├── .gitignore ├── DESCRIPTION ├── INSTALL ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── bam.R ├── bed.R ├── bigBed.R ├── bigWig.R ├── browser.R ├── chain.R ├── fasta.R ├── gff.R ├── igv.R ├── index.R ├── io.R ├── ncbi.R ├── quickload.R ├── ranges.R ├── readGFF.R ├── tabix.R ├── test_rtracklayer_package.R ├── trackDb.R ├── trackTable.R ├── trackhub.R ├── twobit.R ├── ucsc.R ├── utils.R ├── web.R ├── wig.R └── zzz.R ├── TODO ├── cleanup ├── configure ├── configure.ac ├── data ├── cpneTrack.rda └── targets.rda ├── demo ├── 00Index └── targets.R ├── inst ├── CITATION ├── extdata │ └── demo.narrowPeak.gz ├── notes │ ├── design.org │ ├── requirements.tex │ └── use-cases.tex ├── scripts │ ├── cpneTrack.R │ └── twobit.R ├── tests │ ├── bed.bw │ ├── bed.wig │ ├── genes.gff3 │ ├── gtf.gff │ ├── multi.wig │ ├── quickload │ │ ├── T_species_Oct_2011 │ │ │ ├── T_species_Oct_2011.2bit │ │ │ ├── annots.xml │ │ │ ├── bedData.bed.gz │ │ │ ├── bedData.bed.gz.tbi │ │ │ ├── bedGraphData.bw │ │ │ └── mod_chromInfo.txt │ │ └── contents.txt │ ├── step.wig │ ├── test.2bit │ ├── test.R │ ├── test.bb │ ├── test.bed │ ├── test.bed15 │ ├── test.bedGraph │ ├── test.bedpe │ ├── test.bw │ ├── test.gtf │ ├── test.xmfa │ ├── trackhub │ │ ├── genomes.txt │ │ ├── hg19 │ │ │ ├── trackDb.txt │ │ │ └── wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb │ │ └── hub.txt │ ├── v1.gff │ ├── v2.gff │ ├── v3.gff │ ├── variableStep.bw │ └── variableStep.wig └── unitTests │ ├── test_bb.R │ ├── test_bed.R │ ├── test_bedGraph.R │ ├── test_bw.R │ ├── test_gff.R │ ├── test_trackhub.R │ ├── test_twoBit.R │ ├── test_ucsc.R │ └── test_wig.R ├── man ├── BEDFile-class.Rd ├── BamFile-methods.Rd ├── Bed15TrackLine-class.Rd ├── BigBedFile.Rd ├── BigBedSelection.rd ├── BigWigFile.Rd ├── BigWigSelection-class.Rd ├── BrowserViewList-class.Rd ├── Chain-class.Rd ├── FastaFile-class.Rd ├── GFFFile-class.Rd ├── GRangesForUCSCGenome.Rd ├── GenomicData.Rd ├── GenomicSelection.Rd ├── IntegerRangesList-methods.Rd ├── Quickload-class.Rd ├── QuickloadGenome-class.Rd ├── TabixFile-methods.Rd ├── TrackDb-class.Rd ├── TrackHub-class.Rd ├── TrackHubGenome-class.Rd ├── TwoBitFile-class.Rd ├── UCSCData-class.Rd ├── UCSCFile-class.Rd ├── UCSCSchema-class.Rd ├── UCSCTableQuery-class.Rd ├── WIGFile-class.Rd ├── activeView-methods.Rd ├── asBED.Rd ├── asGFF.Rd ├── basicTrackLine-class.Rd ├── blocks-methods.Rd ├── browseGenome.Rd ├── browserSession-class.Rd ├── browserSession-methods.Rd ├── browserView-class.Rd ├── browserView-methods.Rd ├── browserViews-methods.Rd ├── cpneTrack.Rd ├── genomeBrowsers.Rd ├── laySequence-methods.Rd ├── layTrack-methods.Rd ├── liftOver.Rd ├── readGFF.Rd ├── targets.Rd ├── tracks-methods.Rd ├── ucscGenomes.Rd ├── ucscSession-class.Rd ├── ucscTrackLine-class.Rd ├── ucscTrackModes-class.Rd ├── ucscTrackModes-methods.Rd ├── ucscView-class.Rd ├── wigToBigWig.Rd └── wigTrackLine-class.Rd ├── src ├── IRanges_stubs.c ├── Makevars.common ├── Makevars.in ├── Makevars.win ├── R_init_rtracklayer.c ├── S4Vectors_stubs.c ├── XVector_stubs.c ├── bbiHelper.c ├── bbiHelper.h ├── bigBed.c ├── bigBed.h ├── bigBedHelper.c ├── bigBedHelper.h ├── bigWig.c ├── bigWig.h ├── chain_io.c ├── handlers.c ├── handlers.h ├── readGFF.c ├── readGFF.h ├── rtracklayer.h ├── twoBit.c ├── twoBit.h ├── ucsc │ ├── _cheapcgi.c │ ├── _portimpl.c │ ├── _portimpl.h │ ├── asParse.c │ ├── asParse.h │ ├── bPlusTree.c │ ├── bPlusTree.h │ ├── base64.c │ ├── base64.h │ ├── basicBed.c │ ├── basicBed.h │ ├── bbiFile.h │ ├── bbiRead.c │ ├── bbiWrite.c │ ├── bigBed.c │ ├── bigBed.h │ ├── bigWig.h │ ├── binRange.c │ ├── binRange.h │ ├── bits.c │ ├── bits.h │ ├── bwgCreate.c │ ├── bwgInternal.h │ ├── bwgQuery.c │ ├── cheapcgi.h │ ├── cirTree.c │ ├── cirTree.h │ ├── common.c │ ├── common.h │ ├── dlist.c │ ├── dlist.h │ ├── dnaseq.c │ ├── dnaseq.h │ ├── dnautil.c │ ├── dnautil.h │ ├── dystring.c │ ├── dystring.h │ ├── errAbort.c │ ├── errAbort.h │ ├── errCatch.h │ ├── filePath.c │ ├── filePath.h │ ├── hash.c │ ├── hash.h │ ├── hmmstats.c │ ├── hmmstats.h │ ├── htmlColor.c │ ├── htmlColor.h │ ├── htmlPage.c │ ├── htmlPage.h │ ├── https.c │ ├── https.h │ ├── internet.c │ ├── internet.h │ ├── linefile.c │ ├── linefile.h │ ├── localmem.c │ ├── localmem.h │ ├── memalloc.c │ ├── memalloc.h │ ├── memgfx.c │ ├── memgfx.h │ ├── net.c │ ├── net.h │ ├── obscure.c │ ├── obscure.h │ ├── os.c │ ├── osunix.c │ ├── oswin9x.c │ ├── portable.h │ ├── portimpl.h │ ├── rangeTree.c │ ├── rangeTree.h │ ├── rbTree.c │ ├── rbTree.h │ ├── sig.h │ ├── sqlList.c │ ├── sqlList.h │ ├── sqlNum.c │ ├── sqlNum.h │ ├── tokenizer.c │ ├── tokenizer.h │ ├── twoBit.c │ ├── twoBit.h │ ├── udc.c │ ├── udc.h │ ├── verbose.c │ ├── verbose.h │ ├── wildcmp.c │ ├── zlibFace.c │ └── zlibFace.h ├── utils.c └── utils.h ├── tests └── rtracklayer_unit_tests.R └── vignettes ├── example.bed └── rtracklayer.Rnw /.gitignore: -------------------------------------------------------------------------------- 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