├── .clang-format ├── .dir-locals.el ├── .gitignore ├── .travis.yml ├── CODING_STYLE.txt ├── LICENSE.txt ├── Makefile ├── README.md ├── __init__.py ├── alignmentDepth ├── Makefile └── halAlignmentDepth.cpp ├── analysis ├── Makefile ├── __init__.py ├── constraintTurnover │ ├── __init__.py │ └── turnoverModel.py ├── halContiguousRegions.py ├── halContiguousRegionsTest.py ├── neutralIndel │ ├── __init__.py │ ├── backgroundRate.py │ ├── bedConservation.py │ ├── bedHistogram.py │ ├── bedMutations.py │ ├── estimateTurnoverParams.py │ ├── getBedLength.py │ ├── halTreeNIBackground.py │ ├── halTreeNIConservation.py │ ├── halTreeNITurnover.py │ └── turnoverRate.py └── syntenyRates.py ├── api ├── Makefile ├── __init__.py ├── doc │ ├── doxy.cfg │ └── naming-conventions.txt ├── hdf5_impl │ ├── hdf5Alignment.cpp │ ├── hdf5Alignment.h │ ├── hdf5BottomSegment.cpp │ ├── hdf5BottomSegment.h │ ├── hdf5Common.h │ ├── hdf5DnaArray.h │ ├── hdf5DnaDriver.cpp │ ├── hdf5DnaDriver.h │ ├── hdf5ExternalArray.cpp │ ├── hdf5ExternalArray.h │ ├── hdf5Genome.cpp │ ├── hdf5Genome.h │ ├── hdf5MetaData.cpp │ ├── hdf5MetaData.h │ ├── hdf5Sequence.cpp │ ├── hdf5Sequence.h │ ├── hdf5SequenceIterator.cpp │ ├── hdf5SequenceIterator.h │ ├── hdf5TopSegment.cpp │ ├── hdf5TopSegment.h │ ├── hdf5UDCFuseDriver.cpp │ └── hdf5UDCFuseDriver.h ├── hdf5_tests │ ├── allTests.cpp │ ├── allTests.h │ ├── hdf5DnaTypeTest.cpp │ ├── hdf5ExternalArrayTest.cpp │ ├── hdf5SegmentTypeTest.cpp │ ├── hdf5SequenceTypeTest.cpp │ ├── hdf5Test.cpp │ └── hdf5Test.h ├── impl │ ├── halAlignmentInstance.cpp │ ├── halBottomSegment.cpp │ ├── halBottomSegmentIterator.cpp │ ├── halCLParser.cpp │ ├── halColumnIterator.cpp │ ├── halCommon.cpp │ ├── halGappedBottomSegmentIterator.cpp │ ├── halGappedTopSegmentIterator.cpp │ ├── halGenome.cpp │ ├── halMappedSegment.cpp │ ├── halPositionCache.cpp │ ├── halRearrangement.cpp │ ├── halSegment.cpp │ ├── halSegmentIterator.cpp │ ├── halSegmentMapper.cpp │ ├── halSequence.cpp │ ├── halTopSegment.cpp │ ├── halTopSegmentIterator.cpp │ ├── halValidate.cpp │ └── udc2.c ├── inc │ ├── hal.h │ ├── halAlignment.h │ ├── halAlignmentInstance.h │ ├── halBottomSegment.h │ ├── halBottomSegmentIterator.h │ ├── halCLParser.h │ ├── halColumnIterator.h │ ├── halColumnIteratorStack.h │ ├── halCommon.h │ ├── halDefs.h │ ├── halDnaDriver.h │ ├── halDnaIterator.h │ ├── halGappedBottomSegmentIterator.h │ ├── halGappedSegmentIterator.h │ ├── halGappedTopSegmentIterator.h │ ├── halGenome.h │ ├── halMappedSegment.h │ ├── halMappedSegmentContainers.h │ ├── halMetaData.h │ ├── halPositionCache.h │ ├── halRearrangement.h │ ├── halSegment.h │ ├── halSegmentIterator.h │ ├── halSegmentMapper.h │ ├── halSegmentedSequence.h │ ├── halSequence.h │ ├── halSequenceIterator.h │ ├── halSlicedSegment.h │ ├── halTopSegment.h │ ├── halTopSegmentIterator.h │ ├── halValidate.h │ └── udc2.h ├── mmap_impl │ ├── mmapAlignment.cpp │ ├── mmapAlignment.h │ ├── mmapArray.h │ ├── mmapBottomSegment.cpp │ ├── mmapBottomSegment.h │ ├── mmapBottomSegmentData.h │ ├── mmapDnaDriver.cpp │ ├── mmapDnaDriver.h │ ├── mmapFile.cpp │ ├── mmapFile.h │ ├── mmapGenome.cpp │ ├── mmapGenome.h │ ├── mmapGenomeSiteMap.cpp │ ├── mmapGenomeSiteMap.h │ ├── mmapMetaData.h │ ├── mmapPerfectHashTable.cpp │ ├── mmapPerfectHashTable.h │ ├── mmapPhf.cpp │ ├── mmapPhf.h │ ├── mmapPhf.md │ ├── mmapRbTree.cpp │ ├── mmapRbTree.h │ ├── mmapSequence.cpp │ ├── mmapSequence.h │ ├── mmapSequenceData.h │ ├── mmapSequenceIterator.h │ ├── mmapString.h │ ├── mmapTopSegment.cpp │ ├── mmapTopSegment.h │ └── mmapTopSegmentData.h └── tests │ ├── halAlignmentTreesTest.cpp │ ├── halApiTestSupport.cpp │ ├── halApiTestSupport.h │ ├── halBottomSegmentTest.cpp │ ├── halColumnIteratorTest.cpp │ ├── halGappedSegmentIteratorTest.cpp │ ├── halGenomeTest.cpp │ ├── halMappedSegmentTest.cpp │ ├── halMetaDataTest.cpp │ ├── halRandNumberGen.h │ ├── halRandomData.cpp │ ├── halRandomData.h │ ├── halRearrangementTest.cpp │ ├── halSegmentTestSupport.h │ ├── halSequenceTest.cpp │ ├── halTopSegmentTest.cpp │ ├── halValidateTest.cpp │ └── udc2Test.c ├── assemblyHub ├── Makefile ├── README.md ├── __init__.py ├── alignabilityTrack.py ├── assemblyHubCommon.py ├── bedCommon.py ├── bedTrack.py ├── conservationTrack.py ├── docs │ ├── __init__.py │ ├── alignabilityDocs.py │ ├── conservationDocs.py │ ├── gcPercentDocs.py │ ├── hubCentralDocs.py │ ├── makeDocs.py │ └── repeatMaskerDocs.py ├── gcPercentTrack.py ├── groupExclusiveRegions.py ├── hal2assemblyHub.py ├── hal2assemblyHubDoc.pdf ├── halGenerateComparisonHub.py ├── prepareHubFiles.py ├── prepareLodFiles.py ├── rmskTrack.py ├── snakeTrack.py ├── treeCommon.py └── wigTrack.py ├── benchmarks ├── benchMark.py ├── mafMutations.cpp ├── results │ └── .gitignore └── runAndGetResources.py ├── blockViz ├── Makefile ├── __init__.py ├── impl │ ├── hal2chain.cpp │ └── halBlockViz.cpp ├── inc │ └── halBlockViz.h └── tests │ ├── blockVizBed.cpp │ ├── blockVizBenchmark.py │ ├── blockVizMaf.cpp │ ├── blockVizTest.cpp │ ├── expected │ ├── blockVizHdf5Tests.out │ └── blockVizMmapTests.out │ └── timing.sh ├── doc └── to-do.org ├── extra ├── dotplot │ ├── README.md │ ├── example.png │ ├── plotDotplot.R │ └── runDotplot.py └── insertionStats │ ├── getInsertionStats.py │ └── plotInsertionStats.R ├── extract ├── Makefile ├── __init__.py ├── impl │ ├── hal4dExtract.cpp │ ├── hal4dExtractMain.cpp │ ├── halAlignedExtract.cpp │ ├── halExtract.cpp │ ├── halMaskExtractMain.cpp │ ├── halMaskExtractor.cpp │ └── halSingleCopyRegionsExtract.cpp ├── inc │ ├── hal4dExtract.h │ └── halMaskExtractor.h └── tests │ ├── hal4dExtractTest.cpp │ └── input │ └── small.mmap1.0.hal.bz2 ├── fasta ├── Makefile └── hal2fasta.cpp ├── include.mk ├── liftover ├── Makefile ├── halLiftoverStatus.py ├── impl │ ├── halBedLine.cpp │ ├── halBedScanner.cpp │ ├── halBlockLiftover.cpp │ ├── halBlockMapper.cpp │ ├── halColumnLiftover.cpp │ ├── halLiftover.cpp │ ├── halLiftoverMain.cpp │ ├── halWiggleLiftover.cpp │ ├── halWiggleLiftoverMain.cpp │ ├── halWiggleLoader.cpp │ └── halWiggleScanner.cpp ├── inc │ ├── halBedLine.h │ ├── halBedScanner.h │ ├── halBlockLiftover.h │ ├── halBlockMapper.h │ ├── halColumnLiftover.h │ ├── halLiftover.h │ ├── halWiggleLiftover.h │ ├── halWiggleLoader.h │ ├── halWiggleScanner.h │ └── halWiggleTiles.h └── tests │ ├── expected │ ├── halLiftoverBed12ExtraTest.bed │ ├── halLiftoverBed12Test.bed │ ├── halLiftoverBed3Test.bed │ ├── halLiftoverBed4ExtraTest.bed │ ├── halLiftoverPsl12Test.psl │ └── halLiftoverPsl3Test.psl │ ├── halLiftoverTests.cpp │ ├── halLiftoverTests.h │ └── input │ ├── test1.bed12 │ ├── test1.bed12+2 │ ├── test1.bed3 │ └── test1.bed4+2 ├── lod ├── Makefile ├── __init__.py ├── halLodBenchmark.py ├── halLodInterpolate.py ├── impl │ ├── halLodBlock.cpp │ ├── halLodExtract.cpp │ ├── halLodExtractMain.cpp │ ├── halLodGraph.cpp │ ├── halLodManager.cpp │ └── halLodSegment.cpp └── inc │ ├── halLodBlock.h │ ├── halLodExtract.h │ ├── halLodGraph.h │ ├── halLodManager.h │ └── halLodSegment.h ├── maf ├── Makefile ├── __init__.py ├── hal2mafMP.py ├── impl │ ├── hal2maf.cpp │ ├── halMafBed.cpp │ ├── halMafBlock.cpp │ ├── halMafExport.cpp │ ├── halMafScanDimensions.cpp │ ├── halMafScanReference.cpp │ ├── halMafScanner.cpp │ ├── halMafWriteGenomes.cpp │ ├── maf2hal.cpp │ └── naiveLiftUp.py ├── inc │ ├── halMafBed.h │ ├── halMafBlock.h │ ├── halMafExport.h │ ├── halMafScanDimensions.h │ ├── halMafScanReference.h │ ├── halMafScanner.h │ └── halMafWriteGenomes.h └── tests │ ├── expected │ ├── hal2mafMPBySeqTest_Genome_0_seq.maf │ ├── hal2mafMPRefTargetsGenomesTest.maf │ ├── hal2mafMPTargetGenomesTest.maf │ ├── hal2mafSeqPartTest.maf │ ├── hal2mafSeqTest.maf │ └── hal2mafSmallTest.maf │ ├── halMafBlockTest.cpp │ ├── halMafBlockTest.h │ ├── halMafExportTest.cpp │ ├── halMafTests.cpp │ ├── halMafTests.h │ └── input │ └── small-Genome_0.bed ├── modify ├── Makefile ├── ancestorsML.cpp ├── ancestorsML.h ├── ancestorsMLBed.cpp ├── ancestorsMLBed.h ├── ancestorsMLMP.py ├── ancestorsMLMain.cpp ├── ancestorsMLTest.cpp ├── findRegionsExclusivelyInGroup.cpp ├── halAddToBranch.cpp ├── halAppendSubtree.cpp ├── halRemoveGenome.cpp ├── halRemoveSubtree.cpp ├── halRenameGenomes.cpp ├── halRenameSequences.cpp ├── halReplaceGenome.cpp ├── halSetMetadata.cpp ├── halUpdateBranchLengths.cpp ├── halWriteNucleotides.cpp ├── markAncestors.cpp ├── markAncestors.h ├── renameFile.cpp └── renameFile.h ├── mutations ├── Makefile ├── __init__.py ├── impl │ ├── __init__.py │ ├── halBranchMutations.cpp │ ├── halBranchMutationsMain.cpp │ ├── halIndels.cpp │ ├── halMutationsStats.cpp │ ├── halSnps.cpp │ ├── halSummarizeMutations.cpp │ ├── halSummarizeMutationsMain.cpp │ └── halTreeMutations.py └── inc │ ├── halAverage.h │ ├── halBranchMutations.h │ ├── halMutationsStats.h │ └── halSummarizeMutations.h ├── paf ├── Makefile ├── hal2paf.cpp └── tests │ ├── expected │ ├── hal2pafMouseRatTest.paf.gz │ └── hal2pafSmallMMapTest.paf.gz │ └── input │ └── mr.hal ├── phyloP ├── Makefile ├── halPhyloPMP.py ├── 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