111:10000000:00000000
14 | templateCall position=10 index=0
15 | hash=00000000:00000000:00000000:00000000:00111111:11111111:10000000:00000000
16 | done
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska11-empty.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=3
3 | set name=1234 length=23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maska15-empty.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=15 e=0
2 | number windows=7
3 | set name=1234 length=23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maskw18-empty.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=18 e=0
2 | number windows=3
3 | set name=1234 length=23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cg2maskw18a1-empty.txt:
--------------------------------------------------------------------------------
1 | CG2 l=29 w=18 e=0
2 | number windows=4
3 | set name=1234 length=23
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/hash/ngs/instances/resources/cgmaska15testEmpty.txt:
--------------------------------------------------------------------------------
1 | CG l=35 w=18 a=1.5
2 | number windows=6
3 | set name=1234 length=23
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/resources/Size1ToStringtrue:
--------------------------------------------------------------------------------
1 | IndexImplementation
2 | Hash Bits=16
3 | Initial Number of hashes=1
4 | Number of hash codes=1
5 | Memory Usage bytes length
6 | 2 1 Hash
7 | 4 1 Value
8 | 6 6 Initial Position
9 | 4 16 Bit vector
10 | 16 Total bytes
11 |
12 | Hash counts 0 1 2
13 | 1 1 1
14 | Bucket counts 0 1 2
15 | 1 1 1
16 |
17 | Hash Value
18 | [0] 0 0
19 |
20 | Frozen
21 | Performance statistics not available.
22 | Initial position
23 | pointer bits=2
24 | shift bits=14
25 | length=6
26 | Index [6]
27 | [0] 0, 1, 1, 1, 1, 1
28 |
29 |
30 | Bit vector
31 | HashBitVector bits=16 vectorBits=4 shift=12
32 | BitVector[16]
33 | [0] 1000000000 000000
34 |
35 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/resources/ToStringEmpty1false:
--------------------------------------------------------------------------------
1 | IndexImplementation
2 | Hash Bits=16
3 | Initial Number of hashes=0
4 | Number of hash codes=0
5 | Memory Usage bytes length
6 | 20 10 Hash
7 | 40 10 Value
8 | 10 10 Initial Position
9 | 32 256 Bit vector
10 | 102 Total bytes
11 |
12 | Hash counts 0 1 2
13 | 0 0 0
14 | Bucket counts 0 1 2
15 | 0 0 0
16 | Melted
17 |
18 | Memory Usage bytes length
19 | 20 10 Hash
20 | 40 10 Value
21 | 10 10 Initial Position
22 | 32 256 Bit vector
23 | 102 Total bytes
24 |
25 | Hash counts 0 1 2
26 | 0 0 0
27 | Bucket counts 0 1 2
28 | 0 0 0
29 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/resources/ToStringEmpty1true:
--------------------------------------------------------------------------------
1 | IndexImplementation
2 | Hash Bits=16
3 | Initial Number of hashes=0
4 | Number of hash codes=0
5 | Memory Usage bytes length
6 | 20 10 Hash
7 | 40 10 Value
8 | 10 10 Initial Position
9 | 32 256 Bit vector
10 | 102 Total bytes
11 |
12 | Hash counts 0 1 2
13 | 0 0 0
14 | Bucket counts 0 1 2
15 | 0 0 0
16 | Gaseous
17 |
18 | Memory Usage bytes length
19 | 20 10 Hash
20 | 40 10 Value
21 | 10 10 Initial Position
22 | 32 256 Bit vector
23 | 102 Total bytes
24 |
25 | Hash counts 0 1 2
26 | 0 0 0
27 | Bucket counts 0 1 2
28 | 0 0 0
29 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/index/resources/ToStringEmpty2true:
--------------------------------------------------------------------------------
1 | IndexImplementation
2 | Hash Bits=16
3 | Initial Number of hashes=0
4 | Number of hash codes=0
5 | Memory Usage bytes length
6 | 20 10 Hash
7 | 40 10 Value
8 | 10 10 Initial Position
9 | 32 256 Bit vector
10 | 102 Total bytes
11 |
12 | Hash counts 0 1 2
13 | 0 0 0
14 | Bucket counts 0 1 2
15 | 0 0 0
16 | Frozen
17 | Performance statistics not available.
18 | Initial position
19 | pointer bits=3
20 | shift bits=13
21 | length=10
22 | Index [10]
23 |
24 |
25 | Bit vector
26 | HashBitVector bits=16 vectorBits=8 shift=8
27 | BitVector[256]
28 | [0] 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000
29 | [100] 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000
30 | [200] 0000000000 0000000000 0000000000 0000000000 0000000000 000000
31 |
32 | Performance statistics not available.
33 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/metagenomics/resources/constructacomplicated2:
--------------------------------------------------------------------------------
1 | Total genomes:7
2 | Total blocks:2
3 | No hits:1
4 | block size:2 times:1
5 | block size:4 times:1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/metagenomics/resources/empty:
--------------------------------------------------------------------------------
1 | Total genomes:2
2 | Total blocks:0
3 | No hits:2
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/metagenomics/resources/fragstats:
--------------------------------------------------------------------------------
1 | Total genomes:7
2 | Total blocks:3
3 | No hits:0
4 | block size:2 times:2
5 | block size:3 times:1
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/metagenomics/resources/taxonomy.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 110662 1129 species Synechococcus sp. CC9605
10 | 316278 1129 species Synechococcus sp. RCC307
11 | 316279 1129 species Synechococcus sp. CC9902
12 | 321327 1129 species Synechococcus sp. JA-3-3Ab
13 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
14 | 1142 1118 genus Synechocystis
15 | 1148 1142 species Synechocystis sp. PCC 6803
16 | 43988 1118 genus Cyanothece
17 | 41431 43988 species Cyanothece sp. PCC 8801
18 | 43989 43988 species Cyanothece sp. ATCC 51142
19 | 65393 43988 species Cyanothece sp. PCC 7424
20 | 395961 43988 species Cyanothece sp. PCC 7425
21 | 395962 43988 species Cyanothece sp. PCC 8802
22 | 497965 43988 species Cyanothece sp. PCC 7822
23 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/metagenomics/resources/taxonomy_remove.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 110662 1129 species Synechococcus sp. CC9605
10 | 316278 1129 species Synechococcus sp. RCC307
11 | 316279 1129 species Synechococcus sp. CC9902
12 | 321327 1129 species Synechococcus sp. JA-3-3Ab
13 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
14 | 1142 1118 genus Synechocystis
15 | 1148 1142 species Synechocystis sp. PCC 6803
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ml/resources/testBaggedVersion_1:
--------------------------------------------------------------------------------
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/src/test/resources/com/rtg/ml/resources/testBinaryTreeVersion_1:
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/src/test/resources/com/rtg/ngs/longread/resources/longreadtask-testsingleend.txt:
--------------------------------------------------------------------------------
1 | 0 256 test 1 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
2 | 0 256 test 36 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
3 | 0 256 test 71 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
4 | 0 256 test 106 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
5 | 0 256 test 141 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/longread/resources/longreadtask-testsingleendmtrev.txt:
--------------------------------------------------------------------------------
1 | 0 272 test 1 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
2 | 0 272 test 36 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
3 | 0 272 test 71 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
4 | 0 272 test 106 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
5 | 0 272 test 141 0 70= * 0 0 ACGTACGTACGTACGTACGTACGTACGTACGTACGACGTACGTACGTACGTACGTACGTACGTACGTACG * AS:i:0 NM:i:0 IH:i:5 NH:i:5
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/longread/resources/testOffEdge2.txt:
--------------------------------------------------------------------------------
1 | read1 256 simulatedSequence1 1 0 60S40= * 0 0 CATCGTTAAAACAAAGGACGCCAAAAGTTCCTGTGCGTTGATCCTGTTGCGGCGAATACACTTGCTTTGCCTGGCGTGGGACAACCCATATCGGAAATGC * AS:i:0 NM:i:0 IH:i:2 NH:i:2
2 | read3 0 simulatedSequence1 1 37 5S95= * 0 0 GGGGGCTTGCTTTGCCTGGCGTGGGACAACCCATATCGGAAATGCAACACTAAGAGGTGTAGATATTACGTCCCATTTACTTCATGGGCTACGTCCGAAC * AS:i:0 NM:i:0 IH:i:1 NH:i:1
3 | read2 0 simulatedSequence1 306 37 95=5S * 0 0 TACGATCGGGAGCTCACGTCACATCAGCGATGTCTCATCGTTAAAACAAAGGACGCCAAAAGTTCCTGTGCGTTGATCCTGTTGCGGCGAATACAGGGGG * AS:i:0 NM:i:0 IH:i:1 NH:i:1
4 | read1 256 simulatedSequence1 341 0 60=40S * 0 0 CATCGTTAAAACAAAGGACGCCAAAAGTTCCTGTGCGTTGATCCTGTTGCGGCGAATACACTTGCTTTGCCTGGCGTGGGACAACCCATATCGGAAATGC * AS:i:0 NM:i:0 IH:i:2 NH:i:2
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/longread/resources/testOffEdge2paired.txt:
--------------------------------------------------------------------------------
1 | read1 99 simulatedSequence1 1 55 5S95= = 306 410 GGGGGCTTGCTTTGCCTGGCGTGGGACAACCCATATCGGAAATGCAACACTAAGAGGTGTAGATATTACGTCCCATTTACTTCATGGGCTACGTCCGAAC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | read1 147 simulatedSequence1 306 55 95=5S = 1 -410 TACGATCGGGAGCTCACGTCACATCAGCGATGTCTCATCGTTAAAACAAAGGACGCCAAAAGTTCCTGTGCGTTGATCCTGTTGCGGCGAATACAGGGGG * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/dawtt-unmapped:
--------------------------------------------------------------------------------
1 | 0 133 * 0 0 * * 0 0 GGAGGCCCTCTTGTCTTGCA * XC:A:A
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/dawtt-unmated:
--------------------------------------------------------------------------------
1 | 0 73 t 1 37 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 IH:i:1 NH:i:1
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/mapFlagsExtended.txt:
--------------------------------------------------------------------------------
1 | Usage: rtg map [OPTION]... -o DIR -t SDF -i SDF
2 | [OPTION]... -o DIR -t SDF -l SDF -r SDF
3 |
4 | Optional flags:
5 | --Xbam write BAM instead of SAM
6 | --Xexclude do not write repeated reads
7 | --Xhelp print help on extended command-line flag usage
8 | --Xmask=STRING mask class name
9 | --Xscoreindel=INT set max score indel for topn threshold
10 | (Default is 7)
11 | --Xtemp-files=DIR directory for temporary SAM files
12 | --Xtemp-files-gzipped=BOOL gzip temporary SAM files (Default is false)
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/mapf-endtoend-alignments:
--------------------------------------------------------------------------------
1 | 0 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1 XM:i:1
2 | 1 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6 XM:i:1
3 | 2 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6 XM:i:1
4 | 3 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1 XM:i:1
5 | 4 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6
6 | 6 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1
7 | 0 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0 XM:i:1
8 | 1 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0 XM:i:1
9 | 2 145 t 37 255 13=1X2=7X7= * 0 0 TCAGCCCACACTGCTCTTTTTAAAAAGGGG * AS:i:8 NM:i:8 XM:i:1
10 | 3 145 t 37 255 13=1X2=7X7= * 0 0 TCAGCCCACACTGCTCTTTTTAAAAAGGGG * AS:i:8 NM:i:8 XM:i:1
11 | 7 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/mapf-endtoend-unmapped:
--------------------------------------------------------------------------------
1 | 4 133 * 0 0 * * 0 0 AGAGTGCTGTGGGAGCTTTAGAACAGTTGCAG * XC:A:D
2 | 5 77 * 0 0 * * 0 0 CTGCAACTGTTCTAAAGCTCCCACAGCACTCT * XC:A:D
3 | 5 141 * 0 0 * * 0 0 CCCCTTTTTAAAAAGAGCAGTGTGGGCTGA * XC:A:D
4 | 6 133 * 0 0 * * 0 0 AGAGTGCTGTGGGAGCTTTAGAACAGTTGCAG * XC:A:D
5 | 7 69 * 0 0 * * 0 0 CTGCAACTGTTCTAAAGCTCCCACAGCACTCT * XC:A:D
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg.txt:
--------------------------------------------------------------------------------
1 | 0 67 genome 1 255 4= = 9 8 AGGT 3456 AS:i:0 NM:i:0 XA:i:0 IH:i:1
2 | 0 131 genome 9 255 4= = 1 -8 TAGC 3456 AS:i:0 NM:i:0 XA:i:0 IH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg_0.txt:
--------------------------------------------------------------------------------
1 | 0 67 genome 1 55 25=6N10= = 53 93 TGACTGCATGCATGCACATTGCTACATTGCTATGC 34563456345634563456345634563456345 AS:i:0 XU:Z:25=6N10= XA:i:0 IH:i:1 NH:i:1
2 | 0 131 genome 53 55 10=6N25= = 1 -93 GCCTAAGGGCCTAAGGGATACAAAGATACAAAGCC 34563456345634563456345634563456345 AS:i:0 XU:Z:10=6N25= XA:i:0 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg_1.txt:
--------------------------------------------------------------------------------
1 | 0 179 genome 1 55 25=6N10= = 53 93 GGCTTTGTATCTTTGTATCCCTTAGGCCCTTAGGC 54365436543654365436543654365436543 AS:i:0 XU:Z:25=6N10= XA:i:0 IH:i:1 NH:i:1
2 | 0 115 genome 53 55 10=6N25= = 1 -93 GCATAGCAATGTAGCAATGTGCATGCATGCAGTCA 54365436543654365436543654365436543 AS:i:0 XU:Z:10=6N25= XA:i:0 IH:i:1 NH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg_2.txt:
--------------------------------------------------------------------------------
1 | 0 67 genome 1 55 18=2X5=6N10= = 53 93 TGACTGCATGCATGCACAAAGCTACATTGCTATGC 34563456345634563456345634563456345 AS:i:2 XU:Z:18=2X5=6N10= XR:Z:AA XA:i:4 IH:i:1 NH:i:1
2 | 0 131 genome 53 55 10=6N5=2X18= = 1 -93 GCCTAAGGGCCTAAGAAATACAAAGATACAAAGCC 34563456345634563456345634563456345 AS:i:2 XU:Z:10=6N5=2X18= XR:Z:AA XA:i:4 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg_rev.txt:
--------------------------------------------------------------------------------
1 | 0 179 genome 1 255 4= = 9 8 GCTA 6543 AS:i:0 NM:i:0 XA:i:0 IH:i:1
2 | 0 115 genome 9 255 4= = 1 -8 ACCT 6543 AS:i:0 NM:i:0 XA:i:0 IH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngscg_side.txt:
--------------------------------------------------------------------------------
1 | 0 115 genome 1 255 4= = 9 8 ACCT 6543 AS:i:0 NM:i:0 XA:i:0 IH:i:1
2 | 0 179 genome 9 255 4= = 1 -8 GCTA 6543 AS:i:0 NM:i:0 XA:i:0 IH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngspe.txt:
--------------------------------------------------------------------------------
1 | 0 99 genome 1 55 4= = 9 12 AGGT * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | 0 147 genome 9 55 4= = 1 -12 GCTA * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngspe_ns.txt:
--------------------------------------------------------------------------------
1 | 0 99 genome 1 55 1X3= = 9 12 NGGT * AS:i:0 NM:i:1 XA:i:0 IH:i:1 NH:i:1
2 | 0 147 genome 9 55 1X1=1X1= = 1 -12 NCNA * AS:i:0 NM:i:2 XA:i:0 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngspe_rev.txt:
--------------------------------------------------------------------------------
1 | 0 163 genome 1 55 4= = 9 12 TAGC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | 0 83 genome 9 55 4= = 1 -12 ACCT * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/ngspe_side.txt:
--------------------------------------------------------------------------------
1 | 0 83 genome 1 55 4= = 9 12 ACCT * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | 0 163 genome 9 55 4= = 1 -12 TAGC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 |
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/no-sex-ref.sam:
--------------------------------------------------------------------------------
1 | 0 99 genome1 1 55 4= = 9 12 AGGT * AS:i:0 NM:i:0 XA:i:0 RG:Z:READGROUP1 IH:i:1 NH:i:1
2 | 0 147 genome1 9 55 4= = 1 -12 GCTA * AS:i:0 NM:i:0 XA:i:0 RG:Z:READGROUP1 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/peops_tc.txt:
--------------------------------------------------------------------------------
1 | 0 147 t 1 255 20M = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
2 | 0 99 t 1 255 20M = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
3 | 0 147 t 1 255 20M = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
4 | 0 99 t 1 255 20M = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
5 | 0 147 t 1 255 20M = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
6 | 0 99 t 1 255 20M = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
7 | 0 147 t 1 255 20M = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
8 | 0 99 t 1 255 20M = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/proteinalignresults.txt:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-position %identity template-protein read-protein match alignment-score bit-score e-score
2 | templateName +1 0 1 100 kwrknrkskknq kwrknrkskknq kwrknrkskknq -67 30.4 1.5E-8
3 | templateName -1 4 1 100 kwrknrkskknq kwrknrkskknq kwrknrkskknq -67 30.4 1.5E-8
4 | templateName -2 6 2 100 wrknrkskknq wrknrkskknq wrknrkskknq -62 28.5 5.8E-8
5 | templateName +2 2 2 100 wrknrkskknq wrknrkskknq wrknrkskknq -62 28.5 5.8E-8
6 | templateName -1 7 2 100 wrknrkskknqr wrknrkskknqr wrknrkskknqr -67 30.4 1.5E-8
7 | templateName -3 5 2 100 wrknrkskknq wrknrkskknq wrknrkskknq -62 28.5 5.8E-8
8 | templateName +1 3 2 100 wrknrkskknqr wrknrkskknqr wrknrkskknqr -67 30.4 1.5E-8
9 | templateName +3 1 2 100 wrknrkskknq wrknrkskknq wrknrkskknq -62 28.5 5.8E-8
10 | templateName +3 8 10 100 knqrnynhdaa knqrnynhdaa knqrnynhdaa -62 28.5 5.8E-8
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/proteinalignresults_one_sub.txt:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-position %identity template-protein read-protein match alignment-score bit-score e-score
2 | templateName -1 4 1 100 kwrknrkskknq kwrknrkskknq kwrknrkskknq -67 30.4 1.5E-8
3 | templateName +1 0 1 91 kwrknrkskknq kwrknrqskknq kwrknr+skknq -63 28.9 4.5E-8
4 | templateName -3 5 2 90 wrknrkskknq crknrkskknq rknrkskknq -49 23.5 1.9E-6
5 | templateName -2 6 2 90 wrknrkskknq wpknrkskknq w knrkskknq -55 25.8 3.8E-7
6 | templateName -1 7 2 91 wrknrkskknqr wrnnrkskknqr wr nrkskknqr -62 28.5 5.8E-8
7 | templateName +3 1 2 90 wrknrkskknq wrkdrkskknq wrk+rkskknq -57 26.6 2.2E-7
8 | templateName +1 3 2 91 wrknrkskknqr wrknrkstknqr wrknrks knqr -61 28.1 7.6E-8
9 | templateName +3 8 10 100 knqrnynhdaa knqrnynhdaa knqrnynhdaa -62 28.5 5.8E-8
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/rammap.txt:
--------------------------------------------------------------------------------
1 | 0 67 template 1 255 150= = 215 214 CATAATGACGGCTGGGCTACTGGACATATGTACGCGGTCTCCGGGAACAAGCAGCATGGAGTTTCCCCTGACGTATCGGTGATGTGATTGACATAACGATCAGATTTCAAAAGGAGTTCGCGCATTCCAGAGGACGCTATGCACGTTGGT * AS:i:0 NM:i:0 XA:i:0 IH:i:1
2 | 0 131 template 215 255 150= = 1 -214 ACAAGTACAAGGAGGCGGACTATCGCACTCCAAGTTAGCCGGTTTGAACATAGAAGCTCTCCCGAGCTCGCGCTATCCATCGATGTGGATGAGGAGTCAGCAATAAACTCGCTGATAGCCTGATCCAGTCAACTTTATCCATGTCAGGCA * AS:i:0 NM:i:0 XA:i:0 IH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/srsf-unmated:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:unsorted
2 | @SQ SN:chr20 LN:62435964
3 | 1 65 chr20 28833 255 4M5M * 0 0 AGCT <<<< AS:i:3 NM:i:1
4 | 3 129 chr20 28734 255 35M * 0 0 ACCT <<<< AS:i:0 NM:i:0
5 | 3 129 chr20 28834 255 35M * 0 0 ACCT <<<< AS:i:1 NM:i:0
6 | 20 65 chr20 28934 255 35M * 0 0 ACCT <<<< AS:i:4 NM:i:0
7 | 66 65 chr20 28934 255 35M * 0 0 ACCT <<<< AS:i:4 NM:i:0
8 | 67 129 chr20 28934 255 35M * 0 0 ACCT <<<< AS:i:4 NM:i:0
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/svprep-left.fasta:
--------------------------------------------------------------------------------
1 | >read0/0/0/simulatedSequence1/65/F/20.
2 | GTGGGCGGCCACTAGTTGAT
3 | >read1/0/0/simulatedSequence1/24/F/20.
4 | TAACGCGCAAAAGGACCCTG
5 | >read2/0/0/simulatedSequence1/26/R/20.
6 | CTCAGGGTCCTTTTGCGCGT
7 | >read3/0/0/simulatedSequence1/9/R/20.
8 | CGTTATCCTATGCACAAGCT
9 | >read4/0/0/simulatedSequence1/46/F/20.
10 | ACCTACCACCCGGGGGCCTG
11 | >read5/0/0/simulatedSequence1/22/R/20.
12 | GGGTCCTTTTGCGCGTTATC
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/svprep-right.fasta:
--------------------------------------------------------------------------------
1 | >read0/0/0/simulatedSequence1/72/R/20.
2 | TTCTACTATCAACTAGTGGC
3 | >read1/0/0/simulatedSequence1/30/R/20.
4 | AGGTCTCAGGGTCCTTTTGC
5 | >read2/0/0/simulatedSequence1/24/F/20.
6 | TAACGCGCAAAAGGACCCTG
7 | >read3/0/0/simulatedSequence1/4/F/20.
8 | CTGATAGCTTGTGCATAGGA
9 | >read4/0/0/simulatedSequence1/56/R/20.
10 | TGTTTTCCCACAGGCCCCCG
11 | >read5/0/0/simulatedSequence1/19/F/20.
12 | TAGGATAACGCGCAAAAGGA
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/svprep-template.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | AGACTGATAGCTTGTGCATAGGATAACGCGCAAAAGGACCCTGAGACCTACCACCCGGGGGCCTGTGGGCGGCCACTAGTTGATAGTAGAACGGGACGGT
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeop_un.txt:
--------------------------------------------------------------------------------
1 | 1 73 template 1 255 8M * 0 0 ACTAGCAG * AS:i:1 NM:i:1
2 | 2 137 template 1 255 8M * 0 0 ACTAGCAG * AS:i:1 NM:i:1
3 | 1 141 * 0 0 * * 0 0 ACTAGCAG *
4 | 2 77 * 0 0 * * 0 0 ACACTTGG *
5 |
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeop_unmapped.txt:
--------------------------------------------------------------------------------
1 | 1 77 * 0 0 * * 0 0 ACTAGCAG *
2 | 1 141 * 0 0 * * 0 0 ACTAGCAG *
3 | 2 77 * 0 0 * * 0 0 ACACTTGG *
4 | 2 141 * 0 0 * * 0 0 ACTAGCAG *
5 |
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeops_pe_unfiltered.txt:
--------------------------------------------------------------------------------
1 | 0 145 t 1 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
2 | 0 65 t 1 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeops_pe_unfiltered_sortedAppend.txt:
--------------------------------------------------------------------------------
1 | 0 145 t 1 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
2 | 0 65 t 1 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
3 | 1 145 t 21 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
4 | 1 65 t 21 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
5 | 2 145 t 41 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
6 | 2 65 t 41 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XM:i:1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeops_sortedAppend.txt:
--------------------------------------------------------------------------------
1 | 0 147 t 1 55 20= = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | 0 99 t 1 55 20= = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 | 1 147 t 21 55 20= = 21 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
4 | 1 99 t 21 55 20= = 21 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
5 | 2 147 t 41 55 20= = 41 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
6 | 2 99 t 41 55 20= = 41 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/tnpeops_tc.txt:
--------------------------------------------------------------------------------
1 | 0 147 t 1 55 20= = 1 -20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
2 | 0 99 t 1 55 20= = 1 20 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 XA:i:0 IH:i:1 NH:i:1
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmated-unmapped:
--------------------------------------------------------------------------------
1 | 0 133 * 0 0 * * 0 0 GGAGGCCCTCTTGTCTTGCA * XC:A:A RG:Z:RG23
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmated-unmated:
--------------------------------------------------------------------------------
1 | 0 73 t 1 37 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0 RG:Z:RG23 IH:i:1 NH:i:1
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmated-unmated-cal:
--------------------------------------------------------------------------------
1 | #CL null
2 | @nh:RG23 0 1
3 | @covar readgroup basequality sequence equal diff ins del
4 | RG23 20 t 20 0 0 0
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmated-unmated-region-cal:
--------------------------------------------------------------------------------
1 | #CL null
2 | @nh:RG23
3 | @sequence 150 t
4 | @covar readgroup basequality sequence equal diff ins del
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmatedaugment-unmapped:
--------------------------------------------------------------------------------
1 | 1 133 t 72 0 * = 29 0 CAGATGTATTGGATTTAGGG * XC:A:A RG:Z:RG23 XN:i:48
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/topnpeops-checkunmatedaugment-unmated:
--------------------------------------------------------------------------------
1 | 2 65 t 7 37 20= = 110 123 ACAAGAGGGCCTCCTTCTTT * AS:i:0 NM:i:0 RG:Z:RG23 IH:i:1 NH:i:1 XM:i:0 XN:i:129
2 | 1 73 t 29 37 20= * 0 0 GTGATGCTGATCGACTCACC * AS:i:0 NM:i:0 RG:Z:RG23 IH:i:1 NH:i:1
3 | 2 129 t 110 37 20= = 7 -123 AATCGATGGCTCGGGATCGA * AS:i:0 NM:i:0 RG:Z:RG23 IH:i:1 NH:i:1 XM:i:0 XN:i:26
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/upeops-endtoend-alignments:
--------------------------------------------------------------------------------
1 | 0 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1 XM:i:1
2 | 1 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6 XM:i:1
3 | 2 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6 XM:i:1
4 | 3 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1 XM:i:1
5 | 4 65 t 1 255 9=6X14= * 0 0 ACACACTGCGGTCTGAGAGGGCCTCCCAC * AS:i:6 NM:i:6
6 | 6 65 t 1 255 12=1D14= * 0 0 ACACACTGCAAGCAAGAGGGCCTCCC * AS:i:2 NM:i:1
7 | 0 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0 XM:i:1
8 | 1 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0 XM:i:1
9 | 2 145 t 37 255 13=1X2=7X7= * 0 0 TCAGCCCACACTGCTCTTTTTAAAAAGGGG * AS:i:8 NM:i:8 XM:i:1
10 | 3 145 t 37 255 13=1X2=7X7= * 0 0 TCAGCCCACACTGCTCTTTTTAAAAAGGGG * AS:i:8 NM:i:8 XM:i:1
11 | 7 145 t 37 255 30= * 0 0 TCAGCCCACACTGGTCGGGGGCCAAAGGGG * AS:i:0 NM:i:0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/upeops-endtoend-unmapped:
--------------------------------------------------------------------------------
1 | 4 133 * 0 0 * * 0 0 AGAGTGCTGTGGGAGCTTTAGAACAGTTGCAG * XC:A:D
2 | 5 77 * 0 0 * * 0 0 CTGCAACTGTTCTAAAGCTCCCACAGCACTCT * XC:A:D
3 | 5 141 * 0 0 * * 0 0 CCCCTTTTTAAAAAGAGCAGTGTGGGCTGA * XC:A:D
4 | 6 133 * 0 0 * * 0 0 AGAGTGCTGTGGGAGCTTTAGAACAGTTGCAG * XC:A:D
5 | 7 69 * 0 0 * * 0 0 CTGCAACTGTTCTAAAGCTCCCACAGCACTCT * XC:A:D
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/upeops-unmapped:
--------------------------------------------------------------------------------
1 | 0 133 * 0 0 * * 0 0 GGAGGCCCTCTTGTCTTGCA * XC:A:A
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/upeops-unmated:
--------------------------------------------------------------------------------
1 | 0 65 t 1 255 20= * 0 0 TGCAAGACAAGAGGGCCTCC * AS:i:0 NM:i:0
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/ngs/resources/usrf-unmated:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:unsorted
2 | @SQ SN:chr20 LN:62435964
3 | 3 393 chr20 28734 0 35M * 0 0 ACCT <<<< AS:i:0 NM:i:0 IH:i:2 NH:i:2
4 | 1 73 chr20 28833 37 4M5M * 0 0 AGCT <<<< AS:i:3 NM:i:1 IH:i:1 NH:i:1
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/mapxtestresults_partial.txt:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-start template-end template-length read-start read-end read-length template-protein read-protein alignment identical %identical positive %positive mismatches raw-score bit-score e-score
2 | templateName -1 4 1 12 22 1 36 36 kwrknrkskknq kwrknrkskknq kwrknrkskknq 12 100 12 100 0 -67 30.4 1.5e-8
3 | templateName +2 2 2 12 22 2 34 36 wrknrkskknq wrknrkskknq wrknrkskknq 11 100 11 100 0 -62 28.5 5.8e-8
4 | templateName +1 3 2 13 22 1 36 36 wrknrkskknqr wrknrkskknqr wrknrkskknqr 12 100 12 100 0 -67 30.4 1.5e-8
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-exp-unmapped.tsv:
--------------------------------------------------------------------------------
1 | #read-id reason-unmapped
2 | 2
3 | 3
4 | 4
5 | 5
6 | 6
7 | 7
8 | 8
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-exp1-alignments.tsv:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-start template-end template-length read-start read-end read-length template-protein read-protein alignment identical %identical positive %positive mismatches raw-score bit-score e-score
2 | templateName +1 0 1 12 22 1 36 36 kwrknrkskknq kwrknrkskknq kwrknrkskknq 12 100 12 100 0 -67 30.4 1.5e-8
3 | templateName +3 1 2 12 22 3 35 36 wrknrkskknq wrknrkskknq wrknrkskknq 11 100 11 100 0 -62 28.5 5.8e-8
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-exp2-alignments.tsv:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-start template-end template-length read-start read-end read-length template-protein read-protein alignment identical %identical positive %positive mismatches raw-score bit-score e-score
2 | templateName +1 0 1 12 22 1 36 36 kwrknrkskknq kwrknrkskknq kwrknrkskknq 12 100 12 100 0 -67 30.4 1.5e-8
3 | templateName +3 1 2 12 22 3 35 36 wrknrkskknq wrknrkskknq wrknrkskknq 11 100 11 100 0 -62 28.5 5.8e-8
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-no-prot-alignments.tsv:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-start template-end template-length read-start read-end read-length identical %identical positive %positive mismatches raw-score bit-score e-score
2 | templateName +1 0 1 12 22 1 36 36 12 100 12 100 0 -67 30.4 1.5e-8
3 | templateName +3 1 2 12 22 3 35 36 11 100 11 100 0 -62 28.5 5.8e-8
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-no-prot-unmapped.tsv:
--------------------------------------------------------------------------------
1 | #read-id reason-unmapped
2 | 2
3 | 3
4 | 4
5 | 5
6 | 6
7 | 7
8 | 8
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-prot-alignments.tsv:
--------------------------------------------------------------------------------
1 | #template-name frame read-id template-start template-end template-length read-start read-end read-length template-protein read-protein alignment identical %identical positive %positive mismatches raw-score bit-score e-score
2 | templateName +1 0 1 12 22 1 12 12 kwrknrkskknq kwrknrkskknq kwrknrkskknq 12 100 12 100 0 -67 30.4 1.5e-8
3 | templateName +1 1 2 13 22 1 12 12 wrknrkskknqr wrknrkskknqr wrknrkskknqr 12 100 12 100 0 -67 30.4 1.5e-8
4 | templateName +1 2 11 22 22 1 12 12 nqrnynhdaada nqrnynhdaada nqrnynhdaada 12 100 12 100 0 -67 30.4 1.5e-8
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/pop-prot-unmapped.tsv:
--------------------------------------------------------------------------------
1 | #read-id reason-unmapped
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/unmapped.tsv:
--------------------------------------------------------------------------------
1 | #read-id reason-unmapped
2 | 7
3 | 8 f
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/protein/resources/unmapped_rename.tsv:
--------------------------------------------------------------------------------
1 | #read-name reason-unmapped
2 | testRead7
3 | testRead8 f
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/expected_1.fastq:
--------------------------------------------------------------------------------
1 | @first3
2 | CTGACCCCAC
3 | +
4 | CCCFFFFFHH
5 | @first
6 | CTGACCCCAC
7 | +
8 | CCCFFFFFHH
9 | @first2
10 | CTGACCCCAC
11 | +
12 | CCCFFFFFHH
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/expected_2.fastq:
--------------------------------------------------------------------------------
1 | @first3
2 | ATTAAAAATA
3 | +
4 | EEDDEECDBD
5 | @first
6 | ATTAAAAATA
7 | +
8 | EEDDEECDBD
9 | @first2
10 | ATTAAAAATA
11 | +
12 | EEDDEECDBD
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/pair-aligner-zero-phred-del.fq:
--------------------------------------------------------------------------------
1 | @left
2 | ATGATAGATAAATCAAAGAAGCTGCTATAGGCGGTGGCTACC
3 | +
4 | KKKKKKKKKK!!!!KKKKKKKKKKKKKKKKKKKKKKKKKKKK
5 | @right
6 | GGTAGCCACCGCCTATAGCAGCTTCTTTTATCTATCAT
7 | +
8 | KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/pair-aligner-zero-phred-ins.fq:
--------------------------------------------------------------------------------
1 | @left
2 | ACGATGACGTAGATGTGTACCGTTATATGC
3 | +
4 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5 | @right
6 | GCATATAACGGTACCCACATCTACGTCATCGT
7 | +
8 | AAAAAAAAAAAAA!!AAAAAAAAAAAAAAAAA
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/petrim-e2e-probes.fragment-lengths.tsv:
--------------------------------------------------------------------------------
1 | #fragment-length count
2 | 47 1
3 | 50 1
4 | 59 1
5 | 60 1
6 | 61 1
7 | 67 1
8 | 68 1
9 | 79 1
10 | 86 1
11 | 93 1
12 | 95 1
13 | 104 1
14 | 109 2
15 | 113 1
16 | 114 1
17 | 116 2
18 | 119 1
19 | 134 1
20 | 136 1
21 | 144 1
22 | 155 1
23 | 159 1
24 | 175 1
25 | 178 1
26 | 201 1
27 | 204 1
28 | 207 1
29 | 258 1
30 | 276 1
31 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/petrim-e2e-probes.left-read-lengths.tsv:
--------------------------------------------------------------------------------
1 | #read-length count
2 | 4 1
3 | 11 3
4 | 16 1
5 | 18 1
6 | 21 1
7 | 26 1
8 | 27 1
9 | 29 1
10 | 30 3
11 | 31 1
12 | 39 1
13 | 57 1
14 | 66 1
15 | 75 1
16 | 84 1
17 | 85 1
18 | 87 1
19 | 88 1
20 | 107 1
21 | 126 1
22 | 130 1
23 | 145 1
24 | 146 1
25 | 149 2
26 | 150 15
27 | 151 6
28 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/petrim-e2e-probes.overlap-lengths.tsv:
--------------------------------------------------------------------------------
1 | #overlap-length count
2 | 25 1
3 | 33 1
4 | 40 3
5 | 43 1
6 | 45 1
7 | 46 1
8 | 49 1
9 | 55 1
10 | 56 1
11 | 58 2
12 | 59 3
13 | 67 1
14 | 85 1
15 | 94 2
16 | 96 1
17 | 100 1
18 | 103 1
19 | 112 2
20 | 113 1
21 | 121 1
22 | 126 1
23 | 135 1
24 | 141 1
25 | 146 1
26 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/petrim-e2e-probes.right-read-lengths.tsv:
--------------------------------------------------------------------------------
1 | #read-length count
2 | 17 1
3 | 20 1
4 | 29 1
5 | 30 1
6 | 31 1
7 | 37 1
8 | 38 1
9 | 49 1
10 | 56 1
11 | 63 1
12 | 65 1
13 | 74 1
14 | 79 2
15 | 83 2
16 | 84 1
17 | 86 1
18 | 89 1
19 | 104 1
20 | 106 1
21 | 114 1
22 | 125 1
23 | 129 1
24 | 145 1
25 | 147 1
26 | 148 1
27 | 149 1
28 | 150 6
29 | 151 16
30 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/petrim-e2e-probes.summary.txt:
--------------------------------------------------------------------------------
1 | Total input pairs 50
2 | No alignment 9 18.00%
3 | Poor alignment 10 20.00%
4 | Overlapping 31 62.00%
5 | R1 read through 10 20.00%
6 | R2 read through 1 2.00%
7 | R1 read into R2 probe 15 30.00%
8 | R2 read into R1 probe 25 50.00%
9 | Total output pairs 50 100.00%
10 |
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/softclip2fastq_1.fq:
--------------------------------------------------------------------------------
1 | @1 g1:3/0/50S30M/start
2 | ATCGACTGATCGACTGATCGACTGATCGACTGATCGACTGAAAATTTTCC
3 | +
4 | AABBAABBAABBAABBAABBAABB````````````````AAAAAAAABB
5 | @2 g1:3/16/40M40S/end
6 | AAAATTTTCCCCGGGGAAAATTTTCCCCGGGGAAAATTTT
7 | +
8 | ````````````````CCCCCCCCBBBBBBBBAAAAAAAA
9 | @4_1 g1:3/65/50S30M/start
10 | ATCGACTGATCGACTGATCGACTGATCGACTGATCGACTGAAAATTTTCC
11 | +
12 | AABBAABBAABBAABBAABBAABB````````````````AAAAAAAABB
13 | @5_2 g1:3/129/40M40S/end
14 | AAAATTTTCCCCGGGGAAAATTTTCCCCGGGGAAAATTTT
15 | +
16 | ````````````````CCCCCCCCBBBBBBBBAAAAAAAA
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/reader/resources/softclip2fastq_2.fq:
--------------------------------------------------------------------------------
1 | @1 g1:3/0/50S30M/end
2 | AAAATTTTCCCCGGGGAAAATTTTCCCCGG
3 | +
4 | ````````````````CCCCCCCCBBBBBB
5 | @2 g1:3/16/40M40S/start
6 | ATCGACTGATCGACTGATCGACTGATCGACTGATCGACTG
7 | +
8 | AABBAABBAABBAABBAABBAABB````````````````
9 | @4_1 g1:3/65/50S30M/end
10 | AAAATTTTCCCCGGGGAAAATTTTCCCCGG
11 | +
12 | ````````````````CCCCCCCCBBBBBB
13 | @5_2 g1:3/129/40M40S/start
14 | ATCGACTGATCGACTGATCGACTGATCGACTGATCGACTG
15 | +
16 | AABBAABBAABBAABBAABBAABB````````````````
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/report/resources/test.html:
--------------------------------------------------------------------------------
1 | test
2 | __REPLACE__ before __SECOND_REPLACEMENT__ after
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/expected.cigar_ops.tsv:
--------------------------------------------------------------------------------
1 | #strand length X I D S
2 | + 1 0 0 0 0
3 | - 1 0 0 0 0
4 | + 2 0 0 0 0
5 | - 2 0 0 0 0
6 | + 3 0 0 0 0
7 | - 3 0 0 0 0
8 | + 4 0 0 0 0
9 | - 4 0 0 0 0
10 | + 5 0 0 0 0
11 | - 5 0 0 0 0
12 | + 6 0 0 0 0
13 | - 6 0 0 0 0
14 | + 7 0 0 0 0
15 | - 7 0 0 0 0
16 | + 8 0 0 0 0
17 | - 8 0 0 0 0
18 | + 9 0 0 0 0
19 | - 9 0 0 0 0
20 | + 10 0 0 0 0
21 | - 10 0 0 0 0
22 | + 11 0 0 0 0
23 | - 11 0 0 0 0
24 | + 12 0 0 0 0
25 | - 12 0 0 0 0
26 | + 13 0 0 0 0
27 | - 13 0 0 0 0
28 | + 14 0 0 0 0
29 | - 14 0 0 0 0
30 | + 15 0 0 0 0
31 | - 15 0 0 0 0
32 | + 16 0 0 0 0
33 | - 16 0 0 0 0
34 | + 17 0 0 0 0
35 | - 17 0 0 0 0
36 | + 18 0 0 0 0
37 | - 18 0 0 0 0
38 | + 19 0 0 0 0
39 | - 19 0 0 0 0
40 | + 20+ 0 0 0 0
41 | - 20+ 0 0 0 0
42 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/expected.on_target.tsv:
--------------------------------------------------------------------------------
1 | #group total mapped on_target fraction_of_total fraction_of_mapped
2 | Reads 19 19 18 0.9474 0.9474
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/expected.out.txt:
--------------------------------------------------------------------------------
1 | group total mapped on target fraction of total fraction of mapped
2 | ----------------------------------------------------------------------
3 | Reads 19 19 18 0.9474 0.9474
4 |
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/expected.probes.tsv:
--------------------------------------------------------------------------------
1 | #delta + -
2 | -3 0 0
3 | -2 0 0
4 | -1 3 3
5 | 0 3 3
6 | 1 3 3
7 | 2 0 0
8 | 3 0 0
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/expected.summary.tsv:
--------------------------------------------------------------------------------
1 | #strand alignments stripped fraction nt/read
2 | + 10 9 0.9000 43.3
3 | - 9 9 1.0000 40.0
4 | Both 19 18 0.9474 41.7
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/negative_strand_probe_counts.bed:
--------------------------------------------------------------------------------
1 | #chrom start end name score strand count
2 | seq 1000 1040 probe_name_2 848 - 3
3 | seq 2000 2060 probe_name_3 880 - 3
4 | seq 3000 3020 probe_name_4 695 - 3
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/positive_strand_probe_counts.bed:
--------------------------------------------------------------------------------
1 | #chrom start end name score strand count
2 | seq 700 750 probe_name_1 741 + 3
3 | seq 4000 4030 probe_name_5 576 + 3
4 | seq 5000 5050 probe_name_6 880 + 3
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/probe/resources/probes.bed:
--------------------------------------------------------------------------------
1 | seq 700 750 probe_name_1 741 +
2 | seq 1000 1040 probe_name_2 848 -
3 | seq 2000 2060 probe_name_3 880 -
4 | seq 3000 3020 probe_name_4 695 -
5 | seq 4000 4030 probe_name_5 576 +
6 | seq 5000 5050 probe_name_6 880 +
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/badReadBase.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:simulatedSequence2 LN:100000
3 | @RG ID:a PL:ILLUMINA SM:a
4 | read1 163 simulatedSequence2 1 255 5= = 630 239 AARAA +++++ AS:i:1 NM:i:1 MQ:i:255 XA:i:2 IH:i:1 RG:Z:a
5 | read2 163 simulatedSequence2 2 255 5= = 630 239 AAAAA +++++ AS:i:1 NM:i:1 MQ:i:255 XA:i:2 IH:i:1 RG:Z:a
6 | read3 163 simulatedSequence2 3 255 5= = 630 239 AARAA +++++ AS:i:1 NM:i:1 MQ:i:255 XA:i:2 IH:i:1 RG:Z:a
7 | read4 163 simulatedSequence2 4 255 5= = 630 239 AAAAA +++++ AS:i:1 NM:i:1 MQ:i:255 XA:i:2 IH:i:1 RG:Z:a
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/sfm-rmdup-stdout:
--------------------------------------------------------------------------------
1 | SAM records read: 24
2 | SAM records written: 18
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/simplestdout:
--------------------------------------------------------------------------------
1 | 0 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 IH:i:1
2 | 1 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 IH:i:2
3 | 0 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 RG:Z:RG1
4 | 1 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 RG:Z:RG1
5 | 2 0 g1 5 255 8M * 0 0 CGACTGTT ```````` AS:i:1 IH:i:3
6 | 2 0 g1 5 255 8M * 0 0 CGACTGTT ```````` AS:i:1 RG:Z:RG1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/sam/resources/simplestdout-newheader:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:coordinate
2 | @SQ SN:g1 LN:20
3 | @SQ SN:gempty LN:0
4 | @RG ID:RG1 SM:TEST-UPDATED PL:ILLUMINA
5 | 0 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 IH:i:1
6 | 1 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 IH:i:2
7 | 0 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 RG:Z:RG1
8 | 1 0 g1 3 255 8M * 0 0 ATCGACTG ```````` AS:i:0 RG:Z:RG1
9 | 2 0 g1 5 255 8M * 0 0 CGACTGTT ```````` AS:i:1 IH:i:3
10 | 2 0 g1 5 255 8M * 0 0 CGACTGTT ```````` AS:i:1 RG:Z:RG1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/segregation/resources/regions.bed:
--------------------------------------------------------------------------------
1 | 1 0 705881 10000000000 01100000000 N 1 2
2 | 1 645605 249250621 10000000000 01110000000 X 1 3
3 | 2 0 243199373 10000000000 11011110111 N 1 2
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/similarity/resources/phylogeny_testFlags.txt:
--------------------------------------------------------------------------------
1 | Usage: Phylogeny [OPTION]... -o DIR -d DIR
2 |
3 | Required flags:
4 | -o, --output=DIR directory for output
5 | -d, --subject=DIR directory containing formatted subject dataset
6 |
7 | Optional flags:
8 | -h, --help print help on command-line flag usage
9 | -P, --progress report progress
10 | -r, --repeat-freq=INT maximum repeat frequency (Default is 1000)
11 | -S, --step=INT step size (Default is window size)
12 | -W, --word=INT word size (Default is 25 for slimn and 9 for all other
13 | modes)
14 |
15 |
16 |
17 |
18 |
19 |
20 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/resources/readsimsambad.txt:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:simulatedSequence1 LN:97349
3 | @SQ SN:simulatedSequence2 LN:77578
4 | @SQ SN:simulatedSequence3 LN:17428
5 | @SQ SN:simulatedSequence4 LN:87845
6 | @SQ SN:simulatedSequence5 LN:60274
7 | read850:simulatedSequence1: 16 simulatedSequence1 11029 255 32=1X37=1X29= * 0 0 AGACGTTGATAAATTCAAGCCTCTCGACTCTGTAGTAAGTTTTATCGCAGCTGATAATCAGGACGGGCTGTAAGCTCGATTTGCCGGCGGGATGATCCTC * AS:i:2 NM:i:2 IH:i:1
8 | 123 0 simulatedSequence1 11038 255 37=1X2=1X1=1X44=1D1X12= * 0 0 TAAATTCAAGCCTCTCGACTCTGCAGTAAGTTTTATCACACCGGATAATCAGGACGGGCTGGAAGCTCGATTTGCCGGCGGGATGATATCCAAGAGCGGT * AS:i:6 NM:i:5 IH:i:1
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/del1.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTCCCTCCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGTGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/del2.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTGTCCCTCCTTGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGCCATGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCAACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/dup1.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTGTGTCCCAGTAGTTCCTTGCTTGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGCCACCATGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCAAACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/dup2.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTGTCCCAGTAGTTCCTTGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGCCATGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCAACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/inv1.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTACCCCACTTCCAAGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGTGGTGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCATCTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/inv2.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTGTCCCACTTCCTTGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGCCATGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCAACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/simulation/sv/resources/shorty.fasta:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | TTCTGTCCCAGTTCCTTGCG
3 | >simulatedSequence2
4 | TGCTTATCTACCACGCCATGACGTACTTTC
5 | >simulatedSequence3
6 | ACACTCCGGCGGACAGTCAACTGAACTAGGCACACCTGAC
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/citations.dmp:
--------------------------------------------------------------------------------
1 | 10239 | IIzuka H et al. (1975) | 0 | 0 | | Iizuka, H. et al. \"Method of recovering microbial cells containing protein.\" U.S. Pat. 3,888,736 dated June 10, 1975. [No PubMed record available.] | 188917 |
2 | 12333 | Decock C & Seifert K 2005 | 0 | 0 | | Decock C and Seifert K. 2005. Taxonomy and phylogeny of Synchaetomella lunatospora, a new genus and species of synnematous fungi from Southeast Asia. Antonie van Leeuwenhoek 88(3-4): 231-240. | 241715 241716 |
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/delnodes.dmp:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/taxonomy/resources/delnodes.dmp
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/division.dmp:
--------------------------------------------------------------------------------
1 | 0 | BCT | Bacteria | |
2 | 1 | INV | Invertebrates | |
3 | 2 | MAM | Mammals | |
4 | 3 | PHG | Phages | |
5 | 4 | PLN | Plants | |
6 | 5 | PRI | Primates | |
7 | 6 | ROD | Rodents | |
8 | 7 | SYN | Synthetic | |
9 | 8 | UNA | Unassigned | No species nodes should inherit this division assignment |
10 | 9 | VRL | Viruses | |
11 | 10 | VRT | Vertebrates | |
12 | 11 | ENV | Environmental samples | Anonymous sequences cloned directly from the environment |
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/ids_remove.txt:
--------------------------------------------------------------------------------
1 | 43988
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/ids_remove_all_seqs.txt:
--------------------------------------------------------------------------------
1 | 110662
2 | 1148
3 | 316278
4 | 316279
5 | 321327
6 | 321332
7 | 395961
8 | 395962
9 | 41431
10 | 43989
11 | 497965
12 | 65393
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/ids_remove_seqs.txt:
--------------------------------------------------------------------------------
1 | 110662
2 | 316278
3 | 316279
4 | 321327
5 | 321332
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/ids_subset.txt:
--------------------------------------------------------------------------------
1 | 321327
2 | 321332
3 | 41431
4 | 395961
5 | 395962
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/ids_subtree.txt:
--------------------------------------------------------------------------------
1 | 1129
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/merged.dmp:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/taxonomy/resources/merged.dmp
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/no_rank_rename.txt:
--------------------------------------------------------------------------------
1 | 131567 NEWRANK
2 | 999999 BADID
3 | 1118 ALREADYHASRANK
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxVerifyDire2Err:
--------------------------------------------------------------------------------
1 | Error: 1 taxon ids in the taxonomy lookup are not in the taxonomy
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxVerifyDireErr:
--------------------------------------------------------------------------------
1 | 1 sequences in the taxonomy lookup file are not in the SDF
2 | 1 sequences in the SDF are not in the taxonomy lookup file
3 | Error: 2 sequence names are not in both the SDF and the taxonomy lookup
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxVerifyErr:
--------------------------------------------------------------------------------
1 | Warning: 1 internal nodes have sequences attached
2 | Warning: 3 nodes have no rank
3 | 2 nodes with no rank are internal nodes
4 | 1 nodes with no rank are leaf nodes
5 | 2 nodes with no rank have sequences attached
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxVerifyOut:
--------------------------------------------------------------------------------
1 | TREE STATS
2 | internal nodes: 2
3 | leaf nodes: 3
4 | total nodes: 5
5 |
6 | RANK COUNTS
7 | rank internal leaf total
8 | no rank 2 1 3
9 | strain 0 2 2
10 | TOTAL 2 3 5
11 |
12 | SEQUENCE LOOKUP STATS
13 | total sequences: 4
14 | unique taxon ids: 4
15 | taxon ids in taxonomy: 4
16 | taxon ids not in taxonomy: 0
17 | internal nodes: 1
18 | leaf nodes: 3
19 | no rank nodes: 2
20 |
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 110662 1129 species Synechococcus sp. CC9605
10 | 316278 1129 species Synechococcus sp. RCC307
11 | 316279 1129 species Synechococcus sp. CC9902
12 | 321327 1129 species Synechococcus sp. JA-3-3Ab
13 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
14 | 1142 1118 genus Synechocystis
15 | 1148 1142 species Synechocystis sp. PCC 6803
16 | 43988 1118 genus Cyanothece
17 | 41431 43988 species Cyanothece sp. PCC 8801
18 | 43989 43988 species Cyanothece sp. ATCC 51142
19 | 65393 43988 species Cyanothece sp. PCC 7424
20 | 395961 43988 species Cyanothece sp. PCC 7425
21 | 395962 43988 species Cyanothece sp. PCC 8802
22 | 497965 43988 species Cyanothece sp. PCC 7822
23 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 110662 1129 species Synechococcus sp. CC9605
10 | 316278 1129 species Synechococcus sp. RCC307
11 | 316279 1129 species Synechococcus sp. CC9902
12 | 321327 1129 species Synechococcus sp. JA-3-3Ab
13 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
14 | 1142 1118 genus Synechocystis
15 | 1148 1142 species Synechocystis sp. PCC 6803
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove_all_sequences.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove_all_sequences_lookup.tsv:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove_all_sequences_lookup.tsv
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove_lookup.tsv:
--------------------------------------------------------------------------------
1 | 1148 gi|339272262|dbj|AP012205.1|
2 | 316278 gi|147849409|emb|CT978603.1|
3 | 321327 gi|86553275|gb|CP000239.1|
4 | 321332 gi|86556045|gb|CP000240.1|
5 | 110662 gi|78196017|gb|CP000110.1|
6 | 316279 gi|78167878|gb|CP000097.1|
7 | 1148 gi|47118304|dbj|BA000022.2|
8 | 1148 gi|38423849|dbj|AP006585.1|
9 | 1148 gi|38423692|dbj|AP004311.1|
10 | 1148 gi|38423799|dbj|AP004312.1|
11 | 1148 gi|38423559|dbj|AP004310.1|
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_remove_sequences.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1142 1118 genus Synechocystis
9 | 1148 1142 species Synechocystis sp. PCC 6803
10 | 43988 1118 genus Cyanothece
11 | 41431 43988 species Cyanothece sp. PCC 8801
12 | 43989 43988 species Cyanothece sp. ATCC 51142
13 | 65393 43988 species Cyanothece sp. PCC 7424
14 | 395961 43988 species Cyanothece sp. PCC 7425
15 | 395962 43988 species Cyanothece sp. PCC 8802
16 | 497965 43988 species Cyanothece sp. PCC 7822
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_subset.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 321327 1129 species Synechococcus sp. JA-3-3Ab
10 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
11 | 43988 1118 genus Cyanothece
12 | 41431 43988 species Cyanothece sp. PCC 8801
13 | 395961 43988 species Cyanothece sp. PCC 7425
14 | 395962 43988 species Cyanothece sp. PCC 8802
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_subset_lookup.tsv:
--------------------------------------------------------------------------------
1 | 395962 gi|256592529|gb|CP001704.1|
2 | 395962 gi|256592422|gb|CP001702.1|
3 | 395962 gi|256592565|gb|CP001705.1|
4 | 395962 gi|256592500|gb|CP001703.1|
5 | 395962 gi|256588085|gb|CP001701.1|
6 | 395961 gi|219867555|gb|CP001347.1|
7 | 395961 gi|219867221|gb|CP001345.1|
8 | 395961 gi|219867382|gb|CP001346.1|
9 | 395961 gi|219862254|gb|CP001344.1|
10 | 41431 gi|218169684|gb|CP001289.1|
11 | 41431 gi|218165370|gb|CP001287.1|
12 | 41431 gi|218169729|gb|CP001290.1|
13 | 41431 gi|218169631|gb|CP001288.1|
14 | 321327 gi|86553275|gb|CP000239.1|
15 | 321332 gi|86556045|gb|CP000240.1|
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_subtree.tsv:
--------------------------------------------------------------------------------
1 | #RTG taxonomy version 1.0
2 | #taxID parentID rank name
3 | 1 -1 no rank root
4 | 131567 1 no rank cellular organisms
5 | 2 131567 superkingdom Bacteria
6 | 1117 2 phylum Cyanobacteria
7 | 1118 1117 order Chroococcales
8 | 1129 1118 genus Synechococcus
9 | 110662 1129 species Synechococcus sp. CC9605
10 | 316278 1129 species Synechococcus sp. RCC307
11 | 316279 1129 species Synechococcus sp. CC9902
12 | 321327 1129 species Synechococcus sp. JA-3-3Ab
13 | 321332 1129 species Synechococcus sp. JA-2-3B'a(2-13)
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/taxonomy/resources/taxonomy_subtree_lookup.tsv:
--------------------------------------------------------------------------------
1 | 316278 gi|147849409|emb|CT978603.1|
2 | 321327 gi|86553275|gb|CP000239.1|
3 | 321332 gi|86556045|gb|CP000240.1|
4 | 110662 gi|78196017|gb|CP000110.1|
5 | 316279 gi|78167878|gb|CP000097.1|
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/util/testFile:
--------------------------------------------------------------------------------
1 | test out
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/avrstats.txt:
--------------------------------------------------------------------------------
1 | Date built : 2013-03-26-15-37-53
2 | AVR Version : 1
3 | AVR-ID : 0dedcb06-007e-41fc-94c4-a4773ea7db05
4 | Type : ML
5 | INFO fields : XRX
6 | FORMAT fields : GT,GQ,AB,AR
7 | Parameters : avrbuild -p /rtgshare/users/richard/demo_20130319/positive.vcf.gz -n /rtgshare/users/richard/demo_20130319/negative.vcf.gz -o test/com/rtg/variant/avr/resources/mlmodel.avr --info-annotation XRX --format-annotation GT,GQ,AB,AR
8 |
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/default.avr:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/avr/resources/default.avr
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/gtcomplex.props:
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1 | multiplier.gq.simple.homozygous=2.1
2 | multiplier.gq.simple.heterozygous=0.612
3 | multiplier.gq.complex.homozygous=1.26
4 | multiplier.gq.complex.heterozygous=0.342
5 | multiplier.qual.simple=0.3
6 | multiplier.qual.complex=0.5
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/gtqualcomplexmodel.avr:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/avr/resources/gtqualcomplexmodel.avr
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/mlmodel.avr:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/avr/resources/mlmodel.avr
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/null.avr:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/avr/resources/null.avr
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/avr/resources/testMlAvrPredictModelVersion_1:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/avr/resources/testMlAvrPredictModelVersion_1
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-AddingN:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp("", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-AmbiguousRead:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp("G:G", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-CloneConstructor:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp(":", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-CloneConstructor2:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp(":", 0.500),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-EmptyMatches:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp("", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-EmptyMatchesAll:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp(":", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-FromConvergence:
--------------------------------------------------------------------------------
1 | 6
2 | new Hyp(":", 0.000),
3 | new Hyp("AA:AA", -22.467),
4 | new Hyp("TGCTAA:TGCTAA", -36.113),
5 | new Hyp(":AA", -34.401),
6 | new Hyp("AA:TGCTAA", -55.200),
7 | new Hyp(":TGCTAA", -48.046),
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-FromConvergence2:
--------------------------------------------------------------------------------
1 | 6
2 | new Hyp(":", 0.000),
3 | new Hyp("AA:AA", -22.467),
4 | new Hyp("TGCTAA:TGCTAA", -36.113),
5 | new Hyp(":AA", -34.401),
6 | new Hyp("AA:TGCTAA", -55.200),
7 | new Hyp(":TGCTAA", -48.046),
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-MatchesAllWithSecondOutput:
--------------------------------------------------------------------------------
1 | 6
2 | new Hyp(":", 0.000),
3 | new Hyp("A:A", -14.009),
4 | new Hyp("TT:TT", -22.468),
5 | new Hyp(":A", -14.851),
6 | new Hyp("A:TT", -32.805),
7 | new Hyp(":TT", -23.309),
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-NonDefaultEventRates:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp(":", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-ObviousSingleNtInsertionMatchesHeteroCall:
--------------------------------------------------------------------------------
1 | 6
2 | new Hyp(":", 0.000),
3 | new Hyp("A:A", -14.683),
4 | new Hyp("TT:TT", -23.124),
5 | new Hyp(":A", -15.525),
6 | new Hyp("A:TT", -34.132),
7 | new Hyp(":TT", -23.966),
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-ObviousSingleNtInsertionMatchesHomoCall:
--------------------------------------------------------------------------------
1 | 3
2 | new Hyp(":", 0.000),
3 | new Hyp("A:A", -12.623),
4 | new Hyp(":A", -14.158),
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/HypothesesComplex-PriorsBug:
--------------------------------------------------------------------------------
1 | 1
2 | new Hyp(":", 0.000),
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/complex/resources/insertionpriortest0.txt:
--------------------------------------------------------------------------------
1 | Insertion prior
2 | zeta [0.600000, 0.400000]
3 | zeta` [0.950000, 0.050000]
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/contaminationbug.ref:
--------------------------------------------------------------------------------
1 | >chr17
2 | ACTAAGGAGGCTGAGGTATGAGAATTGCTTGAACCCGGGAGGCGGAGATTGCAGTGAGCCAAGATAATGCCACTGCACTACAGCCTGGGCGACAGAGTGAGATCCTGTCTCAAAAAAAATTTTTTTAATAATAATAAAAATAAATAAAAATAAAAGGAAGTGAAAAAGGAAAG
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotest.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BACT_SAMPLE CANCER
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotest3.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotest5.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotest5b.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 | test1 5 . A G . PASS NCS=0.555;DP=18 GT:DP:RE:AR:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:SS:VAF 0/1:9:0.981:0.000:9:19.54:6.03:9.67:0.00:86.632,0.000:0.00:A,9,0.981:9,0:.:0.000 0/1:9:0.981:0.000:30:19.54:.:9.67:.:0.000,86.632:0.00:G,9,0.981:0,9:1:1.000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotest6.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 | simulatedSequence1 34 . A C . PASS LOH=1.0;NCS=22.493;DP=40 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:SSC:SS:VAF:OCOC:DCOC:OCOF:DCOF 0/1:20:0.204:0.000:109:0.00:21.71:43.43:199.150,199.150:0.00:A,10,0.102,C,10,0.102:10,10:.:.:0.500 0/0:20:0.204:0.000:22:0.00:43.43:43.43:398.301,0.000:0.00:A,20,0.204:20,0:2.2:2:0.000:0:0:0.000:0.000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestLoh.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 | test1 5 . A G . PASS LOH=1.0;NCS=4.355;DP=18 GT:DP:RE:AR:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:SSC:SS:VAF:OCOC:DCOC:OCOF:DCOF 0/1:9:0.981:0.000:19:19.54:6.03:9.67:0.00:86.632,0.000:0.00:A,9,0.981:9,0:.:.:0.000 1/1:9:0.981:0.000:4:0.00:6.03:9.67:0.00:0.000,86.632:0.00:G,9,0.981:0,9:0.2:2:1.000:0:0:0.000:0.000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestLohDiploid.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 | test1 5 . A G . PASS LOH=1.0;NCS=10.719;DP=27 GT:DP:RE:AR:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:SSC:SS:VAF:OCOC:DCOC:OCOF:DCOF 0/1:9:0.981:0.000:12:0.24:3.91:9.67:0.00:48.129,38.503:0.00:A,5,0.545,G,4,0.436:5,4:.:.:0.444 1/1:18:1.962:0.000:18:0.00:12.06:19.35:0.00:0.000,173.263:0.00:G,18,1.962:0,18:1.0:2:1.000:0:0:0.000:0.000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestLohDiploid1.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 | test1 5 . A G . PASS LOH=1.0;NCS=21.386;DP=27 GT:DP:RE:AR:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:SSC:SS:VAF:OCOC:DCOC:OCOF:DCOF 0/1:9:0.981:0.000:21:0.24:3.91:9.67:0.00:48.129,38.503:0.00:A,5,0.545,G,4,0.436:5,4:.:.:0.444 1/1:18:1.962:0.000:131:0.00:12.06:19.35:0.00:0.000,173.263:0.00:G,18,1.962:0,18:2.1:2:1.000:0:0:0.000:0.000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestLongInsert.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestLongInsertNoN.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal cancer
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/cancer/resources/somaticnanotestcontaminationbugtest.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT H318-N H318-T
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/WMD.ped:
--------------------------------------------------------------------------------
1 | WMD-MIC-1433 WMD-MIC-1433-3-1 0 0 1 0
2 | WMD-MIC-1433 WMD-MIC-1433-3-2 0 0 2 0
3 | WMD-MIC-1433 WMD-MIC-1433-4-1 WMD-MIC-1433-3-1 WMD-MIC-1433-3-2 1 2
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-allOutput:
--------------------------------------------------------------------------------
1 | foo 21 . A . 54.3 PASS DP=28 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:73:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:73:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison.vcf:
--------------------------------------------------------------------------------
1 | foo 21 . A C 17.8 PASS DP=32 GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:10:1.900:0.000:17.8:18:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950:5,5:-1.78,-0.01,-4.12 0/0:5:0.950:0.000:0.0:44:0.00:10.86:0.00:36.062,0.000:0.00:A,5,0.950:5,0:0.00,-4.51,-10.01 0/0:6:1.140:0.000:0.2:14:1.45:10.86:0.00:36.062,0.000:0.00:A,5,0.950,G,1,0.190:5,0:-0.02,-1.39,-11.59 0/1:11:2.090:0.000:17.6:18:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950,G,1,0.190:5,5:-1.76,-0.01,-9.12
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison2:
--------------------------------------------------------------------------------
1 | foo 21 . A C 318.5 OC DP=52;CT=0 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:10:1.900:0.000:24:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950:5,5:-2.49,0.00,-3.52 1/1:8:1.520:0.000:24:0.00:17.37:0.00:0.000,57.700:0.00:C,8,1.520:0,8:-9.21,-2.37,0.00 1/1:14:2.660:0.000:25:0.00:30.40:0.00:0.000,100.974:0.00:C,14,2.660:0,14:-17.79,-2.47,0.00 0/1:20:3.800:0.000:8:9.26:30.40:0.00:36.062,100.974:0.00:A,5,0.950,C,14,2.660,G,1,0.190:5,14:-14.05,-0.08,-0.79
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison3:
--------------------------------------------------------------------------------
1 | foo 21 . A C 3.3 PASS DP=30 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-6.49,-16.53 0/1:9:1.710:0.000:3:2.17:13.03:0.00:21.637,43.275:0.00:A,3,0.570,C,6,1.140:3,6:-0.33,-0.28,-4.76 0/0:7:1.330:0.000:22:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.20,-15.05 0/0:7:1.330:0.000:22:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.20,-15.05
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison4:
--------------------------------------------------------------------------------
1 | foo 21 . A C 7.6 PASS DP=34 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:11:2.090:0.000:8:1.78:15.20:0.00:28.850,50.487:0.00:A,4,0.760,C,7,1.330:4,7:-0.76,-0.08,-5.74 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-6.50,-16.88 0/0:7:1.330:0.000:20:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.00,-14.86 0/0:9:1.710:0.000:25:0.00:19.54:0.00:64.912,0.000:0.00:A,9,1.710:9,0:0.00,-2.54,-17.21
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison5:
--------------------------------------------------------------------------------
1 | foo 21 . A C 295.0 PASS DP=32 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:9:1.710:0.000:29:0.00:19.54:0.00:0.000,64.912:0.00:C,9,1.710:0,9:-10.31,-2.89,0.00 1/1:9:1.710:0.000:29:0.00:19.54:0.00:0.000,64.912:0.00:C,9,1.710:0,9:-10.31,-2.89,0.00 1/1:7:1.330:0.000:45:0.00:15.20:0.00:0.000,50.487:0.00:C,7,1.330:0,7:-14.06,-4.51,0.00 1/1:7:1.330:0.000:45:0.00:15.20:0.00:0.000,50.487:0.00:C,7,1.330:0,7:-14.06,-4.51,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparison6:
--------------------------------------------------------------------------------
1 | foo 21 . T G 885.7 PASS DP=83 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:31:5.890:0.000:83:0.28:65.14:0.00:0.000,216.374:0.00:A,1,0.190,G,30,5.700:0,30:-39.77,-8.34,0.00 1/1:21:3.990:0.000:59:0.00:45.60:0.00:0.000,151.462:0.00:G,21,3.990:0,21:-29.13,-5.88,0.00 1/1:31:5.890:0.000:144:0.00:67.32:0.00:0.000,223.586:0.00:G,31,5.890:0,31:-50.85,-14.36,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/familycaller-comparisonPloidy:
--------------------------------------------------------------------------------
1 | foo 21 . A C 36.3 PASS DP=46 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0:5:0.950:0.000:45:43.43:.:0.00:0.000,36.062:0.00:C,5,0.950:0,5:0.00,-4.54 0/1:11:2.090:0.000:36:1.78:15.20:0.00:28.850,50.487:0.00:A,4,0.760,C,7,1.330:4,7:-3.63,0.00,-6.97 0/0:7:1.330:0.000:19:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:-0.01,-1.92,-10.90 0/0:7:1.330:0.000:19:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:-0.01,-1.92,-10.90 0/0:9:1.710:0.000:25:0.00:19.54:0.00:64.912,0.000:0.00:A,9,1.710:9,0:0.00,-2.46,-12.71 1:7:1.330:0.000:33:4.96:10.86:0.00:14.425,36.062:0.00:A,2,0.380,C,5,0.950:2,5:-3.28,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/input.bam:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/input.bam
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/input.bam.bai:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/bayes/multisample/family/resources/input.bam.bai
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-allOutput:
--------------------------------------------------------------------------------
1 | foo 21 . A . 54.1 PASS DP=28 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:73:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00 0/0:7:1.330:0.000:73:0.00:15.20:0.00:50.487:0.00:A,7,1.330:7:0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison.vcf:
--------------------------------------------------------------------------------
1 | foo 21 . A C 35.6 PASS DP=32 GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:10:1.900:0.000:17.8:18:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950:5,5:-1.78,-0.01,-4.12 0/0:5:0.950:0.000:0.0:44:0.00:10.86:0.00:36.062,0.000:0.00:A,5,0.950:5,0:0.00,-4.51,-10.01 0/0:6:1.140:0.000:0.2:14:1.45:10.86:0.00:36.062,0.000:0.00:A,5,0.950,G,1,0.190:5,0:-0.02,-1.39,-11.59 0/1:11:2.090:0.000:17.6:18:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950,G,1,0.190:5,5:-1.76,-0.01,-9.12
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison2:
--------------------------------------------------------------------------------
1 | foo 21 . A C 435.4 OC DP=52;CT=0 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:10:1.900:0.000:24:0.00:10.86:0.00:36.062,36.062:0.00:A,5,0.950,C,5,0.950:5,5:-2.49,0.00,-3.52 1/1:8:1.520:0.000:24:0.00:17.37:0.00:0.000,57.700:0.00:C,8,1.520:0,8:-9.21,-2.37,0.00 1/1:14:2.660:0.000:25:0.00:30.40:0.00:0.000,100.974:0.00:C,14,2.660:0,14:-17.79,-2.47,0.00 0/1:20:3.800:0.000:8:9.26:30.40:0.00:36.062,100.974:0.00:A,5,0.950,C,14,2.660,G,1,0.190:5,14:-14.05,-0.08,-0.79
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison3:
--------------------------------------------------------------------------------
1 | foo 21 . A C 3.3 PASS DP=30 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-6.49,-16.25 0/1:9:1.710:0.000:3:2.17:13.03:0.00:21.637,43.275:0.00:A,3,0.570,C,6,1.140:3,6:-0.33,-0.28,-4.76 0/0:7:1.330:0.000:22:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.20,-15.05 0/0:7:1.330:0.000:22:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.20,-15.05
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison4:
--------------------------------------------------------------------------------
1 | foo 21 . A C 7.7 PASS DP=34 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0/1:11:2.090:0.000:8:1.78:15.20:0.00:28.850,50.487:0.00:A,4,0.760,C,7,1.330:4,7:-0.76,-0.08,-5.74 0/0:7:1.330:0.000:57:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-6.50,-16.80 0/0:7:1.330:0.000:20:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:0.00,-2.00,-14.86 0/0:9:1.710:0.000:25:0.00:19.54:0.00:64.912,0.000:0.00:A,9,1.710:9,0:0.00,-2.54,-17.21
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison5:
--------------------------------------------------------------------------------
1 | foo 21 . A C 487.4 PASS DP=32 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:9:1.710:0.000:29:0.00:19.54:0.00:0.000,64.912:0.00:C,9,1.710:0,9:-10.31,-2.89,0.00 1/1:9:1.710:0.000:29:0.00:19.54:0.00:0.000,64.912:0.00:C,9,1.710:0,9:-10.31,-2.89,0.00 1/1:7:1.330:0.000:45:0.00:15.20:0.00:0.000,50.487:0.00:C,7,1.330:0,7:-14.06,-4.51,0.00 1/1:7:1.330:0.000:45:0.00:15.20:0.00:0.000,50.487:0.00:C,7,1.330:0,7:-14.06,-4.51,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparison6:
--------------------------------------------------------------------------------
1 | foo 21 . T G 1197.5 PASS DP=83 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:31:5.890:0.000:83:0.28:65.14:0.00:0.000,216.374:0.00:A,1,0.190,G,30,5.700:0,30:-39.77,-8.34,0.00 1/1:21:3.990:0.000:59:0.00:45.60:0.00:0.000,151.462:0.00:G,21,3.990:0,21:-29.13,-5.88,0.00 1/1:31:5.890:0.000:144:0.00:67.32:0.00:0.000,223.586:0.00:G,31,5.890:0,31:-50.85,-14.36,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/forwardbackward/resources/familycallerfb-comparisonPloidy:
--------------------------------------------------------------------------------
1 | foo 21 . A C 69.2 PASS DP=46 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 0:5:0.950:0.000:45:43.43:.:0.00:0.000,36.062:0.00:C,5,0.950:0,5:0.00,-4.54 0/1:11:2.090:0.000:36:1.78:15.20:0.00:28.850,50.487:0.00:A,4,0.760,C,7,1.330:4,7:-3.63,0.00,-6.97 0/0:7:1.330:0.000:19:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:-0.01,-1.92,-10.90 0/0:7:1.330:0.000:19:0.00:15.20:0.00:50.487,0.000:0.00:A,7,1.330:7,0:-0.01,-1.92,-10.90 0/0:9:1.710:0.000:25:0.00:19.54:0.00:64.912,0.000:0.00:A,9,1.710:9,0:0.00,-2.46,-12.71 1:7:1.330:0.000:33:4.96:10.86:0.00:14.425,36.062:0.00:A,2,0.380,C,5,0.950:2,5:-3.28,0.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/ref.fasta:
--------------------------------------------------------------------------------
1 | >ref
2 | ATGATTCCGCGCGTGCTTACTCGTTCTGGCGGTGAAAGACAAGGCTCTAT
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/threeSample.ped:
--------------------------------------------------------------------------------
1 | lineage original 0 0 2 0
2 | lineage left 0 original 2 0
3 | lineage right 0 original 2 0
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/threeSample_expected.txt:
--------------------------------------------------------------------------------
1 | ref 9 . G C . PASS DP=21 GT:DP:RE:AR:RQ:GQ:DN:DNP:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL 0/1:6:0.060:0.000:145.1:141:N:141:0.00:6.51:13.03:0.00:59.996,59.996:0.00:C,3,0.030,G,3,0.030:3,3:-14.51,0.00,-14.50 0/1:9:0.090:0.000:195.9:162:.:.:2.17:13.03:19.54:0.00:59.996,119.992:0.00:C,6,0.060,G,3,0.030:3,6:-19.59,0.00,-16.16 0/1:6:0.060:0.000:145.1:141:N:141:0.00:6.51:13.03:0.00:59.996,59.996:0.00:C,3,0.030,G,3,0.030:3,3:-14.51,0.00,-14.50
2 | ref 35 . A T . PASS DP=23 GT:DP:RE:AR:RQ:GQ:DN:DNP:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL:OCOC:DCOC:OCOF:DCOF 0/1:6:0.060:0.000:20.8:21:Y:7:5.79:10.86:13.03:0.00:19.999,99.993:0.00:A,1,0.010,T,5,0.050:1,5:-2.08,0.00,-10.24:0:0:0.000:0.000 0/0:11:0.110:0.000:1.0:7:.:.:0.00:23.89:23.89:0.00:219.985,0.000:0.00:A,11,0.110:11,0:-0.10,-0.67,-34.03 0/0:6:0.060:0.000:1.0:7:N:78:0.00:13.03:13.03:0.00:119.992,0.000:0.00:A,6,0.060:6,0:-0.10,-0.67,-22.60
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/twoSample.ped:
--------------------------------------------------------------------------------
1 | lineage original 0 0 2 0
2 | lineage descended 0 original 2 0
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/twoSampleDisconnected.ped:
--------------------------------------------------------------------------------
1 | lineage original 0 0 2 0
2 | lineage descended 0 0 2 0
3 | lineage descended2 0 descended 2 0
4 | lineage descended3 0 original 2 0
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/lineage/resources/twoSample_expected.txt:
--------------------------------------------------------------------------------
1 | ref 9 . G C . PASS DP=15 GT:DP:RE:AR:RQ:GQ:DN:DNP:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL 0/1:6:0.060:0.000:138.6:105:N:134:0.00:6.51:13.03:0.00:59.996,59.996:0.00:C,3,0.030,G,3,0.030:3,3:-13.86,0.00,-10.54 0/1:9:0.090:0.000:139.7:105:.:.:2.17:13.03:19.54:0.00:59.996,119.992:0.00:C,6,0.060,G,3,0.030:3,6:-13.97,0.00,-10.54
2 | ref 35 . A T . PASS DP=23 GT:DP:RE:AR:RQ:GQ:DN:DNP:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL:OCOC:DCOC:OCOF:DCOF 0/1:6:0.060:0.000:20.8:21:Y:7:5.79:10.86:13.03:0.00:19.999,99.993:0.00:A,1,0.010,T,5,0.050:1,5:-2.08,0.00,-10.24:0:0:0.000:0.000 0/0:17:0.170:0.000:1.0:7:.:.:0.00:36.92:36.92:0.00:339.977,0.000:0.00:A,17,0.170:17,0:-0.10,-0.67,-38.48
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_diploid_lge:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.395
4 | 4 0.395
5 | 5 0.075
6 | 6 0.040
7 | 7 0.030
8 | 8 0.035
9 | 9 0.025
10 | 10 0.000
11 | 11 0.000
12 | 12 0.005
13 | 13 0.000
14 | 14 0.005
15 | 15 0.005
16 | 16 0.005
17 | 17 0.000
18 | 18 0.000
19 | 19 0.000
20 | 20 0.000
21 | 2.765
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_diploid_med:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.460
4 | 4 0.460
5 | 5 0.165
6 | 6 0.045
7 | 7 0.025
8 | 8 0.035
9 | 9 0.005
10 | 10 0.005
11 | 11 0.005
12 | 12 0.010
13 | 13 0.010
14 | 14 0.000
15 | 15 0.000
16 | 16 0.000
17 | 17 0.000
18 | 18 0.000
19 | 19 0.000
20 | 20 0.000
21 | 2.975
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_diploid_small:
--------------------------------------------------------------------------------
1 | 1 0.890
2 | 2 0.890
3 | 3 0.490
4 | 4 0.495
5 | 5 0.315
6 | 6 0.190
7 | 7 0.155
8 | 8 0.080
9 | 9 0.045
10 | 10 0.065
11 | 11 0.030
12 | 12 0.020
13 | 13 0.010
14 | 14 0.010
15 | 15 0.010
16 | 16 0.010
17 | 17 0.010
18 | 18 0.010
19 | 19 0.010
20 | 20 0.010
21 | 3.745
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_haploid_lge:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.105
4 | 4 0.055
5 | 5 0.010
6 | 6 0.040
7 | 7 0.030
8 | 8 0.035
9 | 9 0.025
10 | 10 0.000
11 | 11 0.000
12 | 12 0.005
13 | 13 0.000
14 | 14 0.005
15 | 15 0.005
16 | 16 0.005
17 | 17 0.000
18 | 18 0.000
19 | 19 0.000
20 | 20 0.000
21 | 2.070
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_haploid_med:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.120
4 | 4 0.060
5 | 5 0.055
6 | 6 0.040
7 | 7 0.035
8 | 8 0.030
9 | 9 0.005
10 | 10 0.005
11 | 11 0.000
12 | 12 0.010
13 | 13 0.005
14 | 14 0.000
15 | 15 0.000
16 | 16 0.000
17 | 17 0.000
18 | 18 0.000
19 | 19 0.005
20 | 20 0.000
21 | 2.120
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_haploid_small:
--------------------------------------------------------------------------------
1 | 1 0.890
2 | 2 0.890
3 | 3 0.155
4 | 4 0.125
5 | 5 0.030
6 | 6 0.035
7 | 7 0.040
8 | 8 0.035
9 | 9 0.025
10 | 10 0.015
11 | 11 0.020
12 | 12 0.015
13 | 13 0.015
14 | 14 0.005
15 | 15 0.005
16 | 16 0.005
17 | 17 0.005
18 | 18 0.010
19 | 19 0.005
20 | 20 0.005
21 | 2.330
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_null_lge:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.405
4 | 4 0.395
5 | 5 0.330
6 | 6 0.275
7 | 7 0.210
8 | 8 0.180
9 | 9 0.105
10 | 10 0.140
11 | 11 0.100
12 | 12 0.060
13 | 13 0.030
14 | 14 0.020
15 | 15 0.015
16 | 16 0.030
17 | 17 0.020
18 | 18 0.010
19 | 19 0.010
20 | 20 0.010
21 | 4.095
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_null_med:
--------------------------------------------------------------------------------
1 | 1 0.875
2 | 2 0.875
3 | 3 0.470
4 | 4 0.465
5 | 5 0.390
6 | 6 0.295
7 | 7 0.255
8 | 8 0.180
9 | 9 0.105
10 | 10 0.160
11 | 11 0.120
12 | 12 0.080
13 | 13 0.045
14 | 14 0.025
15 | 15 0.010
16 | 16 0.040
17 | 17 0.030
18 | 18 0.010
19 | 19 0.005
20 | 20 0.000
21 | 4.435
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/it_null_small:
--------------------------------------------------------------------------------
1 | 1 0.890
2 | 2 0.890
3 | 3 0.500
4 | 4 0.495
5 | 5 0.445
6 | 6 0.345
7 | 7 0.290
8 | 8 0.205
9 | 9 0.125
10 | 10 0.180
11 | 11 0.120
12 | 12 0.065
13 | 13 0.055
14 | 14 0.045
15 | 15 0.025
16 | 16 0.040
17 | 17 0.030
18 | 18 0.015
19 | 19 0.015
20 | 20 0.015
21 | 4.790
22 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/pophwhyptest:
--------------------------------------------------------------------------------
1 | Hypotheses
2 | A -11.654
3 | C -0.095
4 | G -2.398
5 | T -10.282
6 | Hypotheses
7 | A:A -14.053
8 | C:C -0.191
9 | G:G -4.795
10 | T:T -12.681
11 | A:C -11.071
12 | C:G -1.800
13 | G:T -11.986
14 | A:G -13.357
15 | C:T -9.693
16 | A:T -19.690
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_diploid_lge:
--------------------------------------------------------------------------------
1 | 1 175 0 96 0 0 79 0 0 0 0 0
2 | 2 175 0 96 0 0 79 0 0 0 0 0
3 | 3 79 0 0 0 0 79 0 0 0 0 0
4 | 4 79 0 0 0 0 79 0 0 0 0 0
5 | 5 15 0 0 0 0 15 0 0 0 0 0
6 | 6 8 0 0 0 0 8 0 0 0 0 0
7 | 7 6 0 0 0 0 6 0 0 0 0 0
8 | 8 7 0 0 0 0 7 0 0 0 0 0
9 | 9 5 0 0 0 0 5 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 1 0 0 0 0 1 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 1 0 0 0 0 1 0 0 0 0 0
15 | 15 1 0 0 0 0 1 0 0 0 0 0
16 | 16 1 0 0 0 0 1 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_diploid_med:
--------------------------------------------------------------------------------
1 | 1 23 0 11 0 0 12 0 0 0 0 0
2 | 2 23 0 11 0 0 12 0 0 0 0 0
3 | 3 12 0 0 0 0 12 0 0 0 0 0
4 | 4 12 0 0 0 0 12 0 0 0 0 0
5 | 5 1 0 1 0 0 0 0 0 0 0 0
6 | 6 0 0 0 0 0 0 0 0 0 0 0
7 | 7 0 0 0 0 0 0 0 0 0 0 0
8 | 8 0 0 0 0 0 0 0 0 0 0 0
9 | 9 0 0 0 0 0 0 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 0 0 0 0 0 0 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 0 0 0 0 0 0 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_diploid_small:
--------------------------------------------------------------------------------
1 | 1 5 0 2 0 0 3 0 0 0 0 0
2 | 2 5 0 2 0 0 3 0 0 0 0 0
3 | 3 3 0 0 0 0 3 0 0 0 0 0
4 | 4 3 0 0 0 0 3 0 0 0 0 0
5 | 5 0 0 0 0 0 0 0 0 0 0 0
6 | 6 0 0 0 0 0 0 0 0 0 0 0
7 | 7 0 0 0 0 0 0 0 0 0 0 0
8 | 8 0 0 0 0 0 0 0 0 0 0 0
9 | 9 0 0 0 0 0 0 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 0 0 0 0 0 0 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 0 0 0 0 0 0 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_haploid_lge:
--------------------------------------------------------------------------------
1 | 1 175 0 96 0 0 79 0 0 0 0 0
2 | 2 175 0 96 0 0 79 0 0 0 0 0
3 | 3 21 0 0 0 0 21 0 0 0 0 0
4 | 4 11 0 0 0 0 11 0 0 0 0 0
5 | 5 2 0 0 0 0 2 0 0 0 0 0
6 | 6 8 0 0 0 0 8 0 0 0 0 0
7 | 7 6 0 0 0 0 6 0 0 0 0 0
8 | 8 7 0 0 0 0 7 0 0 0 0 0
9 | 9 5 0 0 0 0 5 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 1 0 0 0 0 1 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 1 0 0 0 0 1 0 0 0 0 0
15 | 15 1 0 0 0 0 1 0 0 0 0 0
16 | 16 1 0 0 0 0 1 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_haploid_med:
--------------------------------------------------------------------------------
1 | 1 23 0 11 0 0 12 0 0 0 0 0
2 | 2 23 0 11 0 0 12 0 0 0 0 0
3 | 3 3 0 1 0 0 2 0 0 0 0 0
4 | 4 1 0 1 0 0 0 0 0 0 0 0
5 | 5 1 0 1 0 0 0 0 0 0 0 0
6 | 6 0 0 0 0 0 0 0 0 0 0 0
7 | 7 0 0 0 0 0 0 0 0 0 0 0
8 | 8 0 0 0 0 0 0 0 0 0 0 0
9 | 9 0 0 0 0 0 0 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 0 0 0 0 0 0 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 0 0 0 0 0 0 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_haploid_small:
--------------------------------------------------------------------------------
1 | 1 5 0 2 0 0 3 0 0 0 0 0
2 | 2 5 0 2 0 0 3 0 0 0 0 0
3 | 3 0 0 0 0 0 0 0 0 0 0 0
4 | 4 0 0 0 0 0 0 0 0 0 0 0
5 | 5 0 0 0 0 0 0 0 0 0 0 0
6 | 6 0 0 0 0 0 0 0 0 0 0 0
7 | 7 0 0 0 0 0 0 0 0 0 0 0
8 | 8 0 0 0 0 0 0 0 0 0 0 0
9 | 9 0 0 0 0 0 0 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 0 0 0 0 0 0 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 0 0 0 0 0 0 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_null_lge:
--------------------------------------------------------------------------------
1 | 1 175 0 96 0 0 79 0 0 0 0 0
2 | 2 175 0 96 0 0 79 0 0 0 0 0
3 | 3 81 0 2 0 0 79 0 0 0 0 0
4 | 4 79 0 0 0 0 79 0 0 0 0 0
5 | 5 66 0 0 0 0 66 0 0 0 0 0
6 | 6 55 0 1 0 0 54 0 0 0 0 0
7 | 7 42 0 0 0 0 42 0 0 0 0 0
8 | 8 36 0 0 0 0 36 0 0 0 0 0
9 | 9 21 0 0 0 0 21 0 0 0 0 0
10 | 10 28 0 0 0 0 28 0 0 0 0 0
11 | 11 20 0 0 0 0 20 0 0 0 0 0
12 | 12 12 0 0 0 0 12 0 0 0 0 0
13 | 13 6 0 0 0 0 6 0 0 0 0 0
14 | 14 4 0 0 0 0 4 0 0 0 0 0
15 | 15 3 0 0 0 0 3 0 0 0 0 0
16 | 16 6 0 0 0 0 6 0 0 0 0 0
17 | 17 4 0 0 0 0 4 0 0 0 0 0
18 | 18 2 0 0 0 0 2 0 0 0 0 0
19 | 19 2 0 0 0 0 2 0 0 0 0 0
20 | 20 2 0 0 0 0 2 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_null_med:
--------------------------------------------------------------------------------
1 | 1 23 0 11 0 0 12 0 0 0 0 0
2 | 2 23 0 11 0 0 12 0 0 0 0 0
3 | 3 13 0 1 0 0 12 0 0 0 0 0
4 | 4 13 0 1 0 0 12 0 0 0 0 0
5 | 5 13 0 1 0 0 12 0 0 0 0 0
6 | 6 8 0 1 0 0 7 0 0 0 0 0
7 | 7 6 0 0 0 0 6 0 0 0 0 0
8 | 8 5 0 0 0 0 5 0 0 0 0 0
9 | 9 2 0 0 0 0 2 0 0 0 0 0
10 | 10 3 0 0 0 0 3 0 0 0 0 0
11 | 11 4 0 0 0 0 4 0 0 0 0 0
12 | 12 2 0 0 0 0 2 0 0 0 0 0
13 | 13 1 0 0 0 0 1 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 1 0 0 0 0 1 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/population/resources/vc_null_small:
--------------------------------------------------------------------------------
1 | 1 5 0 2 0 0 3 0 0 0 0 0
2 | 2 5 0 2 0 0 3 0 0 0 0 0
3 | 3 3 0 0 0 0 3 0 0 0 0 0
4 | 4 3 0 0 0 0 3 0 0 0 0 0
5 | 5 2 0 0 0 0 2 0 0 0 0 0
6 | 6 1 0 0 0 0 1 0 0 0 0 0
7 | 7 1 0 0 0 0 1 0 0 0 0 0
8 | 8 1 0 0 0 0 1 0 0 0 0 0
9 | 9 0 0 0 0 0 0 0 0 0 0 0
10 | 10 0 0 0 0 0 0 0 0 0 0 0
11 | 11 0 0 0 0 0 0 0 0 0 0 0
12 | 12 0 0 0 0 0 0 0 0 0 0 0
13 | 13 0 0 0 0 0 0 0 0 0 0 0
14 | 14 0 0 0 0 0 0 0 0 0 0 0
15 | 15 0 0 0 0 0 0 0 0 0 0 0
16 | 16 0 0 0 0 0 0 0 0 0 0 0
17 | 17 0 0 0 0 0 0 0 0 0 0 0
18 | 18 0 0 0 0 0 0 0 0 0 0 0
19 | 19 0 0 0 0 0 0 0 0 0 0 0
20 | 20 0 0 0 0 0 0 0 0 0 0 0
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/bed_region_template.fasta:
--------------------------------------------------------------------------------
1 | >seq1
2 | AAAATAAAATAAAATAAAATAAAAT
3 | AAAATAAAATAAAATAAAATAAAAT
4 | AAAATAAAATAAAATAAAATAAAAT
5 | AGCTGCTAAAAAAATAAAATAAAAT
6 | AGCTAAAGCTAAAATAAAATAAAAT
7 | AAAATAAAATAAAATAAAATAAAAT
8 | >seq2
9 | CCCCTCCCCTCCCCTCCCCTCCCCT
10 | CCCCTCCCCTCCCCTCCCCTCCCCT
11 | CCCCTCCCCTCCCCTCCCCTCCCCT
12 | CCCCTCCCCTCCCCTCCCCTCCCCT
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_deletion.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 65 70 complex-called
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_deletion.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_dad sm_daughter2 sm_mom
2 | simulatedSequence1 65 . GTGAT GAT,G 331.4 PASS DP=18;XRX GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 0/1:6:0.002:0.000:136.1:84:1.45:8.69:13.03:0.00:73.619,135.053,0.000:0.00:2,4,0:-13.61,0.00,-15.03,-13.56,-8.38,-29.19 0|2:6:0.004:0.000:203.6:102:1.45:8.69:13.03:0.00:73.619,0.000,119.945:0.00:2,0,4:-20.36,-15.46,-26.15,0.00,-10.20,-19.26 0/2:6:0.001:0.000:59.1:59:13.03:13.03:13.03:0.00:220.856,0.000,0.000:0.00:6,0,0:-5.91,-7.54,-38.12,0.00,-30.59,-31.19
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_deletion_reverse.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 65 70 complex-called
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_deletion_reverse.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_dad sm_daughter2 sm_mom
2 | simulatedSequence1 65 . GTGAT G,GAT 331.4 PASS DP=18;XRX GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 0/1:6:0.004:0.000:221.7:84:1.45:8.69:13.03:0.00:73.619,119.945,0.000:0.00:2,4,0:-22.17,0.00,-15.40,-15.46,-8.38,-24.34 0|2:6:0.002:0.000:118.0:102:1.45:8.69:13.03:0.00:73.619,0.000,135.053:0.00:2,0,4:-11.80,-13.56,-31.00,0.00,-10.20,-18.89 0/2:6:0.001:0.000:59.1:59:13.03:13.03:13.03:0.00:220.856,0.000,0.000:0.00:6,0,0:-5.91,-7.54,-39.21,0.00,-30.59,-30.10
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_fraction.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 65 66 complex-called
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_fraction.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_dad sm_mom
2 | simulatedSequence1 65 . G GAA 145.2 PASS DP=12;XRX GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 0/1:6:0.001:0.000:145.2:75:1.45:8.69:13.03:0.00:79.730,142.741:0.00:2,4:-14.52,0.00,-7.49 0/0:6:0.001:0.000:0.0:105:0.00:13.03:13.03:0.00:239.189,0.000:0.00:6,0:0.00,-10.51,-37.92
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_on2_same.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 65 66 complex-called
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_on2_same.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_dad sm_mom
2 | simulatedSequence1 65 . G GAA 23.1 PASS DP=10;XRX GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 0/1:5:0.001:0.000:23.1:23:0.43:6.51:10.86:0.00:119.594,71.371:0.00:3,2:-2.31,0.00,-12.77 0/0:5:0.001:0.000:0.0:102:0.00:10.86:10.86:0.00:199.324,0.000:0.00:5,0:0.00,-10.21,-32.94
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_on2_split.bed:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_on2_split.bed
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-indel_triggering_on2_split.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_dad sm_mom
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-startOfReferenceN.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_mom
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/populationnanotest-testBedRegionPlusRegion.vcf:
--------------------------------------------------------------------------------
1 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sm_mom
2 | seq1 10 . T G 57.8 BED DP=4;STRL=3;STRU=1 GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL:CLUS 1/1:4:0.040:0.000:57.8:11:0.00:8.69:8.69:0.00:0.000,79.995:0.00:G,4,0.040:0,4:-5.78,-1.08,-0.04:1
3 | seq1 15 . T G 57.8 PASS DP=4;STRL=3;STRU=1 GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL:CLUS 1/1:4:0.040:0.000:57.8:11:0.00:8.69:8.69:0.00:0.000,79.995:0.00:G,4,0.040:0,4:-5.78,-1.08,-0.04:2
4 | seq1 21 . A G 64.1 BED DP=4;STRL=2;STRU=1 GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:RS:AD:GL:CLUS 1/1:4:0.040:0.000:64.1:11:0.00:8.69:8.69:0.00:0.000,79.995:0.00:G,4,0.040:0,4:-6.41,-1.10,-0.04:1
5 | seq1 79 . T TAAA 147.4 PASS DP=4;XRX GT:DP:RE:AR:RQ:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 1/1:4:0.040:0.000:147.4:19:0.00:8.69:8.69:0.00:0.000,79.995:0.00:0,4:-14.74,-1.88,-0.01
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/bayes/multisample/resources/testBedRegion.bed:
--------------------------------------------------------------------------------
1 | seq1 11 18
2 | seq1 60 150
3 | seq2 30 80
4 | seq2 50 90
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/resources/cnv.ratio:
--------------------------------------------------------------------------------
1 | simulatedSequence1 0 1.000
2 | simulatedSequence1 5 3.000
3 | simulatedSequence1 10 1.333
4 | simulatedSequence1 15 2.000
5 | simulatedSequence1 20 2.000
6 | simulatedSequence2 0 2.000
7 | simulatedSequence2 5 0.500
8 | simulatedSequence2 10 2.000
9 | simulatedSequence2 15 4.000
10 | simulatedSequence2 20 2.000
11 | simulatedSequence3 0 0.500
12 | simulatedSequence3 5 0.500
13 | simulatedSequence4 0 2.000
14 | simulatedSequence4 10 2.000
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/resources/cnv1.ratio:
--------------------------------------------------------------------------------
1 | simulatedSequence1 0 1.000
2 | simulatedSequence1 5 3.000
3 | simulatedSequence1 10 1.333
4 | simulatedSequence1 15 2.000
5 | simulatedSequence1 20 2.000
6 | simulatedSequence2 0 2.000
7 | simulatedSequence2 5 0.500
8 | simulatedSequence2 10 2.000
9 | simulatedSequence2 15 4.000
10 | simulatedSequence2 20 2.000
11 | simulatedSequence3 0 0.500
12 | simulatedSequence3 5 0.500
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/resources/testFilter.bam:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/cnv/resources/testFilter.bam
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/resources/testFilter.bam.bai:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/cnv/resources/testFilter.bam.bai
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/case.bed:
--------------------------------------------------------------------------------
1 | #Version RTG Core 2016-12-23 / Core fe80ae5 (2016-12-23), Coverage BED output v1.1
2 | #sequence start end label coverage
3 | simulatedSequence1 1752 2757 Mex01 2000
4 | simulatedSequence1 2822 3835 Mex02 2000
5 | simulatedSequence1 3933 4944 Mex03 2000
6 | simulatedSequence1 4969 5980 Mex04 6
7 | simulatedSequence1 6289 6298 Mex05 6
8 | simulatedSequence1 6335 6352 Mex06 6
9 | simulatedSequence1 6355 6540 Mex07a 2000
10 | simulatedSequence1 6655 6740 Mex07b 2000
11 | simulatedSequence1 6755 6940 Mex07c 2000
12 | simulatedSequence1 6955 7540 Mex07d 2000
13 | simulatedSequence1 7543 7654 Mex08 2000
14 | simulatedSequence1 7704 8015 Mex09a 2000
15 | simulatedSequence1 8104 8155 Mex09b 2000
16 | simulatedSequence1 8204 8295 Mex09c 2000
17 | simulatedSequence1 8304 8415 Mex09d 2000
18 | simulatedSequence1 8428 8444 Mex10 6000
19 | simulatedSequence1 8602 9219 Mex11 6000
20 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/control.bed:
--------------------------------------------------------------------------------
1 | #Version RTG Core 2016-12-23 / Core fe80ae5 (2016-12-23), Coverage BED output v1.1
2 | #sequence start end label coverage
3 | simulatedSequence1 1752 2757 Mex01 2000
4 | simulatedSequence1 2822 3835 Mex02 2000
5 | simulatedSequence1 3933 4944 Mex03 2000
6 | simulatedSequence1 4969 5980 Mex04 2000
7 | simulatedSequence1 6289 6298 Mex05 2000
8 | simulatedSequence1 6335 6352 Mex06 2000
9 | simulatedSequence1 6355 6540 Mex07a 2000
10 | simulatedSequence1 6655 6740 Mex07b 2000
11 | simulatedSequence1 6755 6940 Mex07c 2000
12 | simulatedSequence1 6955 7540 Mex07d 2000
13 | simulatedSequence1 7543 7654 Mex08 2000
14 | simulatedSequence1 7704 8015 Mex09a 2000
15 | simulatedSequence1 8104 8155 Mex09b 2000
16 | simulatedSequence1 8204 8295 Mex09b 2000
17 | simulatedSequence1 8304 8415 Mex09d 2000
18 | simulatedSequence1 8428 8444 Mex10 2000
19 | simulatedSequence1 8602 9219 Mex11 2000
20 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/coverage.bed:
--------------------------------------------------------------------------------
1 | #Version RTG Core 2016-12-23 / Core fe80ae5 (2016-12-23), Coverage BED output v1.1
2 | #CL coverage -t /rtgshare/data/human/ref/1000g_v37_phase2/sdf --bed-regions /nas/private/Toma/2016-08-31-new-onco-regions/os131_r112_ROI.bed --per-region --keep-duplicates -o MI000722-coverage MI000722-deprobe/alignments_deprobed.bam
3 | ##RUN-ID 748c508b-c394-4e52-8b87-0f9cb0fefdc9
4 | #sequence start end label coverage
5 | 1 17526 17572 MTOR__Mex01 3314
6 | 1 18222 18358 MTOR__Mex02 2927
7 | 1 19331 19442 MTOR__Mex03 2527
8 | 1 19690 19801 MTOR__Mex04 2046
9 | 1 22893 22989 MTOR__Mex05 3249
10 | 1 24359 24525 MTOR__Mex06 1485
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.out-gc.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.out-panel.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.out.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.panel.bed:
--------------------------------------------------------------------------------
1 | 1 17526 17572 MTOR__Mex01 1.13222
2 | 1 18222 18358 MTOR__Mex02 1.00000
3 | 1 19331 19442 MTOR__Mex03 0.863341
4 | 1 19690 19801 MTOR__Mex04 1.22262
5 | 1 22893 22989 MTOR__Mex05 1.11001
6 | 1 24359 24525 MTOR__Mex06 0.887387
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.sum-out.txt:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.sum-out.txt
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.summary-gc.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.summary-panel.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.summary.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 8428 9220 Mex02 Full Amplification 3.0001 1.5850 1.5850 DUP,1.585,simulatedSequence1:8429-9220;
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/expected.summary.txt:
--------------------------------------------------------------------------------
1 | Total Segments: 4
2 | Deletions: 1
3 | Duplications: 1
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/panel.bed:
--------------------------------------------------------------------------------
1 | #Version RTG Core 2016-12-23 / Core fe80ae5 (2016-12-23), Coverage BED output v1.1
2 | #sequence start end label normalized-coverage
3 | simulatedSequence1 1752 2757 Mex01 1.0
4 | simulatedSequence1 2822 3835 Mex02 1.0
5 | simulatedSequence1 3933 4944 Mex03 1.0
6 | simulatedSequence1 4969 5980 Mex04 1.0
7 | simulatedSequence1 6289 6298 Mex05 1.0
8 | simulatedSequence1 6335 6352 Mex06 1.0
9 | simulatedSequence1 6355 6540 Mex07a 1.0
10 | simulatedSequence1 6655 6740 Mex07b 1.0
11 | simulatedSequence1 6755 6940 Mex07c 1.0
12 | simulatedSequence1 6955 7540 Mex07d 1.0
13 | simulatedSequence1 7543 7654 Mex08 1.0
14 | simulatedSequence1 7704 8015 Mex09a 1.0
15 | simulatedSequence1 8104 8155 Mex09b 1.0
16 | simulatedSequence1 8204 8295 Mex09b 1.0
17 | simulatedSequence1 8304 8415 Mex09d 1.0
18 | simulatedSequence1 8428 8444 Mex10 1.0
19 | simulatedSequence1 8602 9219 Mex11 1.0
20 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/regions.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 1752 4969 Mex01 1 -
2 | simulatedSequence1 8428 9220 Mex02 1 -
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/singleRecordOutput.txt:
--------------------------------------------------------------------------------
1 | #chrom start end name extent status RDR LR SQS segments
2 | 19 4580 4690 one Full Amplification 2.9079 1.5400 1.5400 DUP,1.54,19:1001-9000;
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/cnv/segment/resources/svof-example.txt:
--------------------------------------------------------------------------------
1 | sequence 1 1 . G . . SVTYPE=DUP;END=42;IMPRECISE;CIPOS=-1,20;CIEND=-20,18;BC=1 GT:LR:RDR:SQS 1:4.3000:19.6983:4.3000
2 | sequence 1 60 . G . . SVTYPE=DUP;END=70;IMPRECISE;CIPOS=-18,5;CIEND=-5,930;BC=1 GT:LR:RDR:SQS 1:8.0000:256.0000:8.0000
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covBedRegionNoTemplate.txt:
--------------------------------------------------------------------------------
1 | Coverage per region:
2 | depth breadth covered size name
3 | 2.00 1.0000 7 7 simulatedSequence1:41-47
4 | 2.20 1.0000 10 10 blah
5 | 2.42 1.0000 19 19 feh
6 | 1.77 1.0000 26 26 simulatedSequence2:18-43
7 | 1.77 0.7419 23 31 simulatedSequence2:64-94
8 | 1.93 0.9091 80 88 all regions
9 |
10 | Fold-80 Penalty: 1.15
11 | Median depth: 2.00
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covBedRegionPerRegion.bed:
--------------------------------------------------------------------------------
1 | simulatedSequence1 40 47 simulatedSequence1:41-47 2.00
2 | simulatedSequence1 55 65 blah 2.11
3 | simulatedSequence1 60 75 feh 2.08
4 | simulatedSequence2 17 43 simulatedSequence2:18-43 1.77
5 | simulatedSequence2 55 59 feh 3.50
6 | simulatedSequence2 63 94 simulatedSequence2:64-94 1.80
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest-out.txt:
--------------------------------------------------------------------------------
1 | Coverage per region:
2 | depth breadth covered size name
3 | 2.00 0.8000 16 20 g1
4 | 1.12 0.3824 13 34 g2
5 | 1.44 0.5370 29 54 all regions
6 |
7 | Fold-80 Penalty: 3.34
8 | Median depth: 1.56
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest1-smooth1.txt:
--------------------------------------------------------------------------------
1 | g1 0 1 g1 0.00
2 | g1 1 3 g1 1.00
3 | g1 3 4 g1 2.00
4 | g1 4 5 g1 3.00
5 | g1 5 6 g1 4.00
6 | g1 6 10 g1 5.00
7 | g1 10 12 g1 4.00
8 | g1 12 13 g1 3.00
9 | g1 13 14 g1 2.00
10 | g1 14 18 g1 1.00
11 | g1 18 20 g1 0.00
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest1.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 2.00
3 | g1 4 5 g1 3.00
4 | g1 5 10 g1 5.00
5 | g1 10 12 g1 4.00
6 | g1 12 13 g1 3.00
7 | g1 13 18 g1 1.00
8 | g1 18 20 g1 0.00
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest2-smooth1.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 1.00
3 | g1 4 6 g1 0.00
4 | g1 6 12 g1 1.00
5 | g1 12 16 g1 0.00
6 | g1 16 18 g1 1.00
7 | g1 18 20 g1 0.00
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest2-smooth2.txt:
--------------------------------------------------------------------------------
1 | g1 0 1 g1 0.00
2 | g1 1 2 g1 1.00
3 | g1 2 4 g1 0.00
4 | g1 4 13 g1 1.00
5 | g1 13 18 g1 0.00
6 | g1 18 19 g1 1.00
7 | g1 19 20 g1 0.00
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest2.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 1.00
3 | g1 4 6 g1 0.00
4 | g1 6 10 g1 1.00
5 | g1 10 11 g1 2.00
6 | g1 11 12 g1 1.00
7 | g1 12 16 g1 0.00
8 | g1 16 18 g1 1.00
9 | g1 18 20 g1 0.00
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest3.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 2.00
3 | g1 4 5 g1 3.00
4 | g1 5 10 g1 5.00
5 | g1 10 12 g1 4.00
6 | g1 12 13 g1 3.00
7 | g1 13 18 g1 1.00
8 | g1 18 20 g1 0.00
9 | g2 0 2 g2 0.00
10 | g2 2 4 g2 2.00
11 | g2 4 5 g2 3.00
12 | g2 5 10 g2 5.00
13 | g2 10 12 g2 4.00
14 | g2 12 13 g2 3.00
15 | g2 13 18 g2 1.00
16 | g2 18 20 g2 0.00
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest3region.txt:
--------------------------------------------------------------------------------
1 | g2 5 7 g2:6-7 5.00
2 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest5.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 18 g1 1.00
3 | g1 18 20 g1 0.00
4 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest5IHfraction.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 5 g1 2.00
3 | g1 5 10 g1 3.00
4 | g1 10 13 g1 2.00
5 | g1 13 18 g1 1.00
6 | g1 18 20 g1 0.00
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestErrorRates.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 coverage 0
2 | g1 2 4 coverage 2
3 | g1 4 5 coverage 3
4 | g1 5 10 coverage 5
5 | g1 10 13 coverage 3
6 | g1 13 18 coverage 1
7 | g1 18 20 coverage 0
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestGapStatsOut.txt:
--------------------------------------------------------------------------------
1 | Histogram of gap lengths:
2 | 1: 0
3 | 2: 3
4 | 3: 0
5 | 4: 0
6 | 5: 0
7 | 6: 0
8 | 7: 0
9 | 8: 0
10 | 9: 0
11 | 10: 0
12 | 11: 0
13 | 12: 0
14 | 13: 0
15 | 14: 0
16 | 15: 0
17 | 16: 0
18 | 17: 0
19 | 18: 0
20 | 19: 0
21 | 20: 0
22 | >20: 1
23 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestLevelsStatsOut.txt:
--------------------------------------------------------------------------------
1 | 0 25 46.30 100.00
2 | 1 11 20.37 53.70
3 | 2 3 5.56 33.33
4 | 3 3 5.56 27.78
5 | 4 9 16.67 22.22
6 | 5 2 3.70 5.56
7 | 6 1 1.85 1.85
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestStats.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 1.00
3 | g1 4 5 g1 2.00
4 | g1 5 12 g1 4.00
5 | g1 12 13 g1 3.00
6 | g1 13 18 g1 1.00
7 | g1 18 20 g1 0.00
8 | g2 0 2 g2 0.00
9 | g2 2 4 g2 2.00
10 | g2 4 5 g2 3.00
11 | g2 5 9 g2 5.00
12 | g2 9 10 g2 6.00
13 | g2 10 12 g2 4.00
14 | g2 12 13 g2 3.00
15 | g2 13 17 g2 1.00
16 | g2 17 40 g2 0.00
17 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestStatsOut.txt:
--------------------------------------------------------------------------------
1 | Coverage per region:
2 | depth breadth covered size name
3 | 2.0000 0.8000 16 20 g1
4 | 1.1176 0.3824 13 34 g2
5 | 1.4444 0.5370 29 54 all regions
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktest_clipping.bed:
--------------------------------------------------------------------------------
1 | t 0 41 t 1.00
2 | t 41 43 t 2.00
3 | t 43 81 t 1.00
4 | t 81 84 t 0.00
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestadditional.txt:
--------------------------------------------------------------------------------
1 | g1 0 0 0 0 0 0 0 0 0.00
2 | g1 1 0 0 0 0 0 0 0 0.00
3 | g1 2 2 2 0 0 0 2 0 2.00
4 | g1 3 2 2 0 0 0 2 0 2.00
5 | g1 4 3 3 0 0 0 3 0 3.00
6 | g1 5 5 5 0 0 0 4 1 4.50
7 | g1 6 5 5 0 0 0 4 1 4.50
8 | g1 7 5 5 0 0 0 4 1 4.50
9 | g1 8 5 5 0 0 0 4 1 4.50
10 | g1 9 5 5 0 0 0 4 1 4.50
11 | g1 10 4 4 0 0 0 3 1 3.50
12 | g1 11 4 4 0 0 0 3 1 3.50
13 | g1 12 3 3 0 0 0 2 1 2.50
14 | g1 13 1 1 0 0 0 1 0 1.00
15 | g1 14 1 1 0 0 0 1 0 1.00
16 | g1 15 1 1 0 0 0 1 0 1.00
17 | g1 16 1 1 0 0 0 1 0 1.00
18 | g1 17 1 1 0 0 0 1 0 1.00
19 | g1 18 0 0 0 0 0 0 0 0.00
20 | g1 19 0 0 0 0 0 0 0 0.00
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestadditionalRC.txt:
--------------------------------------------------------------------------------
1 | g1 0 0 0 0 0 0 0 0 0.00
2 | g1 1 0 0 0 0 0 0 0 0.00
3 | g1 2 2 2 0 1 0 1 1 1.50
4 | g1 3 2 2 0 1 0 1 1 1.50
5 | g1 4 2 3 0 1 0 1 2 2.00
6 | g1 5 4 4 1 1 0 3 2 4.00
7 | g1 6 4 4 1 1 0 3 2 4.00
8 | g1 7 4 4 1 1 0 3 2 4.00
9 | g1 8 4 4 1 1 0 3 2 4.00
10 | g1 9 4 4 1 1 0 3 2 4.00
11 | g1 10 4 2 2 0 1 3 1 3.50
12 | g1 11 4 2 2 0 1 3 1 3.50
13 | g1 12 3 1 2 0 1 3 0 3.00
14 | g1 13 1 0 1 0 1 1 0 1.00
15 | g1 14 1 0 1 0 1 1 0 1.00
16 | g1 15 1 0 1 0 1 1 0 1.00
17 | g1 16 1 0 1 0 1 1 0 1.00
18 | g1 17 1 0 1 0 1 1 0 1.00
19 | g1 18 0 0 0 0 0 0 0 0.00
20 | g1 19 0 0 0 0 0 0 0 0.00
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestih1nh2.txt:
--------------------------------------------------------------------------------
1 | g1 0 2 g1 0.00
2 | g1 2 4 g1 1.00
3 | g1 4 10 g1 2.00
4 | g1 10 12 g1 1.00
5 | g1 12 20 g1 0.00
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/coveragetasktestperbase.txt:
--------------------------------------------------------------------------------
1 | g1 0 0 0 0.00
2 | g1 1 0 0 0.00
3 | g1 2 2 0 2.00
4 | g1 3 2 0 2.00
5 | g1 4 3 0 3.00
6 | g1 5 4 1 4.50
7 | g1 6 4 1 4.50
8 | g1 7 4 1 4.50
9 | g1 8 4 1 4.50
10 | g1 9 4 1 4.50
11 | g1 10 3 1 3.50
12 | g1 11 3 1 3.50
13 | g1 12 2 1 2.50
14 | g1 13 1 0 1.00
15 | g1 14 1 0 1.00
16 | g1 15 1 0 1.00
17 | g1 16 1 0 1.00
18 | g1 17 1 0 1.00
19 | g1 18 0 0 0.00
20 | g1 19 0 0 0.00
21 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covstats-add-median.txt:
--------------------------------------------------------------------------------
1 | Coverage per region:
2 | depth breadth covered size name
3 | 3.75 0.3750 3 8 blah
4 | 3.75 0.3750 3 8 all regions
5 |
6 | Fold-80 Penalty: 11.72
7 | Median depth: 3.75
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covstats-levels.tsv:
--------------------------------------------------------------------------------
1 | #coverage_level count percent cumulative
2 | 0 8 9.41 100.00
3 | 1 13 15.29 90.59
4 | 2 46 54.12 75.29
5 | 3 13 15.29 21.18
6 | 4 5 5.88 5.88
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covstats-stats.tsv:
--------------------------------------------------------------------------------
1 | #depth breadth covered size name
2 | 2.00 1.0000 7 7 simulatedSequence1:41-47
3 | 2.11 1.0000 9 9 blah
4 | 2.41 1.0000 17 17 feh
5 | 1.77 1.0000 26 26 simulatedSequence2:18-43
6 | 1.80 0.7333 22 30 simulatedSequence2:64-94
7 | 1.93 0.9059 77 85 all regions
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/coverage/resources/covstats-summary.txt:
--------------------------------------------------------------------------------
1 | Coverage per region:
2 | depth breadth covered size name
3 | 2.00 1.0000 7 7 simulatedSequence1:41-47
4 | 2.11 1.0000 9 9 blah
5 | 2.41 1.0000 17 17 feh
6 | 1.77 1.0000 26 26 simulatedSequence2:18-43
7 | 1.80 0.7333 22 30 simulatedSequence2:64-94
8 | 1.93 0.9059 77 85 all regions
9 |
10 | Fold-80 Penalty: 1.14
11 | Median depth: 2.00
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/format/resources/vovf-test-several.vcf:
--------------------------------------------------------------------------------
1 | chr10 112109 . C T . PASS DP=38 GT:DP:RE:GQ 0/1:38:4.622:95
2 | chr10 115008 . G C . PASS DP=81 GT:DP:RE:GQ 0/1:81:15.368:164
3 | chr10 2028433 . A C,G . PASS DP=39 GT:DP:RE:GQ:RS 1/2:39:4.118:110:A,3,0.301,C,19,1.900,G,17,1.917
4 | chr10 2399390 . AT A . PASS DP=35 GT:DP:RE:GQ 1/1:35:2.602:98
5 | chr10 2402489 . A AGT 2147483647.0 PASS DP=34 GT:DP:RE:GQ 0/1:34:3.428:128
6 | chr10 82350 . C T 9.2 PASS DP=4 GT:DP:RE:GQ 1/1:4:0.400:9
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/bug1508_reads.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/bug1508_reads.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/bug1524.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/bug1524.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/bug1524.txt:
--------------------------------------------------------------------------------
1 | Failed Filters : 0
2 | Passed Filters : 1
3 | Complex Called : 1
4 | SNPs : 0
5 | MNPs : 0
6 | Insertions : 1
7 | Deletions : 0
8 | Indels : 0
9 | Same as reference : 0
10 | SNP Transitions/Transversions: - (0/0)
11 | Total Het/Hom ratio : 0.00 (0/1)
12 | SNP Het/Hom ratio : - (0/0)
13 | MNP Het/Hom ratio : - (0/0)
14 | Insertion Het/Hom ratio : 0.00 (0/1)
15 | Deletion Het/Hom ratio : - (0/0)
16 | Indel Het/Hom ratio : - (0/0)
17 | Insertion/Deletion ratio : - (1/0)
18 | Indel/SNP+MNP ratio : - (1/0)
19 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/bug1675_reads.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/bug1675_reads.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/calibration_global_sample.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build c27615f (2011-10-27), calibrate v2.0
2 | #CL map -i read_set/ -t template_renamed.sdf/ -o male_mappings --sex male --sam-rg @RG\tPL:ILLUMINA\tSM:male\tID:some_reads
3 | @del:some_reads 0 49 0 1
4 | @ins:some_reads 0 64 3 0 0 0 1
5 | @mnp:some_reads 0 6782 452 65 15 2 1
6 | @nh:some_reads 0 7978
7 | @covar readgroup basequality equal diff ins del
8 | some_reads 20 330000 3021 15 24
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/calibration_sample.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build c27615f (2011-10-27), calibrate v2.0
2 | #CL map -i read_set/ -t template_renamed.sdf/ -o male_mappings --sex male --sam-rg @RG\tPL:ILLUMINA\tSM:male\tID:some_reads
3 | @del:some_reads 0 49 0 1
4 | @ins:some_reads 0 64 3 0 0 0 1
5 | @mnp:some_reads 0 6782 452 65 15 2 1
6 | @nh:some_reads 0 7978
7 | @covar readgroup basequality sequence equal diff ins del
8 | some_reads 20 chr1 295364 3021 15 24
9 | some_reads 20 chr2 463114 4627 59 26
10 | some_reads 20 chrX 26540 258 2 2
11 | some_reads 20 chrY 4749 51 0 0
12 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/cg.txt:
--------------------------------------------------------------------------------
1 | #ASSEMBLY_ID GS000001152-ASM
2 | #DBSNP_BUILD dbSNP build 130
3 | #FORMAT_VERSION 1.3
4 | #GENERATED_AT 2010-Sep-25 04:20:13.034199
5 | #GENERATED_BY dbsnptool
6 | #GENOME_REFERENCE NCBI build 36
7 | #SAMPLE GS00225-DNA_H01
8 | #SOFTWARE_VERSION 1.8.0.32
9 | #TYPE VAR-ANNOTATION
10 |
11 | >locus ploidy allele sequence begin end varType reference alleleSeq totalScore hapLink xRef
12 | 1 2 all chr1 0 901 no-call = ?
13 | 2 2 all chr1 901 908 ref = =
14 | 3 2 all chr1 908 979 no-call = ?
15 | 4 2 all chr1 979 993 ref = =
16 | 5 2 all chr1 993 1000 no-call = ?
17 | 6 2 all chr1 1000 1008 ref = =
18 | 7 2 all chr1 1008 1115 no-call = ?
19 | 8 2 all chr1 1115 1132 ref = =
20 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/complexambigsuppressiontemplate.fa:
--------------------------------------------------------------------------------
1 | >chr13
2 | TCCCAGCTACTCAGGAGTCTGAGGTGGGAGAATTGCTTGATGCCAGGAGGCGGAGGTTGCAGTGAGCCGAGATTGCCCCATTGCACTCCAGCCTTGGCAACTGAGCGAGACTCCGTTTCAAAAAAAAAAAAAAAAAGGAGGAGAAAACAGACATAGAGGAAAAGAGGAGAAGGCCATGTGAAGATGGAGGCAGAGGGGGCCAAAGCCACGGAAGCCAGCAACCACTGGCAGCTGAACCAGGCAAGGAGTGGAGTCTTTTCTAGAGGGACTGTGGCCCTGCTAACA
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/complexhypercomplextemplate.fa:
--------------------------------------------------------------------------------
1 | >chr20
2 | TGCATGACCCTGTGCCTCCGAGGGCCACCAAACTATTTCCATGATAGAATTCCCTCTCGCAGAGGTGCAGAGTCCACTCTGAGTCACTCTACAACACACACACACACACACACCACACAAGCACACACACACCGCACACACAGACACTAGCTACTGAGCTAAGTTGCCCATACACTTGCCTCACCCCGGTTGC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/complexreadorder.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/complexreadorder.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/complexreadorder.sam.gz.tbi:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/complexreadorder.sam.gz.tbi
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/complexssp.fa:
--------------------------------------------------------------------------------
1 | >chr1
2 | CACTAGACCAGGCAGCTCTGTGTGGGGAAGTGTGTCTGTGTGTGCGTGTGTGTGCACAAGTGTGTATGTGTGCATGTGTTTGCACGTGTATATGTGTGCACACATCTGTGTGTATATGCACAGGTGTATGTATACGTGTGTGTTGGTGTATTTGTGTGTGTGTGGAAATGTATGCATGTATGCAGTGTGCATGTGTG
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/coverage_mated.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/coverage_mated.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/coverage_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/variant/resources/coverage_unmated.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/coverage_unmated.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/coverage_unmated.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 1
4 | @nh:TEST 0 5
5 | @covar readgroup basequality sequence equal diff ins del
6 | TEST 20 simulatedSequence1 29 1 0 0
7 | TEST 20 simulatedSequence2 20 0 0 0
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome1_mated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome1 -i reads1 -o out1 --sam-rg=@RG\tID:SAMPLE1\tPL:ILLUMINA\tSM:GENOME1
3 | @del:SAMPLE1 0 10
4 | @ins:SAMPLE1 0 11 1
5 | @mnp:SAMPLE1 0 1124 63 12 0 1
6 | @nh:SAMPLE1 0 1436
7 | @covar readgroup basequality sequence equal diff ins del
8 | SAMPLE1 20 simulatedSequence1 47759 435 6 4
9 | SAMPLE1 20 simulatedSequence2 46981 415 4 5
10 | SAMPLE1 20 simulatedSequence3 47556 441 3 1
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome1_unmated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome1 -i reads1 -o out1 --sam-rg=@RG\tID:SAMPLE1\tPL:ILLUMINA\tSM:GENOME1
3 | @mnp:SAMPLE1 0 32 1
4 | @nh:SAMPLE1 0 31
5 | @covar readgroup basequality sequence equal diff ins del
6 | SAMPLE1 20 simulatedSequence1 592 8 0 0
7 | SAMPLE1 20 simulatedSequence2 1283 17 0 0
8 | SAMPLE1 20 simulatedSequence3 1191 9 0 0
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome2_mated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome2 -i reads2 -o out2 --sam-rg=@RG\tID:SAMPLE2\tPL:ILLUMINA\tSM:GENOME2
3 | @del:SAMPLE2 0 19 4 0 1
4 | @ins:SAMPLE2 0 8 1
5 | @mnp:SAMPLE2 0 2279 150 13 2
6 | @nh:SAMPLE2 0 2994
7 | @covar readgroup basequality sequence equal diff ins del
8 | SAMPLE2 20 simulatedSequence1 95314 878 8 8
9 | SAMPLE2 20 simulatedSequence2 100732 866 2 20
10 | SAMPLE2 20 simulatedSequence3 100718 882 0 3
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome2_unmated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome2 -i reads2 -o out2 --sam-rg=@RG\tID:SAMPLE2\tPL:ILLUMINA\tSM:GENOME2
3 | @mnp:SAMPLE2 0 7
4 | @nh:SAMPLE2 0 3
5 | @covar readgroup basequality sequence equal diff ins del
6 | SAMPLE2 20 simulatedSequence2 99 1 0 0
7 | SAMPLE2 20 simulatedSequence3 194 6 0 0
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome3_mated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome3 -i reads3 -o out3 --sam-rg=@RG\tID:SAMPLE3\tPL:ILLUMINA\tSM:GENOME3
3 | @del:SAMPLE3 0 29 4
4 | @ins:SAMPLE3 0 25 2 2 1
5 | @mnp:SAMPLE3 0 3570 235 25 7 1
6 | @nh:SAMPLE3 0 4478
7 | @covar readgroup basequality sequence equal diff ins del
8 | SAMPLE3 20 simulatedSequence1 143673 1311 16 16
9 | SAMPLE3 20 simulatedSequence2 151176 1414 10 6
10 | SAMPLE3 20 simulatedSequence3 148764 1423 13 15
11 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/genome3_unmated.sam.gz.calibration:
--------------------------------------------------------------------------------
1 | #Version vPOST-2.3 build (), calibrate v2.0
2 | #CL map -t genome3 -i reads3 -o out3 --sam-rg=@RG\tID:SAMPLE3\tPL:ILLUMINA\tSM:GENOME3
3 | @del:SAMPLE3 0 1
4 | @mnp:SAMPLE3 0 6 1
5 | @nh:SAMPLE3 0 11
6 | @covar readgroup basequality sequence equal diff ins del
7 | SAMPLE3 20 simulatedSequence1 498 2 0 1
8 | SAMPLE3 20 simulatedSequence2 297 3 0 0
9 | SAMPLE3 20 simulatedSequence3 297 3 0 0
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/hyper_oldcli.vcf:
--------------------------------------------------------------------------------
1 | simulatedSequence1 1 . C T 40.7 PASS DP=3 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:3:0.031:0.000:7:0.00:6.51:0.00:0.000,59.745:0.00:T,3,0.031:0,3:-4.07,-0.73,-0.09
2 | simulatedSequence1 50 . A T 32.3 PASS DP=3 GT:DP:RE:AR:GQ:ABP:SBP:RPB:AQ:PUR:RS:AD:GL 1/1:3:0.031:0.000:8:0.00:6.51:0.00:0.000,59.745:0.00:T,3,0.031:0,3:-3.23,-0.79,-0.08
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/hypertemplate.fa:
--------------------------------------------------------------------------------
1 | >simulatedSequence1
2 | CCTAATGCCGTTAGGATCAAACGTGCCATCATCTGTGCATGCTAGGGAGACACCCACCGAAGGCGCTTGAGGCTCACTATTTGACGACATGGATAAACAC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/ident-insert2-genome.fa:
--------------------------------------------------------------------------------
1 | >chr9
2 | TGCTGAGAAGTTAAATCTGTCCTTTTGGGGCAATCTAAGGGAGAAAAGCTTAAGACTTCTACATATTAATTTCTGCTAAGACTAAATTATCCTCCACTCCTACCAACATCCCCCCTGCAACAGCAAAAAAAAAAAAAAAAAAAAAAAAATGGCAAAAAGCTAAATGCCTCTTCTGCATTTTTTTTTTCTTTTTGAGACAGGGTCTCACTCTGTCACTCACGCTGGAGTGCAGTGGCACAATCTAGGCTCACTGCAATCTCCGCCCCCAGGTTCAAGCAATTCTCCCACTTCAGCTTCCC
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/n2-mappings2.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.4 SO:coordinate
2 | @SQ SN:ref LN:294
3 | @RG ID:READGROUP2 PL:ILLUMINA SM:CANCER
4 | @CO RUN-ID:a53d8433-0046-4955-99c9-8e2d9c3f51a4
5 | @CO TEMPLATE-SDF-ID:d1ee64e1-af15-4947-aba1-da1530793fa8
6 | 0 0 ref 20 37 83=5X15D38= * 0 0 GATAGTCTTACCCCAAGGCCAAAGTCCTATTTTATTATTTTTATATTCTTACTATATATTATACAAATCTTCATTGCAAGTTTAAAAAAAGTAAAAACATAAGAAATCTAATTTTTGTATATAAAA * AS:i:56 NM:i:20 RG:Z:READGROUP1 IH:i:1 NH:i:1
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/out.rtg.txt:
--------------------------------------------------------------------------------
1 | #ASSEMBLY_ID GS000001152-ASM
2 | #DBSNP_BUILD dbSNP build 130
3 | #FORMAT_VERSION 1.3
4 | #GENERATED_AT 2010-Sep-25 04:20:13.034199
5 | #GENERATED_BY dbsnptool
6 | #GENOME_REFERENCE NCBI build 36
7 | #SAMPLE GS00225-DNA_H01
8 | #SOFTWARE_VERSION 1.8.0.32
9 | #TYPE VAR-ANNOTATION
10 | #name position type reference prediction posterior coverage correction support_statistics
11 | chr1 1 x = ? 0 0 0.000
12 | chr1 909 x = ? 0 0 0.000
13 | chr1 994 x = ? 0 0 0.000
14 | chr1 1009 x = ? 0 0 0.000
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/sam11.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/sam11.sam.gz
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/src/test/resources/com/rtg/variant/resources/sam11.sam.gz.tbi:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/sam11.sam.gz.tbi
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/src/test/resources/com/rtg/variant/resources/test2.calibration:
--------------------------------------------------------------------------------
1 | #CL calibrate C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\unmated.chr22.sam.gz -t C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\chr22 -c basequality
2 | @mnp:readgroup1 0 1
3 | @nh:readgroup1 0 10
4 | @covar basequality equal diff ins del
5 | 2 5 5 0 0
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/test3.calibration:
--------------------------------------------------------------------------------
1 | #CL calibrate C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\unmated.chr22.sam.gz -t C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\chr22 -c basequality
2 | @mnp:readgroup1 0 1
3 | @nh:readgroup1 0 10
4 | @covar basequality equal diff ins del
5 | 2 4000000000 4000000 5000000 6000000
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/test4.calibration:
--------------------------------------------------------------------------------
1 | #CL calibrate C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\unmated.chr22.sam.gz -t C:\Workspace\slim\internal\com\rtg\regression\data\calibrate\chr22 -c basequality
2 | @mnp:readgroup1 0 1
3 | @nh:readgroup1 0 10
4 | @covar readgroup basequality machinecycle:35 equal diff ins del
5 | readgroup1 2 0 40000000000 4000000 1000000 2000000
6 | readgroup1 2 1 4000000000 4000000 5000000 6000000
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/variantnanotest-complexambsuppression.vcf:
--------------------------------------------------------------------------------
1 | chr13 119 . C CAA 118.8 a8.0 DP=12;XRX;STRL=16;STRU=1 GT:DP:RE:AR:GQ:ABP:SBP:RPB:PPB:AQ:PUR:AD:GL 0/1:12:2.024:0.167:45:0.24:3.91:2.90:0.00:117.813,144.699:0.00:6,5:-11.88,0.00,-6.49
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/variantnanotest-identityinsert.vcf:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/resources/variantnanotest-identityinsert.vcf
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/src/test/resources/com/rtg/variant/resources/vcfcomplexsoftcliptest.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:g1 LN:52
3 | @CO TEMPLATE-SDF-ID:00000000-0000-0000-0000-00000000002a
4 | @RG ID:RG1 SM:TEST PL:ILLUMINA
5 | 0a 0 g1 2 255 1S5=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
6 | 0b 0 g1 2 255 1S5=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
7 | 0c 0 g1 3 255 2S4=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
8 | 0d 0 g1 3 255 2S4=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
9 | 0e 0 g1 4 255 3S3=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
10 | 0f 0 g1 4 255 3S3=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
11 | 0g 0 g1 5 255 4S2=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
12 | 0h 0 g1 5 255 4S2=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
13 | 0g 0 g1 6 255 5S1=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
14 | 0h 0 g1 6 255 5S1=3I3= * 0 0 AAATCGTTTACT ```````````` AS:i:1 RG:Z:RG1
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/vcfsnpsoftcliptest.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:g1 LN:52
3 | @CO TEMPLATE-SDF-ID:00000000-0000-0000-0000-00000000002a
4 | @RG ID:RG1 SM:TEST PL:ILLUMINA
5 | 0a 0 g1 2 255 1S4=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
6 | 0b 0 g1 2 255 1S4=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
7 | 0c 0 g1 3 255 2S3=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
8 | 0d 0 g1 3 255 2S3=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
9 | 0e 0 g1 4 255 3S2=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
10 | 0f 0 g1 4 255 3S2=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
11 | 0g 0 g1 5 255 4S1=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
12 | 0h 0 g1 5 255 4S1=1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
13 | 0g 0 g1 6 255 5S1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
14 | 0h 0 g1 6 255 5S1X3= * 0 0 AAATCAACT ````````` AS:i:1 RG:Z:RG1
15 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/resources/vcftesttmpl.fa:
--------------------------------------------------------------------------------
1 | >g1
2 | aaatcgactggtcagctaggagcttgtcattctgactgcaacgggcaatatg
3 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/pattern/resources/discordant_pairs.vcf.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/sv/discord/pattern/resources/discordant_pairs.vcf.gz
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/src/test/resources/com/rtg/variant/sv/discord/pattern/resources/sv_load.txt:
--------------------------------------------------------------------------------
1 | VcfBreakpoint: simulatedSequence1 49999 C]simulatedSequence1:53016]
2 | VcfBreakpoint: simulatedSequence1 50002 [simulatedSequence1:53013[G
3 | VcfBreakpoint: simulatedSequence1 53015 T]simulatedSequence1:50000]
4 | VcfBreakpoint: simulatedSequence1 53012 [simulatedSequence2:50003[C
5 | VcfBreakpoint: simulatedSequence2 53015 T]simulatedSequence1:50000]
6 | VcfBreakpoint: simulatedSequence2 53014 T]simulatedSequence2:50000]
7 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/pattern/resources/sv_patterns.bed:
--------------------------------------------------------------------------------
1 | #Version[...]
2 | #CL foo bar baz
3 | #sequence start end description count
4 | simulatedSequence1 49999 50002 inserted_copy:simulatedSequence1:53015-53012 22
5 | simulatedSequence1 49999 53015 inversion 22
6 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/resources/depth-2.txt:
--------------------------------------------------------------------------------
1 | 2 g1 19 90 g2 14 -57 36 76 g1 20 89 g2 13 -56 36 76
2 | 2 g2 14 -57 g1 19 90 36 76 g2 13 -56 g1 20 89 36 76
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/resources/discordantstats:
--------------------------------------------------------------------------------
1 | Total calls: 3
2 | Passed Filters: 2
3 | Failed Filters: 1
4 | Structural variant breakends: 2
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/resources/end-to-end.txt:
--------------------------------------------------------------------------------
1 | 1 g1 15 -55 g1 21 91 36 76 g1 15 -55 g1 21 91 36 76
2 | 2 g1 19 90 g2 14 -57 36 76 g1 20 89 g2 13 -56 36 76
3 | 1 g1 21 91 g1 15 -55 36 76 g1 21 91 g1 15 -55 36 76
4 | 2 g2 14 -57 g1 19 90 36 76 g2 13 -56 g1 20 89 36 76
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/resources/null-intersection-false.txt:
--------------------------------------------------------------------------------
1 | 5 g1 12 148 g2 83 -57 25 76
2 | 1 g1 21 91 g1 15 -55 36 76 g1 21 91 g1 15 -55 36 76
3 | 1 g1 78 148 g3 83 13 25 65 g1 78 148 g3 83 13 25 65
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/discord/resources/null-intersection-true.txt:
--------------------------------------------------------------------------------
1 | 1 g1 21 91 g1 15 -55 36 76 g1 21 91 g1 15 -55 36 76
2 | 1 g1 78 148 g3 83 13 25 65 g1 78 148 g3 83 13 25 65
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/augmented.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.6 SO:coordinate
2 | @SQ SN:gi0 LN:30
3 | @SQ SN:gi1 LN:30
4 | ba 73 gi0 1 255 10M * 0 0 AAAAAAAAAA IB7?*III (), rgstats v1.3
2 | #CL svprep -i mappings_pe_svdup2
3 | #RG-ID total-ref length-n length-x length-x2 insert-n insert-x insert-x2 insert-n insert-x insert-x2 max-score proper discordant unmated
4 | rtgtest_pe 200000 10071 1007100.0 100710000.0 10042 4026218.0 1633004350.0 10042 4026218.0 1633004350.0 8 10042 24 5
5 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/small_sv_interesting.bed:
--------------------------------------------------------------------------------
1 | #chr start end areas maxscore average
2 | simulatedSequence1 47400 47694 3 1.0889 0.3722
3 | simulatedSequence1 49712 52717 5 2.5766 1.1907
4 | simulatedSequence1 52747 52758 1 0.0000 -0.0721
5 | simulatedSequence1 52766 52767 1 0.0000 -0.0630
6 | simulatedSequence1 52769 52789 1 0.1322 0.1099
7 | simulatedSequence1 52793 52807 1 0.0000 -0.0258
8 | simulatedSequence1 52810 53134 1 1.8786 1.1216
9 | simulatedSequence1 55032 55119 1 0.4204 0.0312
10 | simulatedSequence1 55190 55246 1 0.1123 -0.0294
11 | simulatedSequence1 55779 56265 4 7.5133 1.7407
12 | simulatedSequence1 58291 99999 1 1.7161 0.5013
13 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/smallsvMappings.sam.gz:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/sv/resources/smallsvMappings.sam.gz
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/smallsvMappings.sam.gz.tbi:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/sv/resources/smallsvMappings.sam.gz.tbi
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/smallsvTemplate.dwa:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/sv/resources/smallsvTemplate.dwa
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/svtasktest1_bayes.txt:
--------------------------------------------------------------------------------
1 | #Version
2 | #CL sv
3 | #template-name position normal-cov2 normal-cov4 delete-inner del-bound del-bound-rev dup-bound dup-bound-rev breakpoint novel-ins-bp
4 | g1 1
5 | g1 2
6 | g1 3
7 | g1 4
8 | g1 5
9 | g1 6
10 | g1 7
11 | g1 8
12 | g1 9
13 | g1 10
14 | g1 11
15 | g1 12
16 | g1 13
17 | g1 14
18 | g1 15
19 | g1 16
20 | g1 17
21 | g1 18
22 | g1 19
23 | g1 20
24 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/svtasktest4_bayes.txt:
--------------------------------------------------------------------------------
1 | #Version
2 | #CL sv
3 | #template-name position normal-cov2 normal-cov4 delete-inner del-bound del-bound-rev dup-bound dup-bound-rev breakpoint novel-ins-bp
4 | g1 1
5 | g1 2
6 | g1 3
7 | g1 4
8 | g1 5
9 | g1 6
10 | g1 7
11 | g1 8
12 | g1 9
13 | g1 10
14 | g1 11
15 | g1 12
16 | g1 13
17 | g1 14
18 | g1 15
19 | g1 16
20 | g1 17
21 | g1 18
22 | g1 19
23 | g1 20
24 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/variant/sv/resources/testTemplate.dwa:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/src/test/resources/com/rtg/variant/sv/resources/testTemplate.dwa
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/src/test/resources/com/rtg/vcf/validator/resources/badHeaders.txt:
--------------------------------------------------------------------------------
1 | VCF INFO field DUR not contained in the specified rule set.
2 | VCF INFO field DP does not match the expected meta-data type.
3 | VCF INFO field DPR does not match the expected type, or has wrong type for VCF version.
4 | VCF FORMAT field DP does not match the expected number of values.
5 | VCF FORMAT field AVR does not match the expected meta-data type.
6 |
7 | Number of fields in headers that conflict with rule definitions: 4
8 | Number of fields in headers not defined in rules: 1
9 |
10 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/vcf/validator/resources/boringNormal.vcf:
--------------------------------------------------------------------------------
1 | ##fileformat=VCFv4.1
2 | ##fileDate=20130624
3 | ##source=handmade
4 | ##CL=notepad++.exe
5 | ##RUN-ID=16fd3065-1574-4753-a358-de3b641dfe69
6 | ##TEMPLATE-SDF-ID=3f642190-1b3e-45b4-b8f2-1af6bc71284f
7 | ##reference=c:\Workspace\rtg\internal\com\rtg\regression\data\family\sub21
8 | ##contig=
9 | ##FORMAT=
10 | ##SAMPLE=
11 | ##SAMPLE=
12 | ##SAMPLE=
13 | ##PEDIGREE=
14 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA19239 NA19238 NA19240
15 | chr21 125 . A G 132.6 PASS . GT 0/0 0/0 0/1
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-color.txt:
--------------------------------------------------------------------------------
1 | [36m LOC:[39m g1:11-15
2 | [48;5;237m 1 [49m
3 | [48;5;237m56789012345678[49m
4 | |[4m [24m|
5 | [36m REF:[39m CGACTGGTCAGCTA
6 | [36m GEN:[39m [48;5;22mC[49m (1) SM:SAMPLE snps.vcf
7 | [36m GEN:[39m [48;5;22mT[49m (1) SM:SAMPLE snps.vcf
8 | [36m CALL:[39m [48;5;58mC[49m (2) SM:SAMPLE snps.vcf
9 | [36m CALL:[39m [48;5;58mT[49m (2) SM:SAMPLE snps.vcf
10 | [36m READ:[39m [1mCGACTG[48;5;58mG[49mT [22m > SE NH:1 AS:1
11 | [36m READ:[39m [1m GACTG[48;5;58mG[49mTC [22m > SE NH:1 AS:1
12 | [36m READ:[39m [1m GACTG[48;5;58mG[49mTC [22m > SE NH:1 AS:1
13 | [36m READ:[39m [1m [48;5;58mG[49mTCAGCTA[22m > SE NH:1 AS:1
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-delete-exp.txt:
--------------------------------------------------------------------------------
1 | LOC: g1:9
2 | 89012
3 | |
4 | REF: CTGGT
5 | BED: (* (1) mybed
6 | CALL: * (2) SM:SAMPLE mysnps
7 | CALL: * (2) SM:SAMPLE mysnps
8 | READ: ..... > SE NH:1 AS:0
9 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-deletes.txt:
--------------------------------------------------------------------------------
1 | LOC: g1:9-12
2 | _ 1
3 | 345_6789012345678
4 | | |
5 | REF: ATC_GACTGGTCAGCTA
6 | GEN: C (1) SM:SAMPLE snps.vcf
7 | GEN: T (1) SM:SAMPLE snps.vcf
8 | CALL: C (2) SM:SAMPLE snps.vcf
9 | CALL: T (2) SM:SAMPLE snps.vcf
10 | READ: ..._..... > SE NH:1 AS:0
11 | READ: ..._..... > SE NH:1 AS:0
12 | READ: .A....... > SE NH:1 AS:1
13 | READ: ........ > SE NH:1 AS:1
14 | READ: ........ > SE NH:1 AS:1
15 | READ: ........ > SE NH:1 AS:1
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-inserts.txt:
--------------------------------------------------------------------------------
1 | LOC: g1:9-12
2 | _ 1
3 | 345_6789012345678
4 | | |
5 | REF: ATC_GACTGGTCAGCTA
6 | GEN: C (1) SM:SAMPLE snps.vcf
7 | GEN: T (1) SM:SAMPLE snps.vcf
8 | CALL: C (2) SM:SAMPLE snps.vcf
9 | CALL: T (2) SM:SAMPLE snps.vcf
10 | READ: ..._..... > SE NH:1 AS:0
11 | READ: ..._..... > SE NH:1 AS:0
12 | READ: .A....... > SE NH:1 AS:1
13 | READ: ........ > SE NH:1 AS:1
14 | READ: ........ > SE NH:1 AS:1
15 | READ: ........ > SE NH:1 AS:1
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-nocolor.txt:
--------------------------------------------------------------------------------
1 | LOC: g1:10-12
2 | 1
3 | 3456789012345678
4 | ||
5 | REF: ATCGACTGGTCAGCTA
6 | GEN: C (1) SM:SAMPLE snps.vcf
7 | GEN: T (1) SM:SAMPLE snps.vcf
8 | CALL: C (2) SM:SAMPLE snps.vcf
9 | CALL: T (2) SM:SAMPLE snps.vcf
10 | READ: ATCGACTG > SE NH:1 AS:0
11 | READ: ATCGACTG > SE NH:1 AS:0
12 | READ: CGACTGGT > SE NH:1 AS:1
13 | READ: GACTGGTC > SE NH:1 AS:1
14 | READ: GACTGGTC > SE NH:1 AS:1
15 | READ: GTCAGCTA > SE NH:1 AS:1
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-rg.txt:
--------------------------------------------------------------------------------
1 | LOC: g1:1-12
2 | 1
3 | 123456789012345678
4 | | |
5 | REF: AAATCGACTGGTCAGCTA
6 | GEN: C (1) SM:SAMPLE snps.vcf
7 | GEN: T (1) SM:SAMPLE snps.vcf
8 | CALL: C (2) SM:SAMPLE snps.vcf
9 | CALL: T (2) SM:SAMPLE snps.vcf
10 | READ: GACTGGTC > SE NH:1 AS:1 RG:A SM:NA12 255
11 | READ: GACTGGTC > SE NH:1 AS:1 RG:A SM:NA12 255
12 | READ: GTCAGCTA > SE NH:1 AS:1 RG:A SM:NA12 255
13 | READ: ATCGACTG > SE NH:1 AS:0 RG:B SM:NA12 255
14 | READ: ATCGACTG > SE NH:1 AS:0 RG:B SM:NA12 255
15 | READ: CGACTGGT > SE NH:1 AS:1 RG:B SM:NA12 255
16 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/aview-toomuchtemplate.txt:
--------------------------------------------------------------------------------
1 | [36m LOC:[39m g1:11-24
2 | [48;5;237m 1 2[49m
3 | [48;5;237m5678901234567890[49m
4 | |[4m [24m|
5 | [36m REF:[39m CGACTGGTCAGCTAGG
6 | [36m GEN:[39m [48;5;22mC[49m (1) SM:SAMPLE snps.vcf
7 | [36m GEN:[39m [48;5;22mT[49m (1) SM:SAMPLE snps.vcf
8 | [36m CALL:[39m [48;5;58mC[49m (2) SM:SAMPLE snps.vcf
9 | [36m CALL:[39m [48;5;58mT[49m (2) SM:SAMPLE snps.vcf
10 | [36m READ:[39m [1mCGACTG[48;5;58mG[49mT [22m > SE NH:1 AS:1
11 | [36m READ:[39m [1m GACTG[48;5;58mG[49mTC [22m > SE NH:1 AS:1
12 | [36m READ:[39m [1m GACTG[48;5;58mG[49mTC [22m > SE NH:1 AS:1
13 | [36m READ:[39m [1m [48;5;58mG[49mTCAGCTA [22m > SE NH:1 AS:1
14 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/extracted3.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:chr6 LN:170899992
3 | @PG ID:rtg sam2bam VN:vPOST-2.0.1-DEV build 31832 (2010-09-30)
4 | @CO READ-SDF-ID:2bfa1ee2afe9f259
5 | 29832454 153 chr6 18 255 3X3=5I5=1D7=6N10= * 0 0 ACTAATAGAGCTGATTTCCTTGCCTCTCGAGTA 99944525;;:;:<<<<<;=;<:88793::9:8 AS:i:17 NM:i:9 GS:Z:AAAA GC:Z:3S2G28S GQ:Z:76 IH:i:3
6 | 39867921 89 chr6 20 255 10=6N10=3N3=1X3=3X1=1X1= * 0 0 CAATTGATTCCCTCACCCTCAGTTGCTCAAAAT 88,%)788+8;:8:++::2*077718047,088 AS:i:15 NM:i:7 GS:Z:AAAA GC:Z:28S2G3S GQ:Z:8% IH:i:3
7 | 58432667 89 chr6 20 255 10=6N10=1I2=4X2=1X1=2X * 0 0 CAATTGATTCCCTCACCCTCATCTCAGAGCTTC 783%+3'-:0319(21-1<967-771,5.')38 AS:i:15 NM:i:8 GS:Z:GCGG GC:Z:28S2G3S GQ:Z:8- IH:i:1
8 |
--------------------------------------------------------------------------------
/src/test/resources/com/rtg/visualization/resources/genome.fa:
--------------------------------------------------------------------------------
1 | >chr6
2 | AACCTCCACCTCCCAGGTTCAATTGATTCTCCTTGCCTCACCCTCTCGAGTAGCTGGGATTACAGATGAGGGCCACCAC
3 |
--------------------------------------------------------------------------------
/test/bedRegions.bed:
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https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/test/bedRegions.bed
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/test/bedRegions.bed.gz:
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https://raw.githubusercontent.com/RealTimeGenomics/rtg-core/26368592853ee48a3871858971c6f7b328367150/test/bedRegions.bed.gz
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