├── .travis.yml ├── Dockerfile ├── LICENSE ├── Makefile ├── README.rst ├── blatSrc └── blat.c ├── htslib ├── INSTALL ├── LICENSE ├── Makefile ├── NEWS ├── README ├── bgzf.c ├── bgzip.c ├── config.h ├── config.h.in ├── config.log ├── config.mk ├── config.mk.in ├── config.status ├── configure ├── configure.ac ├── cram │ ├── cram.h │ ├── cram_codecs.c │ ├── cram_codecs.h │ ├── cram_decode.c │ ├── cram_decode.h │ ├── cram_encode.c │ ├── cram_encode.h │ ├── cram_external.c │ ├── cram_index.c │ ├── cram_index.h │ ├── cram_io.c │ ├── cram_io.c.00 │ ├── cram_io.h │ ├── cram_samtools.c │ ├── cram_samtools.h │ ├── cram_stats.c │ ├── cram_stats.h │ ├── cram_structs.h │ ├── files.c │ ├── mFILE.c │ ├── mFILE.h │ ├── misc.h │ ├── open_trace_file.c │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.c │ ├── pooled_alloc.h │ ├── rANS_byte.h │ ├── rANS_static.c │ ├── rANS_static.h │ ├── sam_header.c │ ├── sam_header.h │ ├── string_alloc.c │ ├── string_alloc.h │ ├── thread_pool.c │ ├── thread_pool.h │ ├── vlen.c │ ├── vlen.h │ ├── zfio.c │ └── zfio.h ├── faidx.5 ├── faidx.c ├── hfile.c ├── hfile_internal.h ├── hfile_irods.c ├── hfile_libcurl.c ├── hfile_net.c ├── hts.c ├── hts_internal.h ├── htsfile.1 ├── htsfile.c ├── htslib.mk ├── htslib.pc.in ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.h │ ├── kbitset.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_vars.mk ├── kfunc.c ├── knetfile.c ├── kstring.c ├── md5.c ├── plugin.c ├── regidx.c ├── sam.5 ├── sam.c ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── test │ ├── auxf#values.sam │ ├── auxf.fa │ ├── auxf.fa.fai │ ├── c1#bounds.sam │ ├── c1#clip.sam │ ├── c1#noseq.sam │ ├── c1#pad1.sam │ ├── c1#pad2.sam │ ├── c1#pad3.sam │ ├── c1#unknown.sam │ ├── c1.fa │ ├── c1.fa.fai │ ├── c2#pad.sam │ ├── c2.fa │ ├── c2.fa.fai │ ├── ce#1.sam │ ├── ce#2.sam │ ├── ce#5.sam │ ├── ce#5b.sam │ ├── ce#supp.sam │ ├── ce#tag_depadded.sam │ ├── ce#tag_padded.sam │ ├── ce#unmap.sam │ ├── ce#unmap1.sam │ ├── ce#unmap2.sam │ ├── ce.fa │ ├── ce.fa.fai │ ├── compare_sam.pl │ ├── cross_validate.sh │ ├── faidx.fa │ ├── fieldarith.c │ ├── fieldarith.sam │ ├── hfile.c │ ├── sam.c │ ├── test-regidx.c │ ├── test-vcf-api.c │ ├── test-vcf-api.out │ ├── test-vcf-hdr-in.vcf │ ├── test-vcf-hdr.out │ ├── test-vcf-sweep.c │ ├── test-vcf-sweep.out │ ├── test.pl │ ├── test_view.c │ ├── test_view.pl │ ├── xx#blank.sam │ ├── xx#large_aux.sam │ ├── xx#large_aux2.sam │ ├── xx#minimal.sam │ ├── xx#pair.sam │ ├── xx#rg.sam │ ├── xx#tlen.sam │ ├── xx#tlen2.sam │ ├── xx#triplet.sam │ ├── xx#unsorted.sam │ ├── xx.fa │ └── xx.fa.fai ├── vcf.5 ├── vcf.c ├── vcf_sweep.c └── vcfutils.c ├── inc ├── ace.h ├── aliType.h ├── annoFilter.h ├── annoFormatTab.h ├── annoFormatter.h ├── annoGrator.h ├── annoGratorQuery.h ├── annoOption.h ├── annoRow.h ├── annoStreamVcf.h ├── annoStreamer.h ├── apacheLog.h ├── asParse.h ├── axt.h ├── bPlusTree.h ├── bamFile.h ├── bandExt.h ├── base64.h ├── basicBed.h ├── bbiFile.h ├── bigBed.h ├── bigWig.h ├── binRange.h ├── bits.h ├── blastParse.h ├── boxClump.h ├── boxLump.h ├── bwgInternal.h ├── cda.h ├── cgi_build_rules.mk ├── chain.h ├── chainBlock.h ├── chainConnect.h ├── chainToAxt.h ├── chainToPsl.h ├── cheapcgi.h ├── cirTree.h ├── codebias.h ├── common.h ├── correlate.h ├── crTree.h ├── crudeali.h ├── diGraph.h ├── diGraph.h.97 ├── dlist.h ├── dnaLoad.h ├── dnaMarkov.h ├── dnaMotif.h ├── dnaseq.h ├── dnautil.h ├── dtdParse.h ├── dystring.h ├── emblParse.h ├── ens.h ├── errAbort.h ├── errCatch.h ├── fa.h ├── filePath.h ├── flydna.h ├── fof.h ├── fuzzyFind.h ├── gapCalc.h ├── gdf.h ├── genoFind.h ├── genomeRangeTree.h ├── gfClientLib.h ├── gfPcrLib.h ├── gfWebLib.h ├── gff.h ├── gff3.h ├── gfxPoly.h ├── gifLabel.h ├── hacTree.h ├── hash.h ├── hex.h ├── hgGene.h ├── hgap.h ├── hgdb.h ├── histogram.h ├── hmmPfamParse.h ├── hmmstats.h ├── htmlPage.h ├── htmshell.h ├── https.h ├── intValTree.h ├── internet.h ├── itsa.h ├── iupac.h ├── jointalign.h ├── jpegSize.h ├── keys.h ├── knetUdc.h ├── kxTok.h ├── linefile.h ├── localmem.h ├── log.h ├── maDbRep.h ├── maToFf.h ├── maf.h ├── md5.h ├── memalloc.h ├── memgfx.h ├── metaWig.h ├── mime.h ├── net.h ├── nib.h ├── nibTwo.h ├── nt4.h ├── obscure.h ├── oldGff.h ├── oligoTm.h ├── ooc.h ├── options.h ├── pairHmm.h ├── patSpace.h ├── peakCluster.h ├── phyloTree.h ├── pipeline.h ├── portable.h ├── psGfx.h ├── psPoly.h ├── pscmGfx.h ├── psl.h ├── pslTbl.h ├── pslTransMap.h ├── pthreadWrap.h ├── qa.h ├── quickHeap.h ├── quotedP.h ├── ra.h ├── rainbow.h ├── rangeTree.h ├── rbTree.h ├── regexHelper.h ├── repMask.h ├── rle.h ├── rnautil.h ├── rql.h ├── rudp.h ├── scoreWindow.h ├── seg.h ├── seqOut.h ├── seqStats.h ├── shaRes.h ├── sig.h ├── slog.h ├── snof.h ├── snofmake.h ├── spaceSaver.h ├── spacedColumn.h ├── spacedSeed.h ├── splatAli.h ├── splix.h ├── sqlList.h ├── sqlNum.h ├── srcVersion.h ├── subText.h ├── sufa.h ├── sufx.h ├── supStitch.h ├── synQueue.h ├── tabRow.h ├── textOut.h ├── tokenizer.h ├── trans3.h ├── trix.h ├── twoBit.h ├── udc.h ├── unfin.h ├── vGfx.h ├── vcf.h ├── verbose.h ├── wormdna.h ├── xAli.h ├── xa.h ├── xap.h ├── xenalign.h ├── xmlEscape.h ├── xp.h └── zlibFace.h ├── jkOwnLib ├── README ├── bandExt.c ├── crudeali.c ├── ffAliHelp.c ├── ffSeedExtend.c ├── fuzzyFind.c ├── genoFind.c ├── gfBlatLib.c ├── gfClientLib.c ├── gfInternal.c ├── gfInternal.h ├── gfOut.c ├── gfPcrLib.c ├── gfWebLib.c ├── ooc.c ├── patSpace.c ├── splix.c ├── supStitch.c └── trans3.c └── lib ├── README ├── aliType.c ├── annoFilter.c ├── annoFormatTab.c ├── annoFormatter.c ├── annoGrator.c ├── annoGratorQuery.c ├── annoOption.c ├── annoRow.c ├── annoStreamVcf.c ├── annoStreamer.c ├── apacheLog.c ├── asParse.c ├── axt.c ├── axtAffine.c ├── bPlusTree.c ├── bamFile.c ├── base64.c ├── basicBed.c ├── bbiRead.c ├── bbiWrite.c ├── bigBed.c ├── binRange.c ├── bits.c ├── blastOut.c ├── blastParse.c ├── boxClump.c ├── boxLump.c ├── bwgCreate.c ├── bwgQuery.c ├── bwgValsOnChrom.c ├── cda.c ├── chain.c ├── chainBlock.c ├── chainConnect.c ├── chainToAxt.c ├── chainToPsl.c ├── cheapcgi.c ├── cirTree.c ├── codebias.c ├── colHash.c ├── colHash.h ├── common.c ├── common.pss ├── correlate.c ├── crTree.c ├── dgRange.c ├── diGraph.c ├── diGraph.c.97 ├── dlist.c ├── dnaLoad.c ├── dnaMarkov.c ├── dnaMotif.c ├── dnaMotif.pss ├── dnaseq.c ├── dnautil.c ├── dtdParse.c ├── dystring.c ├── emblParse.c ├── errCatch.c ├── errabort.c ├── fa.c ├── ffAli.c ├── ffScore.c ├── filePath.c ├── fixColor.c ├── flydna.c ├── fof.c ├── fuzzyShow.c ├── gapCalc.c ├── gdf.c ├── gemfont.c ├── gemfont.h ├── genomeRangeTree.c ├── gfNet.c ├── gff.c ├── gff3.c ├── gfxPoly.c ├── gifLabel.c ├── gifcodes.h ├── gifcomp.c ├── gifdecomp.c ├── gifread.c ├── gifwrite.c ├── hacTree.c ├── hash.c ├── hex.c ├── histogram.c ├── hmmPfamParse.c ├── hmmstats.c ├── htmlPage.c ├── htmshell.c ├── https.c ├── intExp.c ├── intValTree.c ├── internet.c ├── itsa.c ├── iupac.c ├── jointalign.c ├── jpegSize.c ├── keys.c ├── knetUdc.c ├── kxTok.c ├── lineFileOnBigBed.c ├── linefile.c ├── localmem.c ├── log.c ├── maf.c ├── mafFromAxt.c ├── mafScore.c ├── md5.c ├── memalloc.c ├── memgfx.c ├── metaWig.c ├── mgCircle.c ├── mgPolygon.c ├── mime.c ├── net.c ├── nib.c ├── nibTwo.c ├── nt4.c ├── numObscure.c ├── obscure.c ├── oldGff.c ├── oligoTm.c ├── options.c ├── osunix.c ├── oswin9x.c ├── pairHmm.c ├── peakCluster.c ├── phyloTree.c ├── pipeline.c ├── pngwrite.c ├── portimpl.c ├── portimpl.h ├── psGfx.c ├── psPoly.c ├── pscmGfx.c ├── psl.as ├── psl.c ├── psl.sql ├── pslGenoShow.c ├── pslShow.c ├── pslTbl.c ├── pslTransMap.c ├── pslWScore.sql ├── pthreadWrap.c ├── qa.c ├── quickHeap.c ├── quotedP.c ├── ra.c ├── rainbow.c ├── rangeTree.c ├── rbTree.c ├── regexHelper.c ├── repMask.c ├── rle.c ├── rnautil.c ├── rqlEval.c ├── 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