├── .gitignore ├── COPYING.LIB ├── LICENSE ├── Makefile ├── README.md ├── bin ├── mapInfoSummary ├── ncbiAssemblyReportConvert └── ucscLiftEdit ├── config.mk ├── doc ├── problem-cases.txt ├── slides │ ├── Makefile │ ├── README │ ├── bin │ │ └── tsvToTbl │ ├── data │ │ ├── liftover.pri.gene.biotype-mapstatus.map-info.matrix │ │ ├── liftover.pri.gene.biotype-targetstatus.map-info.matrix │ │ ├── liftover.pri.lost.tsv │ │ ├── liftover.pri.nonOverlap.tsv │ │ ├── pri.gene.targetstatus.map-info.overview │ │ ├── pri.trans.biocat-targetstatus.map-info.overview │ │ ├── pri.trans.mapstatus.map-info.overview │ │ └── pri.trans.targetstatus.map-info.overview │ ├── drawings │ │ └── transMap2.svg │ ├── gencode-backmap.ltx │ └── images │ │ └── UC-Santa-Cruz-Genomics-Inst_022415.png └── to-do.org ├── etc └── stable-id-map.grch38.tsv ├── lib ├── gencode │ ├── __init__.py │ ├── categoryCounts.py │ └── gencodeBioTypes.py └── pycbio_local │ ├── __init__.py │ ├── ncbi │ ├── __init__.py │ └── assembly.py │ ├── sys │ ├── __init__.py │ ├── fileOps.py │ ├── symEnum.py │ └── typeOps.py │ └── tsv │ ├── __init__.py │ ├── tsvReader.py │ └── tsvRow.py ├── requirements.txt ├── setup.cfg ├── src ├── FIOStream.cc ├── FIOStream.hh ├── Makefile ├── README.gzstream ├── annotationSet.cc ├── annotationSet.hh ├── bedMap.cc ├── bedMap.hh ├── featureMapper.cc ├── featureMapper.hh ├── featureTransMap.cc ├── featureTransMap.hh ├── featureTree.cc ├── featureTree.hh ├── featureTreePolish.cc ├── featureTreePolish.hh ├── frame.cc ├── frame.hh ├── gencode-backmap.cc ├── gencodeParser.cc ├── geneMapper.cc ├── geneMapper.hh ├── globals.hh ├── gxf.cc ├── gxf.hh ├── gzstream.cc ├── gzstream.hh ├── jkinclude.hh ├── pslCursor.hh ├── pslMapping.cc ├── pslMapping.hh ├── pslOps.cc ├── pslOps.hh ├── remapStatus.cc ├── remapStatus.hh ├── transMap.cc ├── transMap.hh ├── transcriptMapper.cc ├── transcriptMapper.hh ├── typeOps.cc ├── typeOps.hh └── version.h.in └── tests ├── Makefile ├── README ├── bin ├── getBigDebug ├── grepGene └── runBigDebug ├── data ├── GCF_000001405.25.assembly.txt ├── GCF_000001405.28.assembly.txt ├── GRCh38.p2-GRCh37.p13.gencode.psl ├── dup-transcripts.v19.gff3 ├── dup-transcripts.v32lift37.gff3 ├── dup-transcripts.v33.gff3 ├── full-par-id-mappings-V43-V44.tsv ├── gapped-transcripts.v33.gff3 ├── gencode.v19.annotation.gff3 ├── gencode.v19.annotation.gtf ├── gencode.v22.annotation.gff3 ├── gencode.v22.annotation.gtf ├── gencode.v22.metadata.PolyA_feature ├── gencode.v25.gff3 ├── gencode.v25.gtf ├── gencode.v29.annotation.gff3 ├── gencode.v31.annotation.gff3 ├── header.txt ├── hg38ToHg19.over.chain ├── idChange.v19.gff3 ├── idChange.v25.gff3 ├── par.V19.gff3 ├── par.V43.gff3 ├── par.V43lift37.gff3 ├── par.V44.gff3 ├── problemRegions.bed ├── sort.v33.gff3 ├── transMove.V19.gff3 ├── transMove.V43lift37.gff3 ├── transMove.V44.gff3 └── v25Lift37.attrs └── expected ├── dupTranscriptsV33Test.map-info ├── dupTranscriptsV33Test.mapped.gff3 ├── gapTest.map-info ├── gapTest.mapped.gff3 ├── gff3MappingVerBaseTest.map-info ├── gff3MappingVerBaseTest.mapped.gff3 ├── gff3MappingVerPrevDiffMapTest.map-info ├── gff3MappingVerPrevDiffMapTest.mapped.gff3 ├── gff3MappingVerPrevNoVerTest.map-info ├── gff3MappingVerPrevNoVerTest.mapped.gff3 ├── gff3NcbiTest.map-info ├── gff3NcbiTest.mapped.gff3 ├── gff3ParNamingTest.map-info ├── gff3ParNamingTest.mapped.gff3 ├── gff3ParNamingTest.mapped.gp ├── gff3UcscSubstituteAuto.mapped.gff3 ├── gff3UcscSubstituteAutoSmallNcRna.map-info ├── gff3UcscSubstituteAutoSmallNcRna.mapped.gff3 ├── gff3UcscSubstituteManOverlap.map-info ├── gff3UcscSubstituteManOverlap.mapped.gff3 ├── gff3UcscSubstituteManOverlap.mapped.gp ├── gff3UcscTest.map-info ├── gff3UcscTest.mapped.gff3 ├── gff3UcscTest.mapped.gp ├── gff3V29RegressTest.map-info ├── gff3V29RegressTest.mapped.gff3 ├── gff3V29RegressTest.mapped.gp ├── gff3V31RegressTest.map-info ├── gff3V31RegressTest.mapped.gff3 ├── gtfMappingVerBaseTest.map-info ├── gtfMappingVerBaseTest.mapped.gtf ├── gtfMappingVerPrevDiffMapTest.map-info ├── gtfMappingVerPrevDiffMapTest.mapped.gtf ├── gtfMappingVerPrevNoVerTest.map-info ├── gtfMappingVerPrevNoVerTest.mapped.gtf ├── gtfNcbiTest.map-info ├── gtfNcbiTest.mapped.gtf ├── gtfParNamingTest.map-info ├── gtfParNamingTest.mapped.gp ├── gtfParNamingTest.mapped.gtf ├── gtfUcscSubstituteManOverlap.map-info ├── gtfUcscSubstituteManOverlap.mapped.gp ├── gtfUcscSubstituteManOverlap.mapped.gtf ├── gtfUcscTest.map-info ├── gtfUcscTest.mapped.gp ├── gtfUcscTest.mapped.gtf ├── idChangeV25Test.map-info ├── idChangeV25Test.mapped.gff3 ├── mapInfoSumGeneAllTest.sum ├── mapInfoSumGeneBiotypeTest.sum ├── mapInfoSumSubTargetTest.sum ├── mapInfoSumTransBiocatMatColFreqMapStatusTest.sum ├── mapInfoSumTransBiocatMatRowFreqMapStatusTest.sum ├── mapInfoSumTransBiocatMatrixMapStatusTest.sum ├── mapInfoSumTransBiocatMultimapTest.sum ├── mapInfoSumTransBiocatTest.sum ├── mapInfoSumTransBiottypeTest.sum ├── mapInfoSumTransMatrixGenomicSizeTest.sum ├── 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