├── HoxD55.q ├── LICENSE ├── README.md ├── bin └── .keep ├── example ├── HoxD55.q ├── danRer10.chrom.sizes ├── hg38.chrom.sizes ├── hg38.danRer10.chain ├── hg38.mm10.chr1.chain.gz ├── hg38.mm10.chr1.cleaned.chain.gz ├── mm10.chrom.sizes └── removedSuspects.bed ├── kent ├── LICENSE ├── README.txt ├── README_ucsc ├── bin │ └── README.txt └── src │ ├── LICENSE │ ├── README │ ├── checkUmask.sh │ ├── hg │ ├── README │ ├── inc │ │ ├── Cstraw.h │ │ ├── HInv.h │ │ ├── acemblyClass.h │ │ ├── adjacency.h │ │ ├── affy10K.h │ │ ├── affy10KDetails.h │ │ ├── affy120KDetails.h │ │ ├── affyAllExonProbe.h │ │ ├── affyAtlas.h │ │ ├── affyGenoDetails.h │ │ ├── affyOffset.h │ │ ├── affyPairs.h │ │ ├── affyTransLifted.h │ │ ├── affyTranscriptome.h │ │ ├── agp.h │ │ ├── agpFrag.h │ │ ├── agpGap.h │ │ ├── alignInfo.h │ │ ├── alignSeqSizes.h │ │ ├── alleleFreqs.h │ │ ├── allpredictions.h │ │ ├── altGraph.h │ │ ├── altGraphX.h │ │ ├── ancientRref.h │ │ ├── annoFormatVep.h │ │ ├── annoGrateWigDb.h │ │ ├── annoGratorGpVar.h │ │ ├── annoStreamDb.h │ │ ├── annoStreamDbFactorSource.h │ │ ├── annoStreamDbKnownGene.h │ │ ├── annoStreamDbPslPlus.h │ │ ├── annoStreamWig.h │ │ ├── api.h │ │ ├── arCOGs.h │ │ ├── arcogdesc.h │ │ ├── atomDb.h │ │ ├── autoUpgrade.h │ │ ├── axtInfo.h │ │ ├── axtLib.h │ │ ├── bacCloneAlias.h │ │ ├── bacCloneXRef.h │ │ ├── bacEndAlias.h │ │ ├── bactigPos.h │ │ ├── barChartBed.h │ │ ├── barChartCategory.h │ │ ├── barChartData.h │ │ ├── barChartSample.h │ │ ├── barChartUi.h │ │ ├── baseMaskCommon.h │ │ ├── bdgpExprLink.h │ │ ├── bdgpGeneInfo.h │ │ ├── bdgpSwissProt.h │ │ ├── bed.h │ │ ├── bed12Source.h │ │ ├── bed12wSeq.h │ │ ├── bed5FloatScore.h │ │ ├── bed5Pval.h │ │ ├── bed6FloatScore.h │ │ ├── bed8Attrs.h │ │ ├── bedCart.h │ │ ├── bedDetail.h │ │ ├── bedGraph.h │ │ ├── bgiGeneInfo.h │ │ ├── bgiGeneSnp.h │ │ ├── bgiSnp.h │ │ ├── bigBedFilter.h │ │ ├── bigBedFind.h │ │ ├── bigBedLabel.h │ │ ├── bigGenePred.h │ │ ├── bigPsl.h │ │ ├── bigTransMap.h │ │ ├── bioImage.h │ │ ├── blastTab.h │ │ ├── blastzNet.h │ │ ├── blatServers.h │ │ ├── borf.h │ │ ├── borkPseudoHom.h │ │ ├── botDelay.h │ │ ├── cart.h │ │ ├── cartDb.h │ │ ├── cartJson.h │ │ ├── cartTrackDb.h │ │ ├── ccdsGeneMap.h │ │ ├── ccdsInfo.h │ │ ├── ccdsNotes.h │ │ ├── cddDesc.h │ │ ├── cddInfo.h │ │ ├── cdsEvidence.h │ │ ├── cdsOrtho.h │ │ ├── cdsPick.h │ │ ├── cdsSpec.h │ │ ├── celeraCoverage.h │ │ ├── celeraDupPositive.h │ │ ├── cgapSage │ │ │ ├── cgapSage.h │ │ │ └── cgapSageLib.h │ │ ├── cgh.h │ │ ├── cgiApoptosis.h │ │ ├── chainCart.h │ │ ├── chainDb.h │ │ ├── chainGap.h │ │ ├── chainLink.h │ │ ├── chainNet.h │ │ ├── chainNetDbLoad.h │ │ ├── chainView.h │ │ ├── chicken13kInfo.h │ │ ├── chr18deletions.h │ │ ├── chromAlias.h │ │ ├── chromBins.h │ │ ├── chromColors.h │ │ ├── chromGraph.h │ │ ├── chromGraphFactory.h │ │ ├── chromInfo.h │ │ ├── chromInserts.h │ │ ├── chromKeeper.h │ │ ├── clonePos.h │ │ ├── cnpIafrate.h │ │ ├── cnpIafrate2.h │ │ ├── cnpLocke.h │ │ ├── cnpRedon.h │ │ ├── cnpSebat.h │ │ ├── cnpSebat2.h │ │ ├── cnpSharp.h │ │ ├── cnpSharp2.h │ │ ├── cnpSharpCutoff.h │ │ ├── cnpSharpSample.h │ │ ├── codeBlast.h │ │ ├── codeBlastScore.h │ │ ├── cogs.h │ │ ├── cogsxra.h │ │ ├── columnInfo.h │ │ ├── contigAcc.h │ │ ├── coordConv.h │ │ ├── cpgIsland.h │ │ ├── cpgIslandExt.h │ │ ├── ctgPos.h │ │ ├── ctgPos2.h │ │ ├── customComposite.h │ │ ├── customFactory.h │ │ ├── customPp.h │ │ ├── customTrack.h │ │ ├── cutter.h │ │ ├── cv.h │ │ ├── cytoBand.h │ │ ├── dbDb.h │ │ ├── dbRIP.h │ │ ├── dbSnpRs.h │ │ ├── defaultDb.h │ │ ├── delConrad2.h │ │ ├── delHinds2.h │ │ ├── dgv.h │ │ ├── dgvPlus.h │ │ ├── dless.h │ │ ├── dnaMarkovSql.h │ │ ├── dnaMotifSql.h │ │ ├── dnaProbe.h │ │ ├── dv.h │ │ ├── dvBed.h │ │ ├── dvXref2.h │ │ ├── easyGene.h │ │ ├── ec.h │ │ ├── ecAttribute.h │ │ ├── ecAttributeCode.h │ │ ├── ecCode.h │ │ ├── edwNavBar.html │ │ ├── encode │ │ │ ├── encodeErge.h │ │ │ ├── encodeErge5race.h │ │ │ ├── encodeErgeBinding.h │ │ │ ├── encodeErgeDNAseI.h │ │ │ ├── encodeErgeExpProm.h │ │ │ ├── encodeErgeHssCellLines.h │ │ │ ├── encodeErgeInVitroFoot.h │ │ │ ├── encodeErgeMethProm.h │ │ │ ├── encodeErgeStableTransf.h │ │ │ ├── encodeErgeSummary.h │ │ │ ├── encodeErgeTransTransf.h │ │ │ ├── encodeExp.h │ │ │ ├── encodeHapMapAlleleFreq.h │ │ │ ├── encodeIndels.h │ │ │ ├── encodePeak.h │ │ │ ├── encodePrimateAlleles.h │ │ │ ├── encodeRegionInfo.h │ │ │ ├── encodeRna.h │ │ │ ├── encodeStanfordPromoters.h │ │ │ ├── encodeStanfordPromotersAverage.h │ │ │ ├── wgEncodeCell.h │ │ │ ├── wgEncodeGencodeAnnotationRemark.h │ │ │ ├── wgEncodeGencodeAttrs.h │ │ │ ├── wgEncodeGencodeEntrezGene.h │ │ │ ├── wgEncodeGencodeExonSupport.h │ │ │ ├── wgEncodeGencodeGeneSource.h │ │ │ ├── wgEncodeGencodeGeneSymbol.h │ │ │ ├── wgEncodeGencodePdb.h │ │ │ ├── wgEncodeGencodePolyAFeature.h │ │ │ ├── wgEncodeGencodePubMed.h │ │ │ ├── wgEncodeGencodeRefSeq.h │ │ │ ├── wgEncodeGencodeTag.h │ │ │ ├── wgEncodeGencodeTranscriptSource.h │ │ │ ├── wgEncodeGencodeTranscriptSupport.h │ │ │ ├── wgEncodeGencodeTranscriptionSupportLevel.h │ │ │ └── wgEncodeGencodeUniProt.h │ │ ├── encode3 │ │ │ ├── encode2Manifest.h │ │ │ └── encode3Valid.h │ │ ├── ensFace.h │ │ ├── ensInfo.h │ │ ├── ensPhusionBlast.h │ │ ├── ensXRefZfish.h │ │ ├── est3.h │ │ ├── estOrientInfo.h │ │ ├── estPair.h │ │ ├── exoFish.h │ │ ├── exonJunctionPrimers.h │ │ ├── expData.h │ │ ├── expRecord.h │ │ ├── exprBed.h │ │ ├── facetField.h │ │ ├── factorSource.h │ │ ├── fbTables.h │ │ ├── featureBits.h │ │ ├── fileUi.h │ │ ├── findKGAlias.h │ │ ├── findKGProtAlias.h │ │ ├── fishClones.h │ │ ├── flyBase2004Xref.h │ │ ├── flyBaseSwissProt.h │ │ ├── flyreg.h │ │ ├── flyreg2.h │ │ ├── fosEndPairs.h │ │ ├── gbExtFile.h │ │ ├── gbMiscDiff.h │ │ ├── gbProtAnn.h │ │ ├── gbRNAs.h │ │ ├── gbSeq.h │ │ ├── gbWarn.h │ │ ├── gcPercent.h │ │ ├── genMapDb.h │ │ ├── genbank.h │ │ ├── genbankBlackList.h │ │ ├── gencodeGeneClass.h │ │ ├── gencodeIntron.h │ │ ├── geneBands.h │ │ ├── geneCheck.h │ │ ├── geneCheckDetails.h │ │ ├── geneCheckWidget.h │ │ ├── geneGraph.h │ │ ├── genePix.h │ │ ├── genePred.h │ │ ├── genePredReader.h │ │ ├── geneSimilarities.h │ │ ├── geneTree.h │ │ ├── genoLay.h │ │ ├── genomeRangeTreeFile.h │ │ ├── genomicDups.h │ │ ├── genomicSuperDups.h │ │ ├── genotype.h │ │ ├── genotypeFreqs.h │ │ ├── geoMirror.h │ │ ├── ggDbRep.h │ │ ├── ggMrnaAli.h │ │ ├── ggPrivate.h │ │ ├── ggTypes.h │ │ ├── glDbRep.h │ │ ├── goa.h │ │ ├── goaPart.h │ │ ├── googleAnalytics.h │ │ ├── gpFx.h │ │ ├── growthCondition.h │ │ ├── grp.h │ │ ├── gtexAse.h │ │ ├── gtexDonor.h │ │ ├── gtexEqtlCluster.h │ │ ├── gtexGeneBed.h │ │ ├── gtexInfo.h │ │ ├── gtexSample.h │ │ ├── gtexSampleData.h │ │ ├── gtexTissue.h │ │ ├── gtexTissueData.h │ │ ├── gtexTissueMedian.h │ │ ├── gtexUi.h │ │ ├── gv.h │ │ ├── gvUi.h │ │ ├── gwasCatalog.h │ │ ├── hAnno.h │ │ ├── hCommon.h │ │ ├── hCytoBand.h │ │ ├── hPrint.h │ │ ├── hVarSubst.h │ │ ├── haplotypes.h │ │ ├── hapmapAlleleFreq.h │ │ ├── hapmapAlleles.h │ │ ├── hapmapAllelesCombined.h │ │ ├── hapmapAllelesOrtho.h │ │ ├── hapmapAllelesSummary.h │ │ ├── hapmapLd.h │ │ ├── hapmapPhaseIIISummary.h │ │ ├── hapmapPrimateAlleles.h │ │ ├── hapmapSnps.h │ │ ├── hapmapSnpsCombined.h │ │ ├── hashJoin.h │ │ ├── hdb.h │ │ ├── hgBam.h │ │ ├── hgColors.h │ │ ├── hgConfig.h │ │ ├── hgExp.h │ │ ├── hgFind.h │ │ ├── hgFindSpec.h │ │ ├── hgGene.h │ │ ├── hgHgvs.h │ │ ├── hgMaf.h │ │ ├── hgRelate.h │ │ ├── hgSeq.h │ │ ├── hgdb.h │ │ ├── hgdpGeo.h │ │ ├── hgnc.h │ │ ├── hic.h │ │ ├── hicUi.h │ │ ├── hubConnect.h │ │ ├── hubPublic.h │ │ ├── hubSearchText.h │ │ ├── hui.h │ │ ├── humanParalog.h │ │ ├── hvGfx.h │ │ ├── imageClone.h │ │ ├── indelShift.h │ │ ├── interact.h │ │ ├── interactUi.h │ │ ├── isochores.h │ │ ├── ispyTables.h │ │ ├── itemAttr.h │ │ ├── itemConf.h │ │ ├── itemDetailsHtml.h │ │ ├── jalview.h │ │ ├── jaxOrtholog.h │ │ ├── jaxQTL.h │ │ ├── jaxQTL2.h │ │ ├── jaxQTL3.h │ │ ├── jgiGene.h │ │ ├── jksql.h │ │ ├── joinMixer.h │ │ ├── joiner.h │ │ ├── jsHelper.h │ │ ├── kg1ToKg2.h │ │ ├── kgAlias.h │ │ ├── kgColor.h │ │ ├── kgMapName.h │ │ ├── kgProtAlias.h │ │ ├── kgXref.h │ │ ├── knownInfo.h │ │ ├── knownMore.h │ │ ├── knownToSuper.h │ │ ├── landmark.h │ │ ├── landmarkUi.h │ │ ├── lav.h │ │ ├── ld.h │ │ ├── ld2.h │ │ ├── ldUi.h │ │ ├── lfs.h │ │ ├── liftOver.h │ │ ├── liftOverChain.h │ │ ├── liftUp.h │ │ ├── llaInfo.h │ │ ├── longRange.h │ │ ├── lowelabArkinOperonScore.h │ │ ├── lowelabPfamHit.h │ │ ├── lowelabTIGROperonScore.h │ │ ├── loweutils.h │ │ ├── lrg.h │ │ ├── lsSnpPdb.h │ │ ├── lsSnpPdbChimera.h │ │ ├── mafFrames.h │ │ ├── mafGene.h │ │ ├── mafSummary.h │ │ ├── makeItemsItem.h │ │ ├── mammalPsg.h │ │ ├── mapSts.h │ │ ├── mathWig.h │ │ ├── mcnBreakpoints.h │ │ ├── mdb.h │ │ ├── megablastInfo.h │ │ ├── metaChromGraph.h │ │ ├── mgiID.h │ │ ├── microarray.h │ │ ├── minChromSize.h │ │ ├── minGeneInfo.h │ │ ├── mouseOrtho.h │ │ ├── mouseSyn.h │ │ ├── mouseSynWhd.h │ │ ├── mrnaMisMatch.h │ │ ├── mysqlTableStatus.h │ │ ├── ncRna.h │ │ ├── ncbiRefLink.h │ │ ├── ncbiRefSeqLink.h │ │ ├── netAlign.h │ │ ├── netCart.h │ │ ├── nonCodingUi.h │ │ ├── omicia.h │ │ ├── omim.h │ │ ├── omimTitle.h │ │ ├── ooUtils.h │ │ ├── oreganno.h │ │ ├── oregannoUi.h │ │ ├── orthoAlleles.h │ │ ├── pairedTagAlign.h │ │ ├── pal.h │ │ ├── pbCommon.h │ │ ├── pbStamp.h │ │ ├── pcrResult.h │ │ ├── pepPred.h │ │ ├── peptideAtlasPeptide.h │ │ ├── peptideMapping.h │ │ ├── pgPhenoAssoc.h │ │ ├── pgPolyphenPred.h │ │ ├── pgSiftPred.h │ │ ├── pgSnp.h │ │ ├── plasEndPairs.h │ │ ├── polyGenotype.h │ │ ├── protFeat.h │ │ ├── protVar.h │ │ ├── pscreen.h │ │ ├── pseudoGeneLink.h │ │ ├── pslReader.h │ │ ├── pslWQueryID.h │ │ ├── pslWScore.h │ │ ├── putaInfo.h │ │ ├── qaSeq.h │ │ ├── rangeTreeFile.h │ │ ├── rankProp.h │ │ ├── recombRate.h │ │ ├── recombRateMouse.h │ │ ├── recombRateRat.h │ │ ├── refLink.h │ │ ├── refSeqStatus.h │ │ ├── retroMrnaInfo.h │ │ ├── rgdQtl.h │ │ ├── rhMapInfo.h │ │ ├── rhMapZfishInfo.h │ │ ├── riken.h │ │ ├── rikenBest.h │ │ ├── rikenCluster.h │ │ ├── rmskAlign.h │ │ ├── rmskJoined.h │ │ ├── rmskOut.h │ │ ├── rmskOut2.h │ │ ├── rnaFold.h │ │ ├── rnaGene.h │ │ ├── rnaGenes.h │ │ ├── rnaGroup.h │ │ ├── rnaHybridization.h │ │ ├── rnaPLFold.h │ │ ├── rnaSecStr.h │ │ ├── roughAli.h │ │ ├── sage.h │ │ ├── sageCounts.h │ │ ├── sageExp.h │ │ ├── samAlignment.h │ │ ├── sample.h │ │ ├── sanger22extra.h │ │ ├── sangerGene.h │ │ ├── sangerGeneToWBGeneID.h │ │ ├── sargassoSeaXra.h │ │ ├── scopDes.h │ │ ├── scoredRef.h │ │ ├── search.h │ │ ├── seqWindow.h │ │ ├── sessionThumbnail.h │ │ ├── sgdAbundance.h │ │ ├── sgdClone.h │ │ ├── sgdDescription.h │ │ ├── sgdOther.h │ │ ├── simpleNucDiff.h │ │ ├── simpleRepeat.h │ │ ├── snakeUi.h │ │ ├── snoRNAs.h │ │ ├── snp.h │ │ ├── snp125.h │ │ ├── snp125CodingCoordless.h │ │ ├── snp125Exceptions.h │ │ ├── snp125Ui.h │ │ ├── snp132Ext.h │ │ ├── snpExceptions.h │ │ ├── snpExtFile.h │ │ ├── snpFasta.h │ │ ├── snpMap.h │ │ ├── snpSeq.h │ │ ├── snpTmp.h │ │ ├── snpUi.h │ │ ├── soTerm.h │ │ ├── softPromoter.h │ │ ├── softberryHom.h │ │ ├── spDb.h │ │ ├── splignAlign.h │ │ ├── sqlProg.h │ │ ├── sqlSanity.h │ │ ├── stanMad.h │ │ ├── stsAlias.h │ │ ├── stsInfo.h │ │ ├── stsInfo2.h │ │ ├── stsInfoMouse.h │ │ ├── stsInfoMouseNew.h │ │ ├── stsInfoRat.h │ │ ├── stsMap.h │ │ ├── stsMapMouse.h │ │ ├── stsMapMouseNew.h │ │ ├── stsMapRat.h │ │ ├── stsMarker.h │ │ ├── suggest.h │ │ ├── switchDbTss.h │ │ ├── synMap.h │ │ ├── synteny100000.h │ │ ├── syntenyBerk.h │ │ ├── syntenySanger.h │ │ ├── tRNAs.h │ │ ├── tableDescriptions.h │ │ ├── tableStatus.h │ │ ├── tablesTables.h │ │ ├── tagAlign.h │ │ ├── tagRepo.h │ │ ├── targetDb.h │ │ ├── taxonDivision.h │ │ ├── taxonGeneticCode.h │ │ ├── taxonName.h │ │ ├── taxonNode.h │ │ ├── taxonXref.h │ │ ├── tfbsCons.h │ │ ├── tfbsConsFactors.h │ │ ├── tfbsConsMap.h │ │ ├── tfbsConsSites.h │ │ ├── tigrCmrGene.h │ │ ├── tigrOperon.h │ │ ├── tilingPath.h │ │ ├── traceInfo.h │ │ ├── trackDb.h │ │ ├── trackHub.h │ │ ├── trackLayout.h │ │ ├── trackTable.h │ │ ├── trackVersion.h │ │ ├── transMapGene.h │ │ ├── transMapInfo.h │ │ ├── transMapSrc.h │ │ ├── transMapStuff.h │ │ ├── transRegCode.h │ │ ├── transRegCodeCondition.h │ │ ├── transRegCodeProbe.h │ │ ├── trashDir.h │ │ ├── txAliDiff.h │ │ ├── txCluster.h │ │ ├── txCommon.h │ │ ├── txEdgeBed.h │ │ ├── txEdgeOrtho.h │ │ ├── txGraph.h │ │ ├── txInfo.h │ │ ├── txRnaAccs.h │ │ ├── ucscRetroInfo.h │ │ ├── ucscRetroOrtho.h │ │ ├── userRegions.h │ │ ├── variant.h │ │ ├── variantProjector.h │ │ ├── variome.h │ │ ├── vcfUi.h │ │ ├── vegaInfo.h │ │ ├── vegaInfoZfish.h │ │ ├── versionInfo.h │ │ ├── visiGene.h │ │ ├── vntr.h │ │ ├── wabAli.h │ │ ├── web.h │ │ ├── wgRna.h │ │ ├── wiggle.h │ │ ├── wikiLink.h │ │ ├── wikiTrack.h │ │ ├── yaleGencodeAssoc.h │ │ └── zdobnovSynt.h │ ├── lib │ │ ├── #makefile# │ │ ├── .gitignore │ │ ├── COGXra.sql │ │ ├── HInv.as │ │ ├── HInv.c │ │ ├── HInv.sql │ │ ├── aaSeq.sql │ │ ├── acemblyClass.as │ │ ├── acemblyClass.c │ │ ├── acemblyClass.sql │ │ ├── acemblyPep.sql │ │ ├── adjacency.as │ │ ├── adjacency.c │ │ ├── affy10K.as │ │ ├── affy10K.c │ │ ├── affy10K.sql │ │ ├── affy10KDetails.as │ │ ├── affy10KDetails.c │ │ ├── affy10KDetails.sql │ │ ├── affy120KDetails.as │ │ ├── affy120KDetails.c │ │ ├── affy120KDetails.sql │ │ ├── affyAllExonProbe.as │ │ ├── affyAllExonProbe.c │ │ ├── affyAllExonProbe.sql │ │ ├── affyAtlas.as │ │ ├── affyAtlas.c │ │ ├── affyAtlas.sql │ │ ├── affyGenoDetails.as │ │ ├── affyGenoDetails.c │ │ ├── affyGenoDetails.sql │ │ ├── affyGnfU74A.sql │ │ ├── affyGnfU74B.sql │ │ ├── affyGnfU74C.sql │ │ ├── affyHuEx1Annot.sql │ │ ├── affyOffset.as │ │ ├── affyOffset.c │ │ ├── affyOffset.sql │ │ ├── affyPairs.as │ │ ├── affyPairs.c │ │ ├── affyPairs.sql │ │ ├── affyRatio.sql │ │ ├── affyTransLifted.as │ │ ├── affyTransLifted.c │ │ ├── affyTransLifted.sql │ │ ├── affyTranscriptome.as │ │ ├── affyTranscriptome.c │ │ ├── affyTranscriptome.sql │ │ ├── affyUcla.sql │ │ ├── agp.c │ │ ├── agpFrag.as │ │ ├── agpFrag.c │ │ ├── agpFrag.sql │ │ ├── agpGap.as │ │ ├── agpGap.c │ │ ├── agpGap.sql │ │ ├── alignInfo.as │ │ ├── alignInfo.c │ │ ├── alignInfo.sql │ │ ├── alignSeqSizes.c │ │ ├── alleleFreqs.as │ │ ├── alleleFreqs.c │ │ ├── alleleFreqs.sql │ │ ├── allenBrainGene.sql │ │ ├── allenBrainUrl.as │ │ ├── allenBrainUrl.sql │ │ ├── allpredictions.c │ │ ├── altGraph.as │ │ ├── altGraph.c │ │ ├── altGraph.sql │ │ ├── altGraphX.as │ │ ├── altGraphX.c │ │ ├── altGraphX.sql │ │ ├── ancientRref.c │ │ ├── ancientRref.sql │ │ ├── annoFormatVep.c │ │ ├── annoGrateWigDb.c │ │ ├── annoGratorGpVar.c │ │ ├── annoStreamDb.c │ │ ├── annoStreamDbFactorSource.c │ │ ├── annoStreamDbPslPlus.c │ │ ├── annoStreamWig.c │ │ ├── api.c │ │ ├── arCOGs.as │ │ ├── arCOGs.c │ │ ├── arCOGs.sql │ │ ├── arcogdesc.as │ │ ├── arcogdesc.c │ │ ├── arcogdesc.sql │ │ ├── arrayVal.sql │ │ ├── atlasOncoGene.as │ │ ├── atomDb.as │ │ ├── atomDb.c │ │ ├── atomDb.sql │ │ ├── author.as │ │ ├── autoUpgrade.c │ │ ├── axtInfo.as │ │ ├── axtInfo.c │ │ ├── axtInfo.sql │ │ ├── axtInfoFillHg10.sql │ │ ├── axtInfoFillHg12.sql │ │ ├── axtInfoFillMm2.sql │ │ ├── axtLib.c │ │ ├── bacCloneAlias.as │ │ ├── bacCloneAlias.c │ │ ├── bacCloneAlias.sql │ │ ├── bacCloneXRef.as │ │ ├── bacCloneXRef.c │ │ ├── bacCloneXRef.sql │ │ ├── bacEndAlias.as │ │ ├── bacEndAlias.c │ │ ├── bacEndAlias.sql │ │ ├── bacEndPairs.sql │ │ ├── bacEndPairsBad.sql │ │ ├── bactigPos.as │ │ ├── bactigPos.c │ │ ├── bactigPos.sql │ │ ├── barChartBed.as │ │ ├── barChartBed.c │ │ ├── barChartBed.sql │ │ ├── barChartCategory.as │ │ ├── barChartCategory.c │ │ ├── barChartCategory.sql │ │ ├── barChartData.as │ │ ├── barChartData.c │ │ ├── barChartData.sql │ │ ├── barChartGeneExpr.as │ │ ├── barChartSample.as │ │ ├── barChartSample.c │ │ ├── barChartSample.sql │ │ ├── barChartUi.c │ │ ├── baseMaskCommon.c │ │ ├── bbiChroms.as │ │ ├── bbiChroms.sql │ │ ├── bdgpExprLink.as │ │ ├── bdgpExprLink.c │ │ ├── bdgpExprLink.sql │ │ ├── bdgpGeneInfo.as │ │ ├── bdgpGeneInfo.c │ │ ├── bdgpGeneInfo.sql │ │ ├── bdgpSwissProt.as │ │ ├── bdgpSwissProt.c │ │ ├── bdgpSwissProt.sql │ │ ├── bed.as │ │ ├── bed.c │ │ ├── bed.sql │ │ ├── bed12Source.as │ │ ├── bed12Source.c │ │ ├── bed12Source.sql │ │ ├── bed12wSeq.as │ │ ├── bed12wSeq.c │ │ ├── bed12wSeq.sql │ │ ├── bed5FloatScore.as │ │ ├── bed5FloatScore.c │ │ ├── bed5FloatScore.sql │ │ ├── bed5Pval.as │ │ ├── bed5Pval.c │ │ ├── bed5Pval.sql │ │ ├── bed5SourceVals.as │ │ ├── bed5Sources.as │ │ ├── bed5Sources.sql │ │ ├── bed6.as │ │ ├── bed6.sql │ │ ├── bed6FloatScore.as │ │ ├── bed6FloatScore.c │ │ ├── bed6FloatScore.sql │ │ ├── bed6FloatVal.as │ │ ├── bed6FloatVal.sql │ │ ├── bed8Attrs.as │ │ ├── bed8Attrs.c │ │ ├── bed8Attrs.sql │ │ ├── bedCart.c │ │ ├── bedDetail.as │ │ ├── bedDetail.c │ │ ├── bedDetail.sql │ │ ├── bedExp.as │ │ ├── bedGraph.as │ │ ├── bedGraph.sql │ │ ├── bgiGeneInfo.as │ │ ├── bgiGeneInfo.c │ │ ├── bgiGeneInfo.sql │ │ ├── bgiGeneSnp.as │ │ ├── bgiGeneSnp.c │ │ ├── bgiGeneSnp.sql │ │ ├── bgiSnp.as │ │ ├── bgiSnp.c │ │ ├── bgiSnp.sql │ │ ├── bigBedFind.c │ │ ├── bigBedLabel.c │ │ ├── bigChain.as │ │ ├── bigGenePred.as │ │ ├── bigGenePred.c │ │ ├── bigLink.as │ │ ├── bigMaf.as │ │ ├── bigNarrowPeak.as │ │ ├── bigPsl.as │ │ ├── bigPsl.c │ │ ├── bigTransMap.as │ │ ├── bigTransMap.c │ │ ├── bioCycGenes.sql │ │ ├── bioCycMapDesc.as │ │ ├── bioCycMapDesc.sql │ │ ├── bioCycPathway.as │ │ ├── bioCycPathway.sql │ │ ├── bioCycPathways.sql │ │ ├── bioImage.c │ │ ├── blastRef.as │ │ ├── blastRef.sql │ │ ├── blastTab.as │ │ ├── blastTab.c │ │ ├── blastTab.sql │ │ ├── blastzNet.as │ │ ├── blastzNet.c │ │ ├── blatServers.as │ │ ├── blatServers.c │ │ ├── blatServers.sql │ │ ├── blatServers.tab │ │ ├── borf.as │ │ ├── borf.c │ │ ├── borf.sql │ │ ├── borkPseudoHom.as │ │ ├── borkPseudoHom.c │ │ ├── borkPseudoHom.sql │ │ ├── botDelay.c │ │ ├── cart.c │ │ ├── cartDb.as │ │ ├── cartDb.c │ │ ├── cartDb.sql │ │ ├── cartJson.c │ │ ├── cartTrackDb.c │ │ ├── ccdsGeneMap.as │ │ ├── ccdsGeneMap.c │ │ ├── ccdsInfo.as │ │ ├── ccdsInfo.c │ │ ├── ccdsInfo.sql │ │ ├── ccdsKgMap.as │ │ ├── ccdsMgcMap.as │ │ ├── ccdsNotes.as │ │ ├── ccdsNotes.c │ │ ├── ccdsNotes.sql │ │ ├── cddDesc.as │ │ ├── cddDesc.c │ │ ├── cddDesc.sql │ │ ├── cddInfo.as │ │ ├── cddInfo.c │ │ ├── cddInfo.sql │ │ ├── cds.as │ │ ├── cdsEvidence.as │ │ ├── cdsEvidence.c │ │ ├── cdsEvidence.sql │ │ ├── cdsOrtho.as │ │ ├── cdsOrtho.c │ │ ├── cdsOrtho.sql │ │ ├── cdsPick.as │ │ ├── cdsPick.c │ │ ├── cdsPick.sql │ │ ├── cdsSpec.as │ │ ├── cdsSpec.c │ │ ├── cdsSpec.sql │ │ ├── ceBlastTab.as │ │ ├── celeraCoverage.as │ │ ├── celeraCoverage.c │ │ ├── celeraCoverage.sql │ │ ├── celeraDupPositive.as │ │ ├── celeraDupPositive.c │ │ ├── celeraDupPositive.sql │ │ ├── celeraOverlay.as │ │ ├── celeraOverlay.sql │ │ ├── cell.as │ │ ├── certificate.sql │ │ ├── cgapAlias.as │ │ ├── cgapAlias.sql │ │ ├── cgapBiocDesc.as │ │ ├── cgapBiocDesc.sql │ │ ├── cgapBiocPathway.as │ │ ├── cgapBiocPathway.sql │ │ ├── cgapSage │ │ │ ├── cgapSage.as │ │ │ ├── cgapSage.c │ │ │ ├── cgapSage.sql │ │ │ ├── cgapSageLib.as │ │ │ ├── cgapSageLib.c │ │ │ └── cgapSageLib.sql │ │ ├── cgh.as │ │ ├── cgh.c │ │ ├── cgh.sql │ │ ├── cgiApoptosis.c │ │ ├── chainCart.c │ │ ├── chainDb.as │ │ ├── chainDb.c │ │ ├── chainDb.sql │ │ ├── chainDbWithNormScore.as │ │ ├── chainGap.as │ │ ├── chainGap.c │ │ ├── chainGap.sql │ │ ├── chainLink.as │ │ ├── chainLink.c │ │ ├── chainNet.c │ │ ├── chainNetDbLoad.c │ │ ├── chem_gene_ixns.sql │ │ ├── chicken13kInfo.as │ │ ├── chicken13kInfo.c │ │ ├── chicken13kInfo.sql │ │ ├── chr18deletions.as │ │ ├── chr18deletions.c │ │ ├── chr18deletions.sql │ │ ├── chromAlias.as │ │ ├── chromAlias.c │ │ ├── chromAlias.sql │ │ ├── chromBins.c │ │ ├── chromGraph.as │ │ ├── chromGraph.c │ │ ├── chromGraph.sql │ │ ├── chromGraphFactory.c │ │ ├── chromInfo.as │ │ ├── chromInfo.c │ │ ├── chromInfo.sql │ │ ├── chromInserts.c │ │ ├── chromKeeper.c │ │ ├── clade.as │ │ ├── clonePos.as │ │ ├── clonePos.c │ │ ├── clonePos.sql │ │ ├── clusterInputAwgDnase.as │ │ ├── clusterInputAwgDnase.c │ │ ├── clusterInputAwgDnase.h │ │ ├── clusterInputAwgDnase.sql │ │ ├── clusterInputDnase.as │ │ ├── clusterInputDnase.sql │ │ ├── clusterInputTrackTable.as │ │ ├── clusterInputTrackTable.sql │ │ ├── clusterInputTrackTable2.as │ │ ├── clusterInputTrackTable2.sql │ │ ├── clusterInputTrackTable3.as │ │ ├── clusterInputTrackTable3.sql │ │ ├── clusterInputTrackTable4.as │ │ ├── clusterInputTrackTable4.sql │ │ ├── clusterInputTrackTable5.sql │ │ ├── clusterInputTrackTableEncode3Tfbs.as │ │ ├── clusterInputTrackTableEncode3Tfbs.sql │ │ ├── cnpIafrate.as │ │ ├── cnpIafrate.c │ │ ├── cnpIafrate.sql │ │ ├── cnpIafrate2.as │ │ ├── cnpIafrate2.c │ │ ├── cnpIafrate2.sql │ │ ├── cnpLocke.as │ │ ├── cnpLocke.c │ │ ├── cnpLocke.sql │ │ ├── cnpRedon.as │ │ ├── cnpRedon.c │ │ ├── cnpRedon.sql │ │ ├── cnpSebat.as │ │ ├── cnpSebat.c │ │ ├── cnpSebat.sql │ │ ├── cnpSebat2.as │ │ ├── cnpSebat2.c │ │ ├── cnpSebat2.sql │ │ ├── cnpSharp.as │ │ ├── cnpSharp.c │ │ ├── cnpSharp.sql │ │ ├── cnpSharp2.as │ │ ├── cnpSharp2.c │ │ ├── cnpSharp2.sql │ │ ├── cnpSharpCutoff.as │ │ ├── cnpSharpCutoff.c │ │ ├── cnpSharpCutoff.sql │ │ ├── cnpSharpSample.as │ │ ├── cnpSharpSample.c │ │ ├── cnpSharpSample.sql │ │ ├── codeBlast.as │ │ ├── codeBlast.c │ │ ├── codeBlast.sql │ │ ├── codeBlastScore.as │ │ ├── codeBlastScore.c │ │ ├── codeBlastScore.sql │ │ ├── cogs.c │ │ ├── cogs.sql │ │ ├── cogsxra.as │ │ ├── cogsxra.c │ │ ├── cogsxra.sql │ │ ├── columnInfo.as │ │ ├── columnInfo.c │ │ ├── columnInfo.sql │ │ ├── contamination.as │ │ ├── contamination.sql │ │ ├── contigAcc.as │ │ ├── contigAcc.c │ │ ├── contigAcc.sql │ │ ├── contrastGene.as │ │ ├── coordConv.c │ │ ├── coriellDelDup.as │ │ ├── coriellDelDup.sql │ │ ├── cosmicNew.as │ │ ├── cosmicRaw.sql │ │ ├── cpgIsland.as │ │ ├── cpgIsland.c │ │ ├── cpgIsland.sql │ │ ├── cpgIslandExt.as │ │ ├── cpgIslandExt.c │ │ ├── cpgIslandExt.sql │ │ ├── ctdSorted.sql │ │ ├── ctgPos.as │ │ ├── ctgPos.c │ │ ├── ctgPos.sql │ │ ├── ctgPos2.as │ │ ├── ctgPos2.c │ │ ├── ctgPos2.sql │ │ ├── customAdjacency.c │ │ ├── customComposite.c │ │ ├── customFactory.c │ │ ├── customPp.c │ │ ├── customTrack.c │ │ ├── cutter.as │ │ ├── cutter.c │ │ ├── cutter.sql │ │ ├── cv.c │ │ ├── cytoBand.as │ │ ├── cytoBand.c │ │ ├── cytoBand.sql │ │ ├── cytoBandIdeo.sql │ │ ├── dbDb.as │ │ ├── dbDb.c │ │ ├── dbDb.sql │ │ ├── dbDb.tab │ │ ├── dbNsfpInterPro.as │ │ ├── dbNsfpLrt.as │ │ ├── dbNsfpMutationAssessor.as │ │ ├── dbNsfpMutationTaster.as │ │ ├── dbNsfpPolyPhen2.as │ │ ├── dbNsfpSeqChange.as │ │ ├── dbNsfpSift.as │ │ ├── dbNsfpUniProt.as │ │ ├── dbNsfpVest.as │ │ ├── dbRIP.as │ │ ├── dbRIP.c │ │ ├── dbRIP.sql │ │ ├── dbSnpRs.as │ │ ├── dbSnpRs.c │ │ ├── dbSnpRs.sql │ │ ├── dbSnpRsHg.sql │ │ ├── dbSnpRsMm.sql │ │ ├── dbSnpRsRn.sql │ │ ├── decipherRaw.sql │ │ ├── decipherSnvsRaw.sql │ │ ├── defaultDb.as │ │ ├── defaultDb.c │ │ ├── defaultDb.sql │ │ ├── delConrad2.as │ │ ├── delConrad2.c │ │ ├── delConrad2.sql │ │ ├── delHinds2.as │ │ ├── delHinds2.c │ │ ├── delHinds2.sql │ │ ├── description.as │ │ ├── development.as │ │ ├── dgv.as │ │ ├── dgv.c │ │ ├── dgv.sql │ │ ├── dgvPlus.as │ │ ├── dgvPlus.c │ │ ├── dgvPlus.sql │ │ ├── dhcHumDerDenAnc.as │ │ ├── distance.as │ │ ├── distance.sql │ │ ├── dless.as │ │ ├── dless.c │ │ ├── dless.sql │ │ ├── dmBlastTab.as │ │ ├── dnaMarkovSql.c │ │ ├── dnaMotif.as │ │ ├── dnaMotif.ps │ │ ├── dnaMotif.pss │ │ ├── dnaMotif.sql │ │ ├── dnaMotifSql.c │ │ ├── dnaProbe.c │ │ ├── dnaProbe.sql │ │ ├── dnaSeq.sql │ │ ├── domainDesc.sql │ │ ├── drBlastTab.as │ │ ├── dupSpMrna.as │ │ ├── dupSpMrna.sql │ │ ├── dv.as │ │ ├── dv.c │ │ ├── dv.sql │ │ ├── dvBed.as │ │ ├── dvBed.c │ │ ├── dvBed.sql │ │ ├── dvXref2.as │ │ ├── dvXref2.c │ │ ├── dvXref2.sql │ │ ├── easyGene.as │ │ ├── easyGene.c │ │ ├── easyGene.sql │ │ ├── ec.c │ │ ├── ecAttribute.c │ │ ├── ecAttributeCode.c │ │ ├── ecCode.c │ │ ├── encode │ │ │ ├── bedLogR.as │ │ │ ├── bedLogR.sql │ │ │ ├── bedMethyl.as │ │ │ ├── bedRnaElements.as │ │ │ ├── bedRnaElements.sql │ │ │ ├── bedRnaJunctions.as │ │ │ ├── bedRrbs.as │ │ │ ├── bedRrbs.sql │ │ │ ├── broadPeak.as │ │ │ ├── broadPeak.sql │ │ │ ├── encodeErge.as │ │ │ ├── encodeErge.c │ │ │ ├── encodeErge.sql │ │ │ ├── encodeErge5race.as │ │ │ ├── encodeErge5race.sql │ │ │ ├── encodeErgeBinding.as │ │ │ ├── encodeErgeBinding.sql │ │ │ ├── encodeErgeDNAseI.as │ │ │ ├── encodeErgeDNAseI.sql │ │ │ ├── encodeErgeExpProm.as │ │ │ ├── encodeErgeExpProm.sql │ │ │ ├── encodeErgeHssCellLines.as │ │ │ ├── encodeErgeHssCellLines.c │ │ │ ├── encodeErgeHssCellLines.sql │ │ │ ├── encodeErgeInVitroFoot.as │ │ │ ├── encodeErgeInVitroFoot.sql │ │ │ ├── encodeErgeMethProm.as │ │ │ ├── encodeErgeMethProm.sql │ │ │ ├── encodeErgeStableTransf.as │ │ │ ├── encodeErgeStableTransf.sql │ │ │ ├── encodeErgeSummary.as │ │ │ ├── encodeErgeSummary.sql │ │ │ ├── encodeErgeTransTransf.as │ │ │ ├── encodeErgeTransTransf.sql │ │ │ ├── encodeExp.as │ │ │ ├── encodeExp.c │ │ │ ├── encodeExp.sql │ │ │ ├── encodeHapMapAlleleFreq.as │ │ │ ├── encodeHapMapAlleleFreq.c │ │ │ ├── encodeHapMapAlleleFreq.sql │ │ │ ├── encodeIndels.as │ │ │ ├── encodeIndels.c │ │ │ ├── encodeIndels.sql │ │ │ ├── encodePeak.as │ │ │ ├── encodePeak.c │ │ │ ├── encodePeak.sql │ │ │ ├── encodePrimateAlleles.as │ │ │ ├── encodePrimateAlleles.sql │ │ │ ├── encodeRegionInfo.as │ │ │ ├── encodeRegionInfo.c │ │ │ ├── encodeRegionInfo.sql │ │ │ ├── encodeRegionInfoCustom.c │ │ │ ├── encodeRegionsMercator.sql │ │ │ ├── encodeRegulomeProb.sql │ │ │ ├── encodeRegulomeQuality.sql │ │ │ ├── encodeRna.as │ │ │ ├── encodeRna.c │ │ │ ├── encodeRna.sql │ │ │ ├── encodeStanfordPromoters.as │ │ │ ├── encodeStanfordPromoters.c │ │ │ ├── encodeStanfordPromoters.sql │ │ │ ├── encodeStanfordPromotersAverage.as │ │ │ ├── encodeStanfordPromotersAverage.c │ │ │ ├── encodeStanfordPromotersAverage.sql │ │ │ ├── encodeStanfordRtPcr.as │ │ │ ├── encodeStanfordRtPcr.sql │ │ │ ├── gappedPeak.as │ │ │ ├── gappedPeak.sql │ │ │ ├── narrowPeak.as │ │ │ ├── narrowPeak.sql │ │ │ ├── openChromCombinedPeaks.as │ │ │ ├── openChromCombinedPeaks.sql │ │ │ ├── pairedTagAlign.as │ │ │ ├── pairedTagAlign.c │ │ │ ├── pairedTagAlign.sql │ │ │ ├── peptideMapping.as │ │ │ ├── peptideMapping.c │ │ │ ├── peptideMapping.sql │ │ │ ├── shortFrags.as │ │ │ ├── tagAlign.as │ │ │ ├── tagAlign.c │ │ │ ├── tagAlign.sql │ │ │ ├── tests │ │ │ │ └── makefile │ │ │ ├── unused │ │ │ │ ├── README │ │ │ │ ├── encodeBuPromCerebrum.sql │ │ │ │ ├── encodeBuPromColon.sql │ │ │ │ ├── encodeBuPromHeart.sql │ │ │ │ ├── encodeBuPromKidney.sql │ │ │ │ ├── encodeBuPromLiver.sql │ │ │ │ ├── encodeBuPromLung.sql │ │ │ │ ├── encodeBuPromSkMuscle.sql │ │ │ │ ├── encodeBuPromSpleen.sql │ │ │ │ ├── encodeBuPromStomach.sql │ │ │ │ ├── encodeBuPromTestis.sql │ │ │ │ ├── encodeErge5race.c │ │ │ │ ├── encodeErgeBinding.c │ │ │ │ ├── encodeErgeDNAseI.c │ │ │ │ ├── encodeErgeExpProm.c │ │ │ │ ├── encodeErgeInVitroFoot.c │ │ │ │ ├── encodeErgeMethProm.c │ │ │ │ ├── encodeErgeStableTransf.c │ │ │ │ ├── encodeErgeSummary.c │ │ │ │ ├── encodeErgeTransTransf.c │ │ │ │ ├── encodePrimateAlleles.c │ │ │ │ └── shortFrags.sql │ │ │ ├── wgEncodeCell.as │ │ │ ├── wgEncodeCell.c │ │ │ ├── wgEncodeCell.sql │ │ │ ├── wgEncodeGencodeAnnotationRemark.as │ │ │ ├── wgEncodeGencodeAnnotationRemark.c │ │ │ ├── wgEncodeGencodeAnnotationRemark.sql │ │ │ ├── wgEncodeGencodeAttrs.as │ │ │ ├── wgEncodeGencodeAttrs.c │ │ │ ├── wgEncodeGencodeAttrs.sql │ │ │ ├── wgEncodeGencodeEntrezGene.as │ │ │ ├── wgEncodeGencodeEntrezGene.c │ │ │ ├── wgEncodeGencodeEntrezGene.sql │ │ │ ├── wgEncodeGencodeExonSupport.as │ │ │ ├── wgEncodeGencodeExonSupport.c │ │ │ ├── wgEncodeGencodeExonSupport.sql │ │ │ ├── wgEncodeGencodeGeneSource.as │ │ │ ├── wgEncodeGencodeGeneSource.c │ │ │ ├── wgEncodeGencodeGeneSource.sql │ │ │ ├── wgEncodeGencodeGeneSymbol.as │ │ │ ├── wgEncodeGencodeGeneSymbol.c │ │ │ ├── wgEncodeGencodeGeneSymbol.sql │ │ │ ├── wgEncodeGencodePdb.as │ │ │ ├── wgEncodeGencodePdb.c │ │ │ ├── wgEncodeGencodePdb.sql │ │ │ ├── wgEncodeGencodePolyAFeature.as │ │ │ ├── wgEncodeGencodePolyAFeature.c │ │ │ ├── wgEncodeGencodePolyAFeature.sql │ │ │ ├── wgEncodeGencodePubMed.as │ │ │ ├── wgEncodeGencodePubMed.c │ │ │ ├── wgEncodeGencodePubMed.sql │ │ │ ├── wgEncodeGencodeRefSeq.as │ │ │ ├── wgEncodeGencodeRefSeq.c │ │ │ ├── wgEncodeGencodeRefSeq.sql │ │ │ ├── wgEncodeGencodeTag.as │ │ │ ├── wgEncodeGencodeTag.c │ │ │ ├── wgEncodeGencodeTag.sql │ │ │ ├── wgEncodeGencodeTranscriptSource.as │ │ │ ├── wgEncodeGencodeTranscriptSource.c │ │ │ ├── wgEncodeGencodeTranscriptSource.sql │ │ │ ├── wgEncodeGencodeTranscriptSupport.as │ │ │ ├── wgEncodeGencodeTranscriptSupport.c │ │ │ ├── wgEncodeGencodeTranscriptSupport.sql │ │ │ ├── wgEncodeGencodeTranscriptionSupportLevel.as │ │ │ ├── wgEncodeGencodeTranscriptionSupportLevel.c │ │ │ ├── wgEncodeGencodeTranscriptionSupportLevel.sql │ │ │ ├── wgEncodeGencodeUniProt.as │ │ │ ├── wgEncodeGencodeUniProt.c │ │ │ ├── wgEncodeGencodeUniProt.sql │ │ │ ├── wgEncodeTreatment.as │ │ │ └── wgEncodeTreatment.sql │ │ ├── encode3 │ │ │ ├── encode2Manifest.c │ │ │ └── encode3Valid.c │ │ ├── ensFace.c │ │ ├── ensGene.as │ │ ├── ensGeneXref.as │ │ ├── ensGeneXref.sql │ │ ├── ensGtp.as │ │ ├── ensGtp.sql │ │ ├── ensInfo.as │ │ ├── ensInfo.c │ │ ├── ensInfo.sql │ │ ├── ensPep.sql │ │ ├── ensPhusionBlast.as │ │ ├── ensPhusionBlast.c │ │ ├── ensPhusionBlast.sql │ │ ├── ensTranscript.as │ │ ├── ensTranscript.sql │ │ ├── ensXRefZfish.as │ │ ├── ensXRefZfish.c │ │ ├── ensXRefZfish.sql │ │ ├── ensemblLift.as │ │ ├── ensemblLift.sql │ │ ├── ensemblSource.as │ │ ├── ensemblSource.sql │ │ ├── ensemblToGeneName.as │ │ ├── ensemblXref.sql │ │ ├── ensemblXref2.sql │ │ ├── ensemblXref3.as │ │ ├── ensemblXref3.sql │ │ ├── entrezMrna.sql │ │ ├── entrezRefProt.sql │ │ ├── entrezRefseq.sql │ │ ├── esRegGeneToModule.as │ │ ├── esRegGeneToMotif.as │ │ ├── esRegModuleToMotif.as │ │ ├── est3.as │ │ ├── est3.c │ │ ├── est3.sql │ │ ├── estOrientInfo.as │ │ ├── estOrientInfo.c │ │ ├── estOrientInfo.sql │ │ ├── estPair.as │ │ ├── estPair.c │ │ ├── estPair.sql │ │ ├── evofold.sql │ │ ├── exoFish.as │ │ ├── exoFish.c │ │ ├── exoFish.sql │ │ ├── expData.as │ │ ├── expData.c │ │ ├── expData.sql │ │ ├── expDistance.as │ │ ├── expRecord.as │ │ ├── expRecord.c │ │ ├── expRecord.sql │ │ ├── exprBed.as │ │ ├── exprBed.c │ │ ├── exprBed.sql │ │ ├── extFile.as │ │ ├── facetField.c │ │ ├── factorMotifs.as │ │ ├── factorSource.as │ │ ├── factorSource.c │ │ ├── factorSource.sql │ │ ├── fbTables.as │ │ ├── fbTables.c │ │ ├── featureBits.c │ │ ├── fileUi.c │ │ ├── findKGAlias.c │ │ ├── findKGProtAlias.c │ │ ├── fishClones.as │ │ ├── fishClones.c │ │ ├── fishClones.sql │ │ ├── flyBase2004Xref.as │ │ ├── flyBase2004Xref.c │ │ ├── flyBase2004Xref.sql │ │ ├── flyBaseSwissProt.as │ │ ├── flyBaseSwissProt.c │ │ ├── flyBaseSwissProt.sql │ │ ├── flyreg.as │ │ ├── flyreg.c │ │ ├── flyreg.sql │ │ ├── flyreg2.as │ │ ├── flyreg2.c │ │ ├── flyreg2.sql │ │ ├── fosEndPairs.as │ │ ├── fosEndPairs.c │ │ ├── fosEndPairs.sql │ │ ├── fosEndPairsBad.sql │ │ ├── fullBed.as │ │ ├── fullBed.sql │ │ ├── gadAll.as │ │ ├── gadAll.sql │ │ ├── gap.sql │ │ ├── gbCdnaInfo.as │ │ ├── gbExtFile.as │ │ ├── gbExtFile.c │ │ ├── gbExtFile.sql │ │ ├── gbHeader.h │ │ ├── gbLoaded.sql │ │ ├── gbMembers.as │ │ ├── gbMembers.sql │ │ ├── gbMiscDiff.as │ │ ├── gbMiscDiff.c │ │ ├── gbProtAnn.as │ │ ├── gbProtAnn.c │ │ ├── gbProtAnn.sql │ │ ├── gbRNAs.as │ │ ├── gbRNAs.c │ │ ├── gbRNAs.sql │ │ ├── gbSeq.as │ │ ├── gbSeq.c │ │ ├── gbSeq.sql │ │ ├── gbWarn.as │ │ ├── gbWarn.c │ │ ├── gcPercent.as │ │ ├── gcPercent.c │ │ ├── gcPercent.sql │ │ ├── gdcCancer.as │ │ ├── genMapDb.as │ │ ├── genMapDb.c │ │ ├── genMapDb.sql │ │ ├── genbank.c │ │ ├── genbankBlackList.c │ │ ├── genbankTables.as │ │ ├── gencodeGeneClass.as │ │ ├── gencodeGeneClass.c │ │ ├── gencodeGeneClass.sql │ │ ├── gencodeIntron.as │ │ ├── gencodeIntron.c │ │ ├── gencodeIntron.sql │ │ ├── geneBands.as │ │ ├── geneBands.c │ │ ├── geneBands.sql │ │ ├── geneCheck.as │ │ ├── geneCheck.c │ │ ├── geneCheck.sql │ │ ├── geneCheckDetails.as │ │ ├── geneCheckDetails.c │ │ ├── geneCheckDetails.sql │ │ ├── geneCheckWidget.c │ │ ├── geneGraph.c │ │ ├── geneName.as │ │ ├── geneNetworkId.sql │ │ ├── genePix.c │ │ ├── genePred.as │ │ ├── genePred.c │ │ ├── genePred.sql │ │ ├── genePredExt.as │ │ ├── genePredReader.c │ │ ├── geneReviewsBB.sql │ │ ├── geneReviewsBed5.as │ │ ├── geneReviewsGrshortNBKid.sql │ │ ├── geneReviewsGrshortTitleNBKid.sql │ │ ├── geneReviewsRefGene.sql │ │ ├── geneSimilarities.c │ │ ├── geneTests.sql │ │ ├── geneTree.as │ │ ├── geneTree.c │ │ ├── geneTree.sql │ │ ├── genericAlias.as │ │ ├── genericAlias.sql │ │ ├── genericNameValue.as │ │ ├── genes_rat.as │ │ ├── genes_rat.sql │ │ ├── genoLay.c │ │ ├── genomeClade.as │ │ ├── genomeRangeTreeFile.c │ │ ├── genomicDups.as │ │ ├── genomicDups.c │ │ ├── genomicDups.sql │ │ ├── genomicSuperDups.as │ │ ├── genomicSuperDups.c │ │ ├── genomicSuperDups.sql │ │ ├── genotype.as │ │ ├── genotype.c │ │ ├── genotype.sql │ │ ├── genotypeFreqs.as │ │ ├── genotypeFreqs.c │ │ ├── genotypeFreqs.sql │ │ ├── genscan.sql │ │ ├── geoMirror.c │ │ ├── ggCluster.c │ │ ├── ggDbIo.c │ │ ├── ggDbRep.as │ │ ├── ggDbRep.c │ │ ├── ggDbRep.sql │ │ ├── ggDoc.as │ │ ├── ggDocEvent.as │ │ ├── ggDump.c │ │ ├── ggEvent.as │ │ ├── ggEventDb.as │ │ ├── ggEventText.as │ │ ├── ggGeneClass.as │ │ ├── ggGeneName.as │ │ ├── ggGraph.c │ │ ├── ggLink.as │ │ ├── ggLinkEvent.as │ │ ├── ggMrnaAli.as │ │ ├── ggMrnaAli.c │ │ ├── ggSymbol.as │ │ ├── ggTypes.c │ │ ├── gisaidXref.sql │ │ ├── glDbRep.as │ │ ├── glDbRep.c │ │ ├── glDbRep.sql │ │ ├── goa.as │ │ ├── goa.c │ │ ├── goa.sql │ │ ├── goaPart.as │ │ ├── goaPart.c │ │ ├── goaPart.sql │ │ ├── googleAnalytics.c │ │ ├── gpFx.c │ │ ├── grcIncidentDb.as │ │ ├── growthCondition.as │ │ ├── growthCondition.c │ │ ├── growthCondition.sql │ │ ├── grp.as │ │ ├── grp.c │ │ ├── grp.sql │ │ ├── gsIdXref.sql │ │ ├── gsIdXref2.sql │ │ ├── gsSubjInfo.sql │ │ ├── gsid │ │ │ ├── vax003.as │ │ │ ├── vax003AaCons.as │ │ │ ├── vax003AaMaf.as │ │ │ ├── vax003Cons.as │ │ │ ├── vax003Maf.as │ │ │ ├── vax004.as │ │ │ ├── vax004AaCons.as │ │ │ ├── vax004AaMaf.as │ │ │ ├── vax004Cons.as │ │ │ └── vax004Maf.as │ │ ├── gsidClinicRec.sql │ │ ├── gsidClinicRecWithSeq.sql │ │ ├── gsidSubjInfo.sql │ │ ├── gsidSubjInfo3.sql │ │ ├── gsidSubjSeq.sql │ │ ├── gtexAse.as │ │ ├── gtexAse.c │ │ ├── gtexAse.sql │ │ ├── gtexBoxplot.c │ │ ├── gtexDonor.as │ │ ├── gtexDonor.c │ │ ├── gtexDonor.sql │ │ ├── gtexEqtl.as │ │ ├── gtexEqtl.sql │ │ ├── gtexEqtlCluster.as │ │ ├── gtexEqtlCluster.c │ │ ├── gtexEqtlCluster.sql │ │ ├── gtexGeneBed.as │ │ ├── gtexGeneBed.c │ │ ├── gtexGeneBed.sql │ │ ├── gtexInfo.as │ │ ├── gtexInfo.c │ │ ├── gtexInfo.sql │ │ ├── gtexSample.as │ │ ├── gtexSample.c │ │ ├── gtexSample.sql │ │ ├── gtexSampleData.as │ │ ├── gtexSampleData.c │ │ ├── gtexSampleData.sql │ │ ├── gtexTissue.as │ │ ├── gtexTissue.c │ │ ├── gtexTissue.sql │ │ ├── gtexTissueData.as │ │ ├── gtexTissueData.c │ │ ├── gtexTissueData.sql │ │ ├── gtexTissueMedian.as │ │ ├── gtexTissueMedian.c │ │ ├── gtexTissueMedian.sql │ │ ├── gtexUi.c │ │ ├── gv.as │ │ ├── gv.c │ │ ├── gv.sql │ │ ├── gvUi.c │ │ ├── gwasCatalog.as │ │ ├── gwasCatalog.c │ │ ├── gwasCatalog.sql │ │ ├── hAnno.c │ │ ├── hCommon.c │ │ ├── hCytoBand.c │ │ ├── hPrint.c │ │ ├── hVarSubst.c │ │ ├── haplotypes.c │ │ ├── hapmapAlleleFreq.as │ │ ├── hapmapAlleleFreq.c │ │ ├── hapmapAlleleFreq.sql │ │ ├── hapmapAlleles.as │ │ ├── hapmapAlleles.c │ │ ├── hapmapAlleles.sql │ │ ├── hapmapAllelesChimp.as │ │ ├── hapmapAllelesCombined.as │ │ ├── hapmapAllelesCombined.c │ │ ├── hapmapAllelesCombined.sql │ │ ├── hapmapAllelesMacaque.as │ │ ├── hapmapAllelesOrtho.as │ │ ├── hapmapAllelesOrtho.c │ │ ├── hapmapAllelesOrtho.sql │ │ ├── hapmapAllelesSummary.as │ │ ├── hapmapAllelesSummary.c │ │ ├── hapmapAllelesSummary.sql │ │ ├── hapmapLd.as │ │ ├── hapmapLd.c │ │ ├── hapmapLd.sql │ │ ├── hapmapPhaseIIISummary.as │ │ ├── hapmapPhaseIIISummary.c │ │ ├── hapmapPhaseIIISummary.sql │ │ ├── hapmapPrimateAlleles.as │ │ ├── hapmapPrimateAlleles.c │ │ ├── hapmapPrimateAlleles.sql │ │ ├── hapmapSnps.as │ │ ├── hapmapSnps.c │ │ ├── hapmapSnps.sql │ │ ├── hapmapSnpsCEU.as │ │ ├── hapmapSnpsCHB.as │ │ ├── hapmapSnpsCombined.as │ │ ├── hapmapSnpsCombined.c │ │ ├── hapmapSnpsCombined.sql │ │ ├── hapmapSnpsJPT.as │ │ ├── hapmapSnpsYRI.as │ │ ├── hashJoin.c │ │ ├── hdb.c │ │ ├── hg16Kg.sql │ │ ├── hg17Kg.sql │ │ ├── hgBam.c │ │ ├── hgBlastTab.as │ │ ├── hgColors.c │ │ ├── hgConfig.c │ │ ├── hgExp.c │ │ ├── hgFind.c │ │ ├── hgFindSpec.as │ │ ├── hgFindSpec.c │ │ ├── hgFindSpec.sql │ │ ├── hgFindSpecCustom.c │ │ ├── hgGene.as │ │ ├── hgGene.c │ │ ├── hgGene.sql │ │ ├── hgHgvs.c │ │ ├── hgHgvsParse.c │ │ ├── hgMaf.c │ │ ├── hgRelate.c │ │ ├── hgSeq.c │ │ ├── hgdpGeo.as │ │ ├── hgdpGeo.c │ │ ├── hgdpGeo.sql │ │ ├── hgnc.as │ │ ├── hgnc.c │ │ ├── hgnc.sql │ │ ├── hgncXref.as │ │ ├── hgncXref.sql │ │ ├── hic.c │ │ ├── hicUi.c │ │ ├── history.as │ │ ├── hivGene.as │ │ ├── hivGene.sql │ │ ├── hprdToCdna.sql │ │ ├── hprdToUniProt.sql │ │ ├── hubConnect.as │ │ ├── hubConnect.c │ │ ├── hubConnect.sql │ │ ├── hubPublic.as │ │ ├── hubPublic.c │ │ ├── hubPublic.sql │ │ ├── hubSearchText.as │ │ ├── hubSearchText.c │ │ ├── hubSearchText.sql │ │ ├── hubStatus.as │ │ ├── hubStatus.sql │ │ ├── huge.sql │ │ ├── hugo.as │ │ ├── hui.c │ │ ├── humanParalog.as │ │ ├── humanParalog.c │ │ ├── humanParalog.sql │ │ ├── hvGfx.c │ │ ├── idName.as │ │ ├── imageClone.as │ │ ├── imageClone.c │ │ ├── immuno.sql │ │ ├── immunoRaw.sql │ │ ├── indelShift.c │ │ ├── interPro.as │ │ ├── interPro.sql │ │ ├── interProXref.as │ │ ├── interProXref.sql │ │ ├── interact.as │ │ ├── interact.c │ │ ├── interact.sql │ │ ├── interactUi.c │ │ ├── isochores.as │ │ ├── isochores.c │ │ ├── isochores.sql │ │ ├── ispyTables.c │ │ ├── ispyTables.sql │ │ ├── itemAttr.as │ │ ├── itemAttr.c │ │ ├── itemAttr.sql │ │ ├── itemConf.as │ │ ├── itemConf.c │ │ ├── itemConf.sql │ │ ├── itemDetailsHtml.as │ │ ├── itemDetailsHtml.c │ │ ├── itemDetailsHtml.sql │ │ ├── jWestBanner.html │ │ ├── jWestHeader.html │ │ ├── jalview.c │ │ ├── jaxAlleleInfo.as │ │ ├── jaxAlleleInfo.sql │ │ ├── jaxAllelePheno.as │ │ ├── jaxAllelePheno.sql │ │ ├── jaxOrtholog.as │ │ ├── jaxOrtholog.c │ │ ├── jaxOrtholog.sql │ │ ├── jaxQTL.as │ │ ├── jaxQTL.c │ │ ├── jaxQTL2.as │ │ ├── jaxQTL2.c │ │ ├── jaxQTL2.sql │ │ ├── jaxQTL3.as │ │ ├── jaxQTL3.c │ │ ├── jaxQTL3.sql │ │ ├── jaxQtl.sql │ │ ├── jaxQtlRaw.sql │ │ ├── jgiFilteredModels.sql │ │ ├── jgiGene.as │ │ ├── jgiGene.c │ │ ├── jgiGene.sql │ │ ├── jksql.c │ │ ├── joinMixer.c │ │ ├── joiner.c │ │ ├── jsHelper.c │ │ ├── keggList.sql │ │ ├── keggMapDesc.as │ │ ├── keggMapDesc.sql │ │ ├── keggPathway.as │ │ ├── keggPathway.sql │ │ ├── keyword.as │ │ ├── kg1ToKg2.as │ │ ├── kg1ToKg2.c │ │ ├── kg1ToKg2.sql │ │ ├── kg2.sql │ │ ├── kgAlias.as │ │ ├── kgAlias.c │ │ ├── kgAlias.sql │ │ ├── kgCandidate.sql │ │ ├── kgCandidate0.sql │ │ ├── kgCandidate2.sql │ │ ├── kgCandidateX.sql │ │ ├── kgCandidateY.sql │ │ ├── kgCandidateZ.sql │ │ ├── kgColor.as │ │ ├── kgColor.c │ │ ├── kgColor.sql │ │ ├── kgMapName.as │ │ ├── kgMapName.c │ │ ├── kgMapName.sql │ │ ├── kgProtAlias.as │ │ ├── kgProtAlias.c │ │ ├── kgProtAlias.sql │ │ ├── kgProtSnpMap.sql │ │ ├── kgPutBack2.sql │ │ ├── kgSpAlias.as │ │ ├── kgSpAlias.sql │ │ ├── kgTemp2.sql │ │ ├── kgXref.as │ │ ├── kgXref.c │ │ ├── kgXref.sql │ │ ├── kgXrefPrevious.as │ │ ├── kiddEichlerToNcbi.as │ │ ├── kiddEichlerToNcbi.sql │ │ ├── knownAttrs.as │ │ ├── knownAttrs.sql │ │ ├── knownBlastTab.as │ │ ├── knownCanonToDecipher.sql │ │ ├── knownCanonical.as │ │ ├── knownCanonical.c │ │ ├── knownCanonical.sql │ │ ├── knownCds.as │ │ ├── knownCds.sql │ │ ├── knownGene.as │ │ ├── knownGene.sql │ │ ├── knownGeneLink.as │ │ ├── knownGeneLink.sql │ │ ├── knownGeneMrna.as │ │ ├── knownGeneMrna.sql │ │ ├── knownGenePep.sql │ │ ├── knownInfo.as │ │ ├── knownInfo.c │ │ ├── knownInfo.sql │ │ ├── knownIsoforms.as │ │ ├── knownIsoforms.sql │ │ ├── knownMore.as │ │ ├── knownMore.c │ │ ├── knownMore.sql │ │ ├── knownTo.as │ │ ├── knownTo.sql │ │ ├── knownToHprd.sql │ │ ├── knownToKeggEntrez.sql │ │ ├── knownToLocusLink.as │ │ ├── knownToSuper.as │ │ ├── knownToSuper.c │ │ ├── knownToSuper.sql │ │ ├── knownToTreefam.sql │ │ ├── knownToVisiGene.as │ │ ├── landmark.as │ │ ├── landmark.c │ │ ├── landmark.sql │ │ ├── landmarkUi.c │ │ ├── lav.c │ │ ├── ld.as │ │ ├── ld.c │ │ ├── ld.sql │ │ ├── ld2.as │ │ ├── ld2.c │ │ ├── ld2.sql │ │ ├── lfs.as │ │ ├── lfs.c │ │ ├── lfs.sql │ │ ├── library.as │ │ ├── liftOver.c │ │ ├── liftOverChain.as │ │ ├── liftOverChain.c │ │ ├── liftOverChain.sql │ │ ├── liftUp.c │ │ ├── lincRNAsCTTemp.as │ │ ├── llaInfo.as │ │ ├── llaInfo.c │ │ ├── llaInfo.sql │ │ ├── logoutJs.h │ │ ├── longRange.c │ │ ├── lowelabArkinOperonScore.as │ │ ├── lowelabArkinOperonScore.c │ │ ├── lowelabArkinOperonScore.sql │ │ ├── lowelabPfamHit.as │ │ ├── lowelabPfamHit.c │ │ ├── lowelabPfamHit.h │ │ ├── lowelabPfamHit.sql │ │ ├── lowelabTIGROperonScore.as │ │ ├── lowelabTIGROperonScore.c │ │ ├── lowelabTIGROperonScore.sql │ │ ├── loweutils.c │ │ ├── lrg.as │ │ ├── lrg.c │ │ ├── lsSnpPdb.as │ │ ├── lsSnpPdb.c │ │ ├── lsSnpPdb.sql │ │ ├── lsSnpPdbChimera.c │ │ ├── lsSnpPdbChimera.py │ │ ├── mafFrames.as │ │ ├── mafFrames.c │ │ ├── mafFrames.sql │ │ ├── mafGene.c │ │ ├── mafSnp160way.as │ │ ├── mafSummary.as │ │ ├── mafSummary.c │ │ ├── mafSummary.sql │ │ ├── makeItemsItem.as │ │ ├── makeItemsItem.c │ │ ├── makeItemsItem.sql │ │ ├── makefile │ │ ├── mammalPsg.as │ │ ├── mammalPsg.c │ │ ├── mammalPsg.sql │ │ ├── mane.as │ │ ├── mapSts.as │ │ ├── mapSts.c │ │ ├── mapSts.sql │ │ ├── mathWig.c │ │ ├── mcnBreakpoints.as │ │ ├── mcnBreakpoints.c │ │ ├── mcnBreakpoints.sql │ │ ├── mdb.c │ │ ├── megablastInfo.as │ │ ├── megablastInfo.c │ │ ├── megablastInfo.sql │ │ ├── metaChromGraph.as │ │ ├── metaChromGraph.c │ │ ├── metaChromGraph.sql │ │ ├── metaDb.as │ │ ├── metaDb.sql │ │ ├── metaInfo.as │ │ ├── metaInfo.sql │ │ ├── mgcMBLabValid.as │ │ ├── mgcMBLabValid.sql │ │ ├── mgiID.as │ │ ├── mgiID.c │ │ ├── mgiID.sql │ │ ├── microarray.c │ │ ├── mim2gene.as │ │ ├── minChromSize.c │ │ ├── minGeneInfo.as │ │ ├── minGeneInfo.c │ │ ├── minGeneInfo.sql │ │ ├── mmBlastTab.as │ │ ├── mouseOrtho.as │ │ ├── mouseOrtho.c │ │ ├── mouseOrtho.sql │ │ ├── mouseSyn.as │ │ ├── mouseSyn.c │ │ ├── mouseSyn.sql │ │ ├── mouseSynWhd.as │ │ ├── mouseSynWhd.c │ │ ├── mouseSynWhd.sql │ │ ├── mouseTraceInfo.sql │ │ ├── mrnaClone.as │ │ ├── mrnaGp.sql │ │ ├── mrnaGp2.sql │ │ ├── mrnaMisMatch.c │ │ ├── mrnaOrientInfo.sql │ │ ├── mrnaRefseq.as │ │ ├── mrnaRefseq.sql │ │ ├── mrnaSeq.sql │ │ ├── mysqlTableStatus.as │ │ ├── mysqlTableStatus.c │ │ ├── namedSessionDb.as │ │ ├── namedSessionDb.sql │ │ ├── ncRna.as │ │ ├── ncRna.c │ │ ├── ncRna.sql │ │ ├── ncbiRefLink.as │ │ ├── ncbiRefLink.c │ │ ├── ncbiRefLink.sql │ │ ├── ncbiRefSeqLink.as │ │ ├── ncbiRefSeqLink.c │ │ ├── ncbiRefSeqLink.sql │ │ ├── nestedRepeats.as │ │ ├── nestedRepeats.sql │ │ ├── netAlign.as │ │ ├── netAlign.c │ │ ├── netAlign.sql │ │ ├── netCart.c │ │ ├── newfoo │ │ │ ├── cytoBand.c │ │ │ └── cytoBand.h │ │ ├── nonCodingUi.c │ │ ├── ntOoaHaplo.as │ │ ├── ntOoaHaplo.sql │ │ ├── omicia.as │ │ ├── omicia.c │ │ ├── omicia.sql │ │ ├── omim2gene.as │ │ ├── omim2gene.sql │ │ ├── omimAv.as │ │ ├── omimAv.sql │ │ ├── omimAvRepl.as │ │ ├── omimAvRepl.sql │ │ ├── omimDisorderMap.as │ │ ├── omimDisorderMap.sql │ │ ├── omimDisorderPhenotype.as │ │ ├── omimDisorderPhenotype.sql │ │ ├── omimField.sql │ │ ├── omimGeneMap.as │ │ ├── omimGeneMap.sql │ │ ├── omimGeneMap2.as │ │ ├── omimGeneMap2.sql │ │ ├── omimGeneSymbol.as │ │ ├── omimGeneSymbol.sql │ │ ├── omimMorbidMap.as │ │ ├── omimPhenotype.as │ │ ├── omimPhenotype.sql │ │ ├── omimTitle.as │ │ ├── omimTitle.c │ │ ├── omimTitle.sql │ │ ├── omimToKnownCanonical.as │ │ ├── omimToKnownCanonical.sql │ │ ├── ooUtils.c │ │ ├── oreganno.as │ │ ├── oreganno.c │ │ ├── oreganno.sql │ │ ├── oregannoUi.c │ │ ├── orfToGene.as │ │ ├── orfToGene.sql │ │ ├── organism.as │ │ ├── orig_makefile │ │ ├── orthoAlleles.as │ │ ├── orthoAlleles.c │ │ ├── orthoAlleles.sql │ │ ├── pal.c │ │ ├── pbAaDistA.sql │ │ ├── pbAaDistC.sql │ │ ├── pbAaDistD.sql │ │ ├── pbAaDistE.sql │ │ ├── pbAaDistF.sql │ │ ├── pbAaDistG.sql │ │ ├── pbAaDistH.sql │ │ ├── pbAaDistI.sql │ │ ├── pbAaDistK.sql │ │ ├── pbAaDistL.sql │ │ ├── pbAaDistM.sql │ │ ├── pbAaDistN.sql │ │ ├── pbAaDistP.sql │ │ ├── pbAaDistQ.sql │ │ ├── pbAaDistR.sql │ │ ├── pbAaDistS.sql │ │ ├── pbAaDistT.sql │ │ ├── pbAaDistV.sql │ │ ├── pbAaDistW.sql │ │ ├── pbAaDistX.as │ │ ├── pbAaDistY.sql │ │ ├── pbAnomLimit.as │ │ ├── pbAnomLimit.sql │ │ ├── pbResAvgStd.as │ │ ├── pbResAvgStd.sql │ │ ├── pbStamp.as │ │ ├── pbStamp.c │ │ ├── pbStamp.sql │ │ ├── pcrResult.c │ │ ├── pdbSP.as │ │ ├── pdbSP.sql │ │ ├── pepCCntDist.as │ │ ├── pepCCntDist.sql │ │ ├── pepExonCntDist.as │ │ ├── pepExonCntDist.sql │ │ ├── pepHydroDist.as │ │ ├── pepHydroDist.sql │ │ ├── pepIPCntDist.as │ │ ├── pepIPCntDist.sql │ │ ├── pepMolWtDist.as │ │ ├── pepMolWtDist.sql │ │ ├── pepMwAa.as │ │ ├── pepMwAa.sql │ │ ├── pepPi.as │ │ ├── pepPi.sql │ │ ├── pepPiDist.as │ │ ├── pepPiDist.sql │ │ ├── pepPred.as │ │ ├── pepPred.c │ │ ├── pepPred.sql │ │ ├── pepResDist.as │ │ ├── pepResDist.sql │ │ ├── peptideAtlasPeptide.as │ │ ├── peptideAtlasPeptide.c │ │ ├── peptideAtlasPeptide.sql │ │ ├── pfamDesc.as │ │ ├── pfamDesc.sql │ │ ├── pfamXref.as │ │ ├── pfamXref.sql │ │ ├── pgPhenoAssoc.as │ │ ├── pgPhenoAssoc.c │ │ ├── pgPhenoAssoc.sql │ │ ├── pgPolyphenPred.as │ │ ├── pgPolyphenPred.c │ │ ├── pgPolyphenPred.sql │ │ ├── pgSiftPred.as │ │ ├── pgSiftPred.c │ │ ├── pgSiftPred.sql │ │ ├── pgSnp.as │ │ ├── pgSnp.c │ │ ├── pgSnp.sql │ │ ├── pga.sql │ │ ├── pileups.as │ │ ├── pileups.sql │ │ ├── plasEndPairs.as │ │ ├── plasEndPairs.c │ │ ├── plasEndPairs.sql │ │ ├── polyGenotype.as │ │ ├── polyGenotype.c │ │ ├── polyGenotype.sql │ │ ├── productName.as │ │ ├── protFeat.as │ │ ├── protFeat.c │ │ ├── protFeat.sql │ │ ├── protHomolog.as │ │ ├── protHomolog.sql │ │ ├── protMrnaBlast.sql │ │ ├── protMrnaBlat.sql │ │ ├── protMrnaScore.sql │ │ ├── protRefBlat.sql │ │ ├── protVar.as │ │ ├── protVar.c │ │ ├── protVar.sql │ │ ├── proteome_pfamDesc.sql │ │ ├── pscreen.as │ │ ├── pscreen.c │ │ ├── pscreen.sql │ │ ├── pseudoGeneLink.as │ │ ├── pseudoGeneLink.c │ │ ├── pseudoGeneLink.sql │ │ ├── pseudoYale60.sql │ │ ├── pseudoYale60Class.sql │ │ ├── pslReader.c │ │ ├── pslWQueryID.as │ │ ├── pslWQueryID.c │ │ ├── pslWQueryID.sql │ │ ├── pslWScore.as │ │ ├── pslWScore.c │ │ ├── pslWScore.sql │ │ ├── pubsArticle.as │ │ ├── pubsArticle.sql │ │ ├── pubsBlat.as │ │ ├── pubsBlat.sql │ │ ├── pubsBlat2.as │ │ ├── pubsBlatPsl.as │ │ ├── pubsBlatPsl.sql │ │ ├── pubsMarker.as │ │ ├── pubsMarker.sql │ │ ├── pubsMarkerSnp.as │ │ ├── pubsMarkerSnp.sql │ │ ├── pubsSequenceAnnot.as │ │ ├── pubsSequenceAnnot.sql │ │ ├── putaInfo.as │ │ ├── putaInfo.c │ │ ├── putaInfo.sql │ │ ├── qaSeq.c │ │ ├── rangeTreeFile.c │ │ ├── rankProp.as │ │ ├── rankProp.c │ │ ├── rdmrRaw.sql │ │ ├── recombRate.as │ │ ├── recombRate.c │ │ ├── recombRate.sql │ │ ├── recombRateMouse.c │ │ ├── recombRateMouse.sql │ │ ├── recombRateRat.c │ │ ├── recombRateRat.sql │ │ ├── refFlat.as │ │ ├── refLink.as │ │ ├── refLink.c │ │ ├── refLink.sql │ │ ├── refRa.sql │ │ ├── refSeqFuncElems.as │ │ ├── refSeqKg.sql │ │ ├── refSeqStatus.as │ │ ├── refSeqStatus.c │ │ ├── refSeqStatus.sql │ │ ├── refseqSeq.sql │ │ ├── regrp.csh │ │ ├── regrp.sql │ │ ├── retroMrnaInfo.as │ │ ├── retroMrnaInfo.c │ │ ├── retroMrnaInfo.sql │ │ ├── rgdEst.sql │ │ ├── rgdEstLink.sql │ │ ├── rgdGene.sql │ │ ├── rgdGene2.sql │ │ ├── rgdGene2KeggPathway.as │ │ ├── rgdGene2KeggPathway.sql │ │ ├── rgdGene2Pep.sql │ │ ├── rgdGene2Raw.as │ │ ├── rgdGene2Raw.sql │ │ ├── rgdGene2ToDescription.sql │ │ ├── rgdGene2ToDisplayId.sql │ │ ├── rgdGene2ToKeggEntrez.as │ │ ├── rgdGene2ToKeggEntrez.sql │ │ ├── rgdGene2ToPDB.sql │ │ ├── rgdGene2ToSuper.sql │ │ ├── rgdGene2ToSymbol.as │ │ ├── rgdGene2ToSymbol.sql │ │ ├── rgdGene2ToUniProt.sql │ │ ├── rgdGene2Xref.as │ │ ├── rgdGene2Xref.sql │ │ ├── rgdGeneCds.sql │ │ ├── rgdGeneLink.sql │ │ ├── rgdGenePathway.as │ │ ├── rgdGeneRaw0.sql │ │ ├── rgdGeneRaw2.sql │ │ ├── rgdGeneRaw2cds.sql │ │ ├── rgdGeneRaw2exon.sql │ │ ├── rgdGeneRaw2gene.sql │ │ ├── rgdGeneRaw3.sql │ │ ├── rgdGeneXref2.sql │ │ ├── rgdPathway.as │ │ ├── rgdQtl.c │ │ ├── rgdQtl.sql │ │ ├── rgdQtlLink.as │ │ ├── rgdQtlLink.sql │ │ ├── rgdSslp.sql │ │ ├── rgdSslpLink.sql │ │ ├── rhMapInfo.as │ │ ├── rhMapInfo.c │ │ ├── rhMapInfo.sql │ │ ├── rhMapZfishInfo.as │ │ ├── rhMapZfishInfo.c │ │ ├── rhMapZfishInfo.sql │ │ ├── riken.c │ │ ├── riken.dtd │ │ ├── rikenBest.as │ │ ├── rikenBest.c │ │ ├── rikenBest.sql │ │ ├── rikenBorf.sql │ │ ├── rikenCluster.as │ │ ├── rikenCluster.c │ │ ├── rikenCluster.sql │ │ ├── rmskAlign.as │ │ ├── rmskAlign.c │ │ ├── rmskAlign.sql │ │ ├── rmskBed6+10.as │ │ ├── rmskJoined.as │ │ ├── rmskJoined.c │ │ ├── rmskJoined.sql │ │ ├── rmskOut.as │ │ ├── rmskOut.c │ │ ├── rmskOut.sql │ │ ├── rmskOut2.as │ │ ├── rmskOut2.c │ │ ├── rmskOut2.sql │ │ ├── rnBlastTab.as │ │ ├── rnaFold.as │ │ ├── rnaFold.c │ │ ├── rnaFold.sql │ │ ├── rnaGene.as │ │ ├── rnaGene.c │ │ ├── rnaGene.sql │ │ ├── rnaGenes.as │ │ ├── rnaGenes.c │ │ ├── rnaGenes.sql │ │ ├── rnaGroup.as │ │ ├── rnaGroup.c │ │ ├── rnaGroup.sql │ │ ├── rnaHybridization.as │ │ ├── rnaHybridization.c │ │ ├── rnaHybridization.sql │ │ ├── rnaPLFold.as │ │ ├── rnaPLFold.c │ │ ├── rnaPLFold.sql │ │ ├── rnaSecStr.as │ │ ├── rnaSecStr.c │ │ ├── rnaSecStr.sql │ │ ├── roughAli.as │ │ ├── roughAli.c │ │ ├── roughAli.sql │ │ ├── sage.as │ │ ├── sage.c │ │ ├── sage.sql │ │ ├── sageCounts.c │ │ ├── sageExp.as │ │ ├── sageExp.c │ │ ├── sageExp.sql │ │ ├── samAlignment.as │ │ ├── samAlignment.c │ │ ├── samAlignment.sql │ │ ├── samSubdir.as │ │ ├── samSubdir.sql │ │ ├── sample.as │ │ ├── sample.c │ │ ├── sample.sql │ │ ├── sanger22extra.as │ │ ├── sanger22extra.c │ │ ├── sanger22extra.sql │ │ ├── sangerGene.as │ │ ├── sangerGene.c │ │ ├── sangerGeneToWBGeneID.as │ │ ├── sangerGeneToWBGeneID.c │ │ ├── sangerGeneToWBGeneID.sql │ │ ├── sangerLinks.as │ │ ├── sangerLinks.sql │ │ ├── sargassoSeaXra.as │ │ ├── sargassoSeaXra.c │ │ ├── sargassoSeaXra.sql │ │ ├── scBlastTab.as │ │ ├── scopDes.as │ │ ├── scopDes.c │ │ ├── scopDes.sql │ │ ├── scopDesc.as │ │ ├── scopDesc.sql │ │ ├── scoredRef.as │ │ ├── scoredRef.c │ │ ├── scoredRef.sql │ │ ├── search.c │ │ ├── seq.as │ │ ├── seqWindow.c │ │ ├── sessionDb.as │ │ ├── sessionDb.sql │ │ ├── sessionThumbnail.c │ │ ├── sex.as │ │ ├── sfAssign.as │ │ ├── sfAssign.sql │ │ ├── sfDes.as │ │ ├── sfDes.sql │ │ ├── sfDescription.as │ │ ├── sfDescription.sql │ │ ├── sgdAbundance.as │ │ ├── sgdAbundance.c │ │ ├── sgdAbundance.sql │ │ ├── sgdClone.as │ │ ├── sgdClone.c │ │ ├── sgdClone.sql │ │ ├── sgdDescription.as │ │ ├── sgdDescription.c │ │ ├── sgdDescription.sql │ │ ├── sgdOther.as │ │ ├── sgdOther.c │ │ ├── sgdOther.sql │ │ ├── sgdOtherDescription.sql │ │ ├── simpleNucDiff.as │ │ ├── simpleNucDiff.c │ │ ├── simpleNucDiff.sql │ │ ├── simpleRepeat.as │ │ ├── simpleRepeat.c │ │ ├── simpleRepeat.sql │ │ ├── snakeUi.c │ │ ├── snoRNAs.as │ │ ├── snoRNAs.c │ │ ├── snoRNAs.h │ │ ├── snoRNAs.sql │ │ ├── snp.as │ │ ├── snp.c │ │ ├── snp.sql │ │ ├── snp125.as │ │ ├── snp125.c │ │ ├── snp125.sql │ │ ├── snp125Coding.as │ │ ├── snp125Coding.sql │ │ ├── snp125CodingCoordless.as │ │ ├── snp125CodingCoordless.c │ │ ├── snp125CodingCoordless.sql │ │ ├── snp125ExceptionDesc.as │ │ ├── snp125ExceptionDesc.sql │ │ ├── snp125Exceptions.as │ │ ├── snp125Exceptions.c │ │ ├── snp125Exceptions.sql │ │ ├── snp125Ui.c │ │ ├── snp126Exceptions.sql │ │ ├── snp132Ext.as │ │ ├── snp132Ext.c │ │ ├── snpArrayAffy10.as │ │ ├── snpArrayAffy10.sql │ │ ├── snpArrayAffy10v2.as │ │ ├── snpArrayAffy10v2.sql │ │ ├── snpArrayAffy250Nsp.as │ │ ├── snpArrayAffy250Nsp.sql │ │ ├── snpArrayAffy250Sty.as │ │ ├── snpArrayAffy250Sty.sql │ │ ├── snpArrayAffy50HindIII.as │ │ ├── snpArrayAffy50HindIII.sql │ │ ├── snpArrayAffy50XbaI.as │ │ ├── snpArrayAffy50XbaI.sql │ │ ├── snpArrayIllumina1M.sql │ │ ├── snpArrayIllumina1MRaw.sql │ │ ├── snpArrayIllumina300.as │ │ ├── snpArrayIllumina300.sql │ │ ├── snpArrayIlluminaHuman660W_Quad.sql │ │ ├── snpArrayIlluminaHuman660W_QuadRaw.sql │ │ ├── snpArrayIlluminaHumanCytoSNP_12.sql │ │ ├── snpArrayIlluminaHumanCytoSNP_12Raw.sql │ │ ├── snpArrayIlluminaHumanOmni1_Quad.sql │ │ ├── snpArrayIlluminaHumanOmni1_QuadRaw.sql │ │ ├── snpExceptions.as │ │ ├── snpExceptions.c │ │ ├── snpExceptions.sql │ │ ├── snpExtFile.as │ │ ├── snpExtFile.c │ │ ├── snpExtFile.sql │ │ ├── snpFasta.as │ │ ├── snpFasta.c │ │ ├── snpFasta.sql │ │ ├── snpFreq.sql │ │ ├── snpMap.as │ │ ├── snpMap.c │ │ ├── snpMap.sql │ │ ├── snpOrthoPanPonRhe.as │ │ ├── snpOrthoPanPonRhe.sql │ │ ├── snpOrthoPanTroRheMac.as │ │ ├── snpOrthoPanTroRheMac.sql │ │ ├── snpSeq.as │ │ ├── snpSeq.c │ │ ├── snpSeq.sql │ │ ├── snpSingle.sql │ │ ├── snpSingleValid.sql │ │ ├── snpTmp.as │ │ ├── snpTmp.c │ │ ├── snpTmp.sql │ │ ├── snpUi.c │ │ ├── soTerm.c │ │ ├── softPromoter.as │ │ ├── softPromoter.c │ │ ├── softPromoter.sql │ │ ├── softberryHom.as │ │ ├── softberryHom.c │ │ ├── softberryHom.sql │ │ ├── source.as │ │ ├── spDb.c │ │ ├── spDeleted.sql │ │ ├── spDisease.as │ │ ├── spDisease.sql │ │ ├── spMrna.as │ │ ├── spMrna.sql │ │ ├── spOldNew.as │ │ ├── spOldNew.sql │ │ ├── spOrganism.as │ │ ├── spOrganism.sql │ │ ├── spPsiBlast.as │ │ ├── spReactomeEvent.as │ │ ├── spReactomeEvent.sql │ │ ├── spReactomeId.as │ │ ├── spReactomeId.sql │ │ ├── spRef.sql │ │ ├── spSecondaryID.as │ │ ├── spSecondaryID.sql │ │ ├── spVariant.as │ │ ├── spVariant.sql │ │ ├── spXref2.as │ │ ├── spXref2.sql │ │ ├── spXref3.as │ │ ├── spXref3.sql │ │ ├── splicProt.sql │ │ ├── splignAlign.as │ │ ├── splignAlign.c │ │ ├── sqlProg.c │ │ ├── sqlSanity.c │ │ ├── stanMad.as │ │ ├── stanMad.c │ │ ├── straw │ │ │ ├── makefile │ │ │ ├── straw.cpp │ │ │ ├── straw.h │ │ │ └── udcWrapper.h │ │ ├── stsAlias.as │ │ ├── stsAlias.c │ │ ├── stsAlias.sql │ │ ├── stsInfo.as │ │ ├── stsInfo.c │ │ ├── stsInfo.sql │ │ ├── stsInfo2.as │ │ ├── stsInfo2.c │ │ ├── stsInfo2.sql │ │ ├── stsInfoMouse.as │ │ ├── stsInfoMouse.c │ │ ├── stsInfoMouse.sql │ │ ├── stsInfoMouseNew.as │ │ ├── stsInfoMouseNew.c │ │ ├── stsInfoMouseNew.sql │ │ ├── stsInfoRat.as │ │ ├── stsInfoRat.c │ │ ├── stsInfoRat.sql │ │ ├── stsMap.as │ │ ├── stsMap.c │ │ ├── stsMap.sql │ │ ├── stsMapMouse.as │ │ ├── stsMapMouse.c │ │ ├── stsMapMouse.sql │ │ ├── stsMapMouseNew.as │ │ ├── stsMapMouseNew.c │ │ ├── stsMapMouseNew.sql │ │ ├── stsMapRat.as │ │ ├── stsMapRat.c │ │ ├── stsMapRat.sql │ │ ├── stsMarker.as │ │ ├── stsMarker.c │ │ ├── stsMarker.sql │ │ ├── suggest.c │ │ ├── swInterPro.as │ │ ├── swInterPro.sql │ │ ├── switchDbTss.as │ │ ├── switchDbTss.c │ │ ├── switchDbTss.sql │ │ ├── synMap.as │ │ ├── synMap.c │ │ ├── synMap.sql │ │ ├── synteny100000.as │ │ ├── synteny100000.c │ │ ├── synteny100000.sql │ │ ├── syntenyBerk.as │ │ ├── syntenyBerk.c │ │ ├── syntenyBerk.sql │ │ ├── syntenySanger.as │ │ ├── syntenySanger.c │ │ ├── syntenySanger.sql │ │ ├── tRNAs.as │ │ ├── tRNAs.c │ │ ├── tRNAs.sql │ │ ├── tableAccessControl.as │ │ ├── tableAccessControl.sql │ │ ├── tableDescriptions.as │ │ ├── tableDescriptions.c │ │ ├── tableDescriptions.sql │ │ ├── tableList.sql │ │ ├── tableStatus.as │ │ ├── tableStatus.c │ │ ├── tableStatus.sql │ │ ├── tablesTables.c │ │ ├── tagRepo.c │ │ ├── tandemDups.as │ │ ├── targetDb.as │ │ ├── targetDb.c │ │ ├── targetDb.sql │ │ ├── taxonDivision.as │ │ ├── taxonDivision.c │ │ ├── taxonDivision.sql │ │ ├── taxonGeneticCode.as │ │ ├── taxonGeneticCode.c │ │ ├── taxonGeneticCode.sql │ │ ├── taxonName.as │ │ ├── taxonName.c │ │ ├── taxonName.sql │ │ ├── taxonNames.sql │ │ ├── taxonNode.as │ │ ├── taxonNode.c │ │ ├── taxonNode.sql │ │ ├── taxonXref.as │ │ ├── taxonXref.c │ │ ├── taxonXref.sql │ │ ├── tests │ │ │ ├── .gitignore │ │ │ ├── annoGratorTester.c │ │ │ ├── annoGratorTests.mk │ │ │ ├── binTest.c │ │ │ ├── binTest.sh │ │ │ ├── customTrackTester.c │ │ │ ├── customTrackTests.mk │ │ │ ├── expected │ │ │ │ ├── annoGrator │ │ │ │ │ ├── bigBedToTabOut.txt │ │ │ │ │ ├── gpFx.txt │ │ │ │ │ ├── insertions.txt │ │ │ │ │ ├── pgSnpDbToTabOut.txt │ │ │ │ │ ├── pgSnpKgDbToGpFx.txt │ │ │ │ │ ├── pgSnpKgDbToTabOutShort.txt │ │ │ │ │ ├── snpBigWigToTabOut.txt │ │ │ │ │ ├── snpConsDbToTabOutShort.txt │ │ │ │ │ ├── vcfEx1.txt │ │ │ │ │ ├── vcfEx2.txt │ │ │ │ │ ├── vepOut.txt │ │ │ │ │ └── vepOutIndelTrim.txt │ │ │ │ ├── customTrack │ │ │ │ │ ├── simpleTest.ct.bed │ │ │ │ │ └── unnamed.ct.bed │ │ │ │ ├── genePred │ │ │ │ │ ├── fileFrameStatTest.gp │ │ │ │ │ ├── fileFrameStatTest.info │ │ │ │ │ ├── fileFrameTest.info │ │ │ │ │ ├── fileIdName2Test.info │ │ │ │ │ ├── fileIdTest.info │ │ │ │ │ ├── fileMinTest.info │ │ │ │ │ ├── fromGffCeSangerTest.gp │ │ │ │ │ ├── fromGffCeSangerTypeTest.gp │ │ │ │ │ ├── fromGffFrameTest.gp │ │ │ │ │ ├── fromGffRegressTest.gp │ │ │ │ │ ├── fromGffSpaceInNameTest.gp │ │ │ │ │ ├── fromGtfImpliedStopTest.gp │ │ │ │ │ ├── fromGtfNscanTest.gp │ │ │ │ │ ├── fromGtfRegressTest.gp │ │ │ │ │ ├── fromGxfAcemblyFrameTest.gp │ │ │ │ │ ├── fromGxfAcemblyTest.gp │ │ │ │ │ ├── fromGxfExonSelFrameTest.gp │ │ │ │ │ ├── fromGxfExonSelTest.gp │ │ │ │ │ ├── fromGxfFrameTest.gp │ │ │ │ │ ├── fromGxfMinTest.gp │ │ │ │ │ ├── fromGxfNcbiTest.gp │ │ │ │ │ ├── fromGxfVegaFrameTest.gp │ │ │ │ │ ├── fromGxfVegaPseudoTest.gp │ │ │ │ │ ├── fromGxfVegaTest.gp │ │ │ │ │ ├── fromPslCdsFrameTest.gp │ │ │ │ │ ├── fromPslIncmplTest.gp │ │ │ │ │ ├── fromPslMinTest.gp │ │ │ │ │ ├── knownGeneTest.info │ │ │ │ │ ├── refFlatTest.info │ │ │ │ │ ├── refGeneTest.info │ │ │ │ │ ├── tableFrameStatTest.gp │ │ │ │ │ ├── tableFrameStatTest.info │ │ │ │ │ ├── tableFrameTest.gp │ │ │ │ │ ├── tableFrameTest.info │ │ │ │ │ ├── tableIdName2Test.info │ │ │ │ │ ├── tableIdTest.info │ │ │ │ │ └── tableMinTest.info │ │ │ │ ├── hdbTest │ │ │ │ ├── hgvs │ │ │ │ │ ├── clinVarHgvs.txt │ │ │ │ │ └── validTerms.txt │ │ │ │ ├── spDbTest │ │ │ │ └── sqlCheck │ │ │ │ │ ├── sqlCheck.1 │ │ │ │ │ ├── sqlCheck.2 │ │ │ │ │ ├── sqlCheck.3 │ │ │ │ │ ├── sqlCheck.4 │ │ │ │ │ ├── sqlCheck.7 │ │ │ │ │ ├── sqlCheck.8 │ │ │ │ │ └── sqlCheck.9 │ │ │ ├── genePredTester.c │ │ │ ├── genePredTests.mk │ │ │ ├── hdbTest.c │ │ │ ├── hgvsTester.c │ │ │ ├── hgvsTests.mk │ │ │ ├── input │ │ │ │ ├── annoGrator │ │ │ │ │ ├── indelTrim.vcf │ │ │ │ │ ├── insertionsPrimary.bb │ │ │ │ │ ├── insertionsPrimary.bed │ │ │ │ │ ├── insertionsPrimary.vcf │ │ │ │ │ ├── insertionsPrimary.vcf.gz.tbi │ │ │ │ │ ├── insertionsSecondary.bb │ │ │ │ │ ├── insertionsSecondary.bed │ │ │ │ │ ├── insertionsSecondary.vcf │ │ │ │ │ ├── insertionsSecondary.vcf.gz.tbi │ │ │ │ │ ├── moreVariants.pgSnp.tab │ │ │ │ │ ├── pgForTestingGpFx.pgSnp.tab │ │ │ │ │ └── vepSample.pgSnp.tab │ │ │ │ ├── customTrack │ │ │ │ │ ├── simpleTest.ct │ │ │ │ │ └── unnamed.ct │ │ │ │ ├── genePred │ │ │ │ │ ├── acembly.gff │ │ │ │ │ ├── ceSangerGene.gff │ │ │ │ │ ├── flybase.gtf │ │ │ │ │ ├── frameBug.gff │ │ │ │ │ ├── incmpl.cds │ │ │ │ │ ├── incmpl.psl │ │ │ │ │ ├── ncbi.gff │ │ │ │ │ ├── nscan.gtf │ │ │ │ │ ├── refSeq.cds │ │ │ │ │ ├── refSeq.psl │ │ │ │ │ ├── refSeqFrame.gp │ │ │ │ │ ├── refSeqFrameStat.gp │ │ │ │ │ ├── refSeqId.gp │ │ │ │ │ ├── refSeqIdName2.gp │ │ │ │ │ ├── refSeqMin.gp │ │ │ │ │ ├── regress.gff │ │ │ │ │ ├── regress.gtf │ │ │ │ │ ├── spaceInName.gff │ │ │ │ │ ├── tigr.gff │ │ │ │ │ ├── twinscan.gtf │ │ │ │ │ ├── vegaGene.gtf │ │ │ │ │ └── vegaPseudo.gtf │ │ │ │ ├── hgvs │ │ │ │ │ ├── clinVarHgvs.txt │ │ │ │ │ └── validTerms.txt │ │ │ │ └── pslReader │ │ │ │ │ ├── mrna.psl │ │ │ │ │ └── mrna.pslx │ │ │ ├── makefile │ │ │ ├── pslReaderTester.c │ │ │ ├── pslReaderTests.mk │ │ │ ├── spDbTest.c │ │ │ ├── sqlCheck.c │ │ │ ├── sqlCheck.mk │ │ │ └── testCommon.mk │ │ ├── tfbsCons.as │ │ ├── tfbsCons.c │ │ ├── tfbsCons.sql │ │ ├── tfbsConsFactors.as │ │ ├── tfbsConsFactors.c │ │ ├── tfbsConsFactors.sql │ │ ├── tfbsConsMap.as │ │ ├── tfbsConsMap.c │ │ ├── tfbsConsMap.sql │ │ ├── tfbsConsSites.as │ │ ├── tfbsConsSites.c │ │ ├── tfbsConsSites.sql │ │ ├── tigrCmrGene.as │ │ ├── tigrCmrGene.c │ │ ├── tigrCmrGene.sql │ │ ├── tigrOperon.as │ │ ├── tigrOperon.c │ │ ├── tigrOperon.sql │ │ ├── tilingPath.as │ │ ├── tilingPath.c │ │ ├── tilingPath.sql │ │ ├── tissue.as │ │ ├── traceInfo.as │ │ ├── traceInfo.c │ │ ├── trackDb.as │ │ ├── trackDb.c │ │ ├── trackDb.sql │ │ ├── trackDbCache.c │ │ ├── trackDbCustom.c │ │ ├── trackHub.c │ │ ├── trackLayout.c │ │ ├── trackTable.as │ │ ├── trackTable.c │ │ ├── trackTable.sql │ │ ├── trackVersion.as │ │ ├── trackVersion.c │ │ ├── trackVersion.sql │ │ ├── transMapGene.as │ │ ├── transMapGene.c │ │ ├── transMapGene.sql │ │ ├── transMapInfo.as │ │ ├── transMapInfo.c │ │ ├── transMapInfo.sql │ │ ├── transMapSrc.as │ │ ├── transMapSrc.c │ │ ├── transMapSrc.sql │ │ ├── transMapStuff.c │ │ ├── transRegCode.as │ │ ├── transRegCode.c │ │ ├── transRegCode.sql │ │ ├── transRegCodeCondition.as │ │ ├── transRegCodeCondition.c │ │ ├── transRegCodeCondition.sql │ │ ├── transRegCodeMotif.as │ │ ├── transRegCodeMotif.sql │ │ ├── transRegCodeProbe.as │ │ ├── transRegCodeProbe.c │ │ ├── transRegCodeProbe.sql │ │ ├── trashDir.c │ │ ├── txAliDiff.as │ │ ├── txAliDiff.c │ │ ├── txAliDiff.sql │ │ ├── txAliDoubleGap.as │ │ ├── txAliMismatch.as │ │ ├── txAliQSkipped.as │ │ ├── txAliShiftyGap.as │ │ ├── txAliShortGap.as │ │ ├── txCluster.as │ │ ├── txCluster.c │ │ ├── txCluster.sql │ │ ├── txCommon.c │ │ ├── txEdgeBed.as │ │ ├── txEdgeBed.c │ │ ├── txEdgeBed.sql │ │ ├── txEdgeOrtho.as │ │ ├── txEdgeOrtho.c │ │ ├── txEdgeOrtho.sql │ │ ├── txGraph.as │ │ ├── txGraph.c │ │ ├── txGraph.sql │ │ ├── txInfo.as │ │ ├── txInfo.c │ │ ├── txInfo.sql │ │ ├── txRnaAccs.as │ │ ├── txRnaAccs.c │ │ ├── txRnaAccs.sql │ │ ├── ucscPfam.sql │ │ ├── ucscRetroCds.sql │ │ ├── ucscRetroInfo.as │ │ ├── ucscRetroInfo.c │ │ ├── ucscRetroInfo.sql │ │ ├── ucscRetroInfo3.sql │ │ ├── ucscRetroOrtho.as │ │ ├── ucscRetroOrtho.c │ │ ├── ucscRetroOrtho.sql │ │ ├── ucscScop.as │ │ ├── ucscScop.sql │ │ ├── ucscToEnsembl.as │ │ ├── ucscToINSDC.as │ │ ├── ucscToINSDC.sql │ │ ├── uniProtAlias.sql │ │ ├── useCount.sql │ │ ├── userDb.as │ │ ├── userDb.sql │ │ ├── userRegions.c │ │ ├── validateGisaid.c │ │ ├── validateGisaid.dummy │ │ ├── varAcc.sql │ │ ├── varProtTemp.sql │ │ ├── varProtein.sql │ │ ├── variant.c │ │ ├── variantProjector.c │ │ ├── variome.as │ │ ├── variome.c │ │ ├── variome.sql │ │ ├── vax003.sql │ │ ├── vax003AEMsa.sql │ │ ├── vax003BMsa.sql │ │ ├── vax004.sql │ │ ├── vax004AaCons.sql │ │ ├── vax004AaMaf.sql │ │ ├── vax004Cons.sql │ │ ├── vax004Maf.sql │ │ ├── vcfUi.c │ │ ├── vegaInfo.as │ │ ├── vegaInfo.c │ │ ├── vegaInfo.sql │ │ ├── vegaInfoZfish.as │ │ ├── vegaInfoZfish.c │ │ ├── vegaInfoZfish.sql │ │ ├── visiGene.c │ │ ├── vntr.as │ │ ├── vntr.c │ │ ├── vntr.sql │ │ ├── wabAli.as │ │ ├── wabAli.c │ │ ├── wabAli.sql │ │ ├── web.c │ │ ├── webUsers.sql │ │ ├── wgEncodeAwgDnaseCombinedSources.as │ │ ├── wgEncodeRegDnaseClusteredSources.as │ │ ├── wgRna.as │ │ ├── wgRna.c │ │ ├── wgRna.sql │ │ ├── wigAsciiToBinary.c │ │ ├── wigDataStream.c │ │ ├── wiggle.as │ │ ├── wiggle.c │ │ ├── wiggle.sql │ │ ├── wiggleCart.c │ │ ├── wiggleUtils.c │ │ ├── wiki.as │ │ ├── wiki.sql │ │ ├── wikiLink.c │ │ ├── wikiTrack.as │ │ ├── wikiTrack.c │ │ ├── wikiTrack.sql │ │ ├── wikibme.sql │ │ ├── yaleGencodeAssoc.as │ │ ├── yaleGencodeAssoc.c │ │ ├── yaleGencodeAssoc.sql │ │ ├── zdobnovSynt.as │ │ ├── zdobnovSynt.c │ │ └── zdobnovSynt.sql │ └── mouseStuff │ │ ├── README │ │ ├── axtChain │ │ ├── axtChain.c │ │ ├── linearGap.txt │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ ├── newStyleLastz.chain │ │ │ └── oldStyleBlastz.chain │ │ │ ├── input │ │ │ ├── hg19.chrM.2bit │ │ │ ├── newStyleLastz.Q.txt │ │ │ ├── newStyleLastz.psl │ │ │ ├── oldStyleBlastz.Q.txt │ │ │ ├── oldStyleBlastz.psl │ │ │ └── susScr3.chrM.2bit │ │ │ └── makefile │ │ ├── axtSort │ │ ├── axtSort.c │ │ └── makefile │ │ ├── axtSwap │ │ ├── axtSwap.c │ │ └── makefile │ │ ├── axtToMaf │ │ ├── axtToMaf.c │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ └── zeroScore.maf │ │ │ ├── input │ │ │ ├── hg15.sizes │ │ │ ├── rn3.sizes │ │ │ ├── zeroScore.axt │ │ │ └── zeroScore.maf │ │ │ └── makefile │ │ ├── axtToPsl │ │ ├── axtToPsl.c │ │ ├── chromSizes.sql │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ └── blockBug.psl │ │ │ ├── input │ │ │ ├── blockBug.axt │ │ │ └── blockBug.sizes │ │ │ └── makefile │ │ ├── chainAntiRepeat │ │ ├── chainAntiRepeat.c │ │ └── makefile │ │ ├── chainBridge │ │ ├── chainBridge.c │ │ ├── makefile │ │ └── tests │ │ │ ├── expected │ │ │ ├── awful.bridged.chain │ │ │ ├── noChange.bridged.chain │ │ │ └── someChange.bridged.chain │ │ │ ├── input │ │ │ ├── hg19ToHg38.awful.chain │ │ │ ├── hg19ToHg38.noChange.chain │ │ │ └── hg19ToHg38.someChange.chain │ │ │ └── makefile │ │ ├── chainCleaner │ │ ├── NetFilterNonNested.perl │ │ ├── chainCleaner.c │ │ └── makefile │ │ ├── chainFilter │ │ ├── chainFilter.c │ │ └── makefile │ │ ├── chainFormat.doc │ │ ├── chainMergeSort │ │ ├── chainMergeSort.c │ │ └── makefile │ │ ├── chainNet │ │ ├── chainNet.c │ │ └── makefile │ │ ├── chainOverlap │ │ ├── chainOverlap.c │ │ └── makefile │ │ ├── chainPreNet │ │ ├── chainPreNet.c │ │ └── makefile │ │ ├── chainSort │ │ ├── chainSort.c │ │ └── makefile │ │ ├── chainSplit │ │ ├── chainSplit.c │ │ └── makefile │ │ ├── chainStitchId │ │ ├── chainStitchId.c │ │ └── makefile │ │ ├── chainSwap │ │ ├── chainSwap.c │ │ └── makefile │ │ ├── chainToAxt │ │ ├── chainToAxt.c │ │ ├── expected │ │ │ └── chrM.axt │ │ ├── input │ │ │ └── chrM.chain │ │ └── makefile │ │ ├── chainToPsl │ │ ├── chainToPsl.c │ │ ├── makefile │ │ └── tests │ │ │ └── makefile │ │ ├── chainToPslBasic │ │ ├── chainToPslBasic.c │ │ └── makefile │ │ ├── lavToAxt │ │ ├── lavToAxt.c │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ ├── crea.axt │ │ │ ├── newStyleLastz.axt │ │ │ └── oldStyleBlastz.axt │ │ │ ├── input │ │ │ ├── crea.lav │ │ │ ├── hCreaGeno.2bit │ │ │ ├── hg19.chrM.2bit │ │ │ ├── hg19.chrM.fa │ │ │ ├── mCreaGeno.2bit │ │ │ ├── newStyleLastz.Q.txt │ │ │ ├── newStyleLastz.lav │ │ │ ├── oldStyleBlastz.Q.txt │ │ │ ├── oldStyleBlastz.lav │ │ │ ├── susScr3.chrM.2bit │ │ │ └── susScr3.chrM.fa │ │ │ └── makefile │ │ ├── lavToPsl │ │ ├── lavToPsl.c │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ ├── newStyleLastz.bed │ │ │ ├── newStyleLastz.psl │ │ │ ├── oldStyleBlastz.bed │ │ │ └── oldStyleBlastz.psl │ │ │ ├── input │ │ │ ├── newStyleLastz.lav │ │ │ ├── oldStyleBlastz.lav │ │ │ └── trimEndsBug.lav │ │ │ └── makefile │ │ ├── mafNoAlign │ │ ├── mafNoAlign.c │ │ └── makefile │ │ ├── mafRanges │ │ ├── mafRanges.c │ │ ├── makefile │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ ├── canFam1.bed │ │ │ ├── canFam1.nao.bed │ │ │ ├── fr1.bed │ │ │ ├── galGal2.bed │ │ │ ├── galGal2.fr1.bed │ │ │ ├── galGal2.nao.bed │ │ │ ├── hg17.bed │ │ │ ├── hg17.danRer1.fr1.bed │ │ │ ├── hg17.galGal2.bed │ │ │ ├── hg17.galGal2.nao.bed │ │ │ └── hg17.nao.bed │ │ │ ├── input │ │ │ └── chrM.maf │ │ │ └── makefile │ │ ├── mafToAxt │ │ ├── mafToAxt.c │ │ └── makefile │ │ ├── mafToFa │ │ ├── mafToFa.c │ │ └── makefile │ │ ├── mafToPsl │ │ ├── mafToPsl.c │ │ └── makefile │ │ ├── makefile │ │ ├── netFilter │ │ ├── makefile │ │ └── netFilter.c │ │ ├── netFormat.doc │ │ ├── netSplit │ │ ├── makefile │ │ └── netSplit.c │ │ ├── netSyntenic │ │ ├── makefile │ │ └── netSyntenic.c │ │ ├── netToAxt │ │ ├── makefile │ │ ├── netToAxt.c │ │ └── tests │ │ │ ├── .gitignore │ │ │ ├── expected │ │ │ ├── testDog.noSplit.axt │ │ │ └── testDog.split.axt │ │ │ ├── input │ │ │ ├── testDog.chain │ │ │ └── testDog.net │ │ │ └── makefile │ │ ├── netToBed │ │ ├── makefile │ │ └── netToBed.c │ │ └── pslMrnaCover │ │ ├── makefile │ │ └── pslMrnaCover.c │ ├── htslib │ ├── INSTALL │ ├── LICENSE │ ├── Makefile │ ├── NEWS │ ├── README │ ├── bgzf.c │ ├── bgzip.c │ ├── config.h │ ├── config.h.in │ ├── 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 │ ├── LICENSE │ ├── ace.h │ ├── aliType.h │ ├── annoAssembly.h │ ├── annoFilter.h │ ├── annoFormatTab.h │ ├── annoFormatter.h │ ├── annoGrateWig.h │ ├── annoGrator.h │ ├── annoGratorQuery.h │ ├── annoOption.h │ ├── annoRow.h │ ├── annoStreamBigBed.h │ ├── annoStreamBigWig.h │ ├── annoStreamLongTabix.h │ ├── annoStreamTab.h │ ├── annoStreamVcf.h │ ├── annoStreamer.h │ ├── apacheLog.h │ ├── asParse.h │ ├── aveStats.h │ ├── axt.h │ ├── bPlusTree.h │ ├── bamFile.h │ ├── bandExt.h │ ├── base64.h │ ├── basicBed.h │ ├── bbiFile.h │ ├── bedTabix.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 │ ├── common.mk │ ├── correlate.h │ ├── crTree.h │ ├── crudeali.h │ ├── csv.h │ ├── diGraph.h │ ├── diGraph.h.97 │ ├── dlist.h │ ├── dnaLoad.h │ ├── dnaMarkov.h │ ├── dnaMotif.h │ ├── dnaseq.h │ ├── dnautil.h │ ├── dtdParse.h │ ├── dyOut.h │ ├── dystring.h │ ├── elmTree.h │ ├── emblParse.h │ ├── ens.h │ ├── errAbort.h │ ├── errCatch.h │ ├── fa.h │ ├── fieldedTable.h │ ├── filePath.h │ ├── flydna.h │ ├── fof.h │ ├── fq.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 │ ├── hmac.h │ ├── hmmPfamParse.h │ ├── hmmstats.h │ ├── htmlColor.h │ ├── htmlPage.h │ ├── htmshell.h │ ├── https.h │ ├── intValTree.h │ ├── internet.h │ ├── itsa.h │ ├── iupac.h │ ├── jointalign.h │ ├── jpegSize.h │ ├── jsonParse.h │ ├── jsonQuery.h │ ├── jsonWrite.h │ ├── keys.h │ ├── knetUdc.h │ ├── kxTok.h │ ├── linefile.h │ ├── localEnvironment.mk │ ├── localmem.h │ ├── log.h │ ├── longTabix.h │ ├── longToList.h │ ├── maDbRep.h │ ├── maToFf.h │ ├── maf.h │ ├── mailViaPipe.h │ ├── md5.h │ ├── memalloc.h │ ├── memgfx.h │ ├── meta.h │ ├── metaWig.h │ ├── mime.h │ ├── net.h │ ├── nib.h │ ├── nibTwo.h │ ├── nt4.h │ ├── obscure.h │ ├── oldGff.h │ ├── oligoTm.h │ ├── ooc.h │ ├── options.h │ ├── pairDistance.h │ ├── pairHmm.h │ ├── paraFetch.h │ ├── patSpace.h │ ├── peakCluster.h │ ├── phyloTree.h │ ├── pipeline.h │ ├── portable.h │ ├── psGfx.h │ ├── psPoly.h │ ├── pscmGfx.h │ ├── psl.h │ ├── pslTbl.h │ ├── pslTransMap.h │ ├── pthreadDoList.h │ ├── pthreadWrap.h │ ├── qa.h │ ├── quickHeap.h │ ├── quotedP.h │ ├── ra.h │ ├── raToStruct.h │ ├── rainbow.h │ ├── rangeTree.h │ ├── rbTree.h │ ├── regexHelper.h │ ├── repMask.h │ ├── rle.h │ ├── rnautil.h │ ├── rql.h │ ├── rqlToSql.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 │ ├── sqlReserved.h │ ├── srcVersion.h │ ├── strex.h │ ├── subText.h │ ├── sufa.h │ ├── sufx.h │ ├── supStitch.h │ ├── synQueue.h │ ├── tabRow.h │ ├── tagSchema.h │ ├── tagStorm.h │ ├── tagToJson.h │ ├── tagToSql.h │ ├── textOut.h │ ├── tokenizer.h │ ├── trans3.h │ ├── trix.h │ ├── twoBit.h │ ├── udc.h │ ├── unfin.h │ ├── userApp.mk │ ├── uuid.h │ ├── vGfx.h │ ├── vcf.h │ ├── vcfBits.h │ ├── verbose.h │ ├── windowsToAscii.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 │ ├── makefile │ ├── ooc.c │ ├── patSpace.c │ ├── splix.c │ ├── supStitch.c │ ├── tests │ │ └── freen │ │ │ ├── freen.c │ │ │ └── makefile │ ├── trans3.c │ ├── version.doc │ ├── xenbig.c │ └── xensmall.c │ ├── lib │ ├── LICENSE │ ├── README │ ├── README-CSP3.txt │ ├── aliType.c │ ├── alpha │ │ └── placeHolder.c │ ├── annoAssembly.c │ ├── annoFilter.c │ ├── annoFormatTab.c │ ├── annoFormatter.c │ ├── annoGrateWig.c │ ├── annoGrator.c │ ├── annoGratorQuery.c │ ├── annoOption.c │ ├── annoRow.c │ ├── annoStreamBigBed.c │ ├── annoStreamBigWig.c │ ├── annoStreamLongTabix.c │ ├── annoStreamTab.c │ ├── annoStreamVcf.c │ ├── annoStreamer.c │ ├── apacheLog.c │ ├── asParse.c │ ├── aveStats.c │ ├── axt.c │ ├── axtAffine.c │ ├── bPlusTree.c │ ├── bamFile.c │ ├── base64.c │ ├── basicBed.c │ ├── bbiRead.c │ ├── bbiWrite.c │ ├── bedTabix.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.ps │ ├── common.pss │ ├── correlate.c │ ├── crTree.c │ ├── csv.c │ ├── dgRange.c │ ├── diGraph.c │ ├── diGraph.c.97 │ ├── dlist.c │ ├── dnaLoad.c │ ├── dnaMarkov.c │ ├── dnaMotif.c │ ├── dnaMotif.pss │ ├── dnaseq.c │ ├── dnautil.c │ ├── dtdParse.c │ ├── dyOut.c │ ├── dystring.c │ ├── elmTree.c │ ├── emblParse.c │ ├── errAbort.c │ ├── errCatch.c │ ├── fa.c │ ├── ffAli.c │ ├── ffScore.c │ ├── fieldedTable.c │ ├── filePath.c │ ├── fixColor.c │ ├── flydna.c │ ├── fof.c │ ├── font │ │ ├── README │ │ ├── mgCourier10.c │ │ ├── mgCourier12.c │ │ ├── mgCourier14.c │ │ ├── mgCourier18.c │ │ ├── mgCourier24.c │ │ ├── mgCourier34.c │ │ ├── mgCourier8.c │ │ ├── mgHelvetica10.c │ │ ├── mgHelvetica12.c │ │ ├── mgHelvetica14.c │ │ ├── mgHelvetica18.c │ │ ├── mgHelvetica24.c │ │ ├── mgHelvetica34.c │ │ ├── mgHelvetica8.c │ │ ├── mgHelveticaBold10.c │ │ ├── mgHelveticaBold12.c │ │ ├── mgHelveticaBold14.c │ │ ├── mgHelveticaBold18.c │ │ ├── mgHelveticaBold24.c │ │ ├── mgHelveticaBold34.c │ │ ├── mgHelveticaBold8.c │ │ ├── mgMenlo12.c │ │ ├── mgSail8.c │ │ ├── mgSixhi6.c │ │ ├── mgTimes10.c │ │ ├── mgTimes12.c │ │ ├── mgTimes14.c │ │ ├── mgTimes18.c │ │ ├── mgTimes24.c │ │ ├── mgTimes34.c │ │ └── mgTimes8.c │ ├── fq.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 │ ├── hmac.c │ ├── hmmPfamParse.c │ ├── hmmstats.c │ ├── htmlColor.c │ ├── htmlPage.c │ ├── htmshell.c │ ├── https.c │ ├── i386 │ │ └── placeHolder.c │ ├── i686 │ │ └── placeHolder.c │ ├── intExp.c │ ├── intValTree.c │ ├── internet.c │ ├── itsa.c │ ├── iupac.c │ ├── jointalign.c │ ├── jpegSize.c │ ├── jsonParse.c │ ├── jsonQuery.c │ ├── jsonWrite.c │ ├── keys.c │ ├── knetUdc.c │ ├── kxTok.c │ ├── lineFileOnBigBed.c │ ├── linefile.c │ ├── localmem.c │ ├── log.c │ ├── longTabix.c │ ├── longToList.c │ ├── maf.c │ ├── maf.doc │ ├── mafFromAxt.c │ ├── mafScore.c │ ├── mailViaPipe.c │ ├── makefile │ ├── md5.c │ ├── memalloc.c │ ├── memgfx.c │ ├── meta.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 │ ├── orig_makefile │ ├── osunix.c │ ├── oswin9x.c │ ├── pairDistance.c │ ├── pairHmm.c │ ├── paraFetch.c │ ├── peakCluster.c │ ├── phyloTree.c │ ├── pipeline.c │ ├── pngwrite.c │ ├── portimpl.c │ ├── portimpl.h │ ├── ppc │ │ └── placeHolder.c │ ├── psGfx.c │ ├── psPoly.c │ ├── pscmGfx.c │ ├── psl.as │ ├── psl.c │ ├── psl.sql │ ├── pslGenoShow.c │ ├── pslShow.c │ ├── pslTbl.c │ ├── pslTransMap.c │ ├── pslWScore.as │ ├── pslWScore.sql │ ├── pthreadDoList.c │ ├── pthreadWrap.c │ ├── qa.c │ ├── quickHeap.c │ ├── quotedP.c │ ├── ra.c │ ├── raToStruct.c │ ├── rainbow.c │ ├── rangeTree.c │ ├── rbTree.c │ ├── regexHelper.c │ ├── repMask.c │ ├── rle.c │ ├── rnautil.c │ ├── rqlEval.c │ ├── rqlParse.c │ ├── rqlToSql.c │ ├── rudp.c │ ├── scoreWindow.c │ ├── seg.c │ ├── seqOut.c │ ├── seqStats.c │ ├── servBrcMcw.c │ ├── servCrunx.c │ ├── servcis.c │ ├── servcl.c │ ├── servmsII.c │ ├── servpws.c │ ├── shaRes.c │ ├── slog.c │ ├── snof.c │ ├── snofmake.c │ ├── snofsig.c │ ├── spaceSaver.c │ ├── spacedColumn.c │ ├── spacedSeed.c │ ├── sparc │ │ └── placeHolder.c │ ├── splatAli.as │ ├── splatAli.c │ ├── sqlList.c │ ├── sqlNum.c │ ├── sqlReserved.c │ ├── strex.c │ ├── strex.doc │ ├── subText.c │ ├── sufa.c │ ├── sufx.c │ ├── synQueue.c │ ├── tabRow.c │ ├── tagSchema.c │ ├── tagStorm.c │ ├── tagToJson.c │ ├── tagToSql.c │ ├── tests │ │ ├── dyStringTester.c │ │ ├── errCatchTest.c │ │ ├── expected │ │ │ ├── base64Decode.out │ │ │ ├── base64Encode.out │ │ │ ├── errCatch.bad │ │ │ ├── errCatch.good │ │ │ ├── gff3DiscontiousTest.out │ │ │ ├── gff3ErrorCasesTest.err │ │ │ ├── gff3SacCerTest.out │ │ │ ├── google.out │ │ │ ├── hacTreeTest.out │ │ │ ├── hashTest1.out │ │ │ ├── htmlExpandUrlTest │ │ │ ├── htmlMime1.out │ │ │ ├── jsonQueryTest.out │ │ │ ├── mime1.out │ │ │ ├── mime2.out │ │ │ ├── mime3.out │ │ │ ├── mime4.out │ │ │ ├── mime5.out │ │ │ ├── mimeAltHead.out │ │ │ ├── mimeAutoBoundary.out │ │ │ ├── mimeBin.out │ │ │ ├── mimeBlat.out │ │ │ ├── noName1.html │ │ │ ├── pipelineExecError.err │ │ │ ├── pipelineExecError.parent.err │ │ │ ├── pipelineWriteErr.out │ │ │ ├── quotedPDecode.out │ │ │ ├── quotedPEncode.out │ │ │ ├── simple1.wc │ │ │ ├── tabixFetch1kGNoGenotypes.out │ │ │ ├── tabixFetch1kGWithGenotypes.out │ │ │ ├── vcfParse1kGNoGenotypes.out │ │ │ ├── vcfParse1kGWithGenotypes.out │ │ │ └── vcfParseOldV3.out │ │ ├── fetchUrlTest.c │ │ ├── fetchUrlViaUdcTest.c │ │ ├── gff3Tester.c │ │ ├── hacTreeTest.c │ │ ├── htmlExpandUrlTest.c │ │ ├── htmlMimeTest.c │ │ ├── htmlPageTest.c │ │ ├── input │ │ │ ├── 20091110_pilot1_vcf_merged_call_sets_YRI.2and3_way.vcf.gz.tbi │ │ │ ├── YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz.tbi │ │ │ ├── YRI.trio.2010_06.novelsequences.sites.vcf.gz.tbi │ │ │ ├── discontinuous.gff3 │ │ │ ├── errorCasesTest.gff3 │ │ │ ├── google.html │ │ │ ├── hacTreeTest.txt │ │ │ ├── hashTest1.txt │ │ │ ├── htmlMime.txt │ │ │ ├── jsonQueryTestJson.txt │ │ │ ├── jsonQueryTestPath.txt │ │ │ ├── mime1.txt │ │ │ ├── mime2.txt │ │ │ ├── mime3.txt │ │ │ ├── mime4.txt │ │ │ ├── mime5.txt │ │ │ ├── mimeAltHead.txt │ │ │ ├── mimeAutoBoundary.txt │ │ │ ├── mimeBin.txt │ │ │ ├── mimeBlat.txt │ │ │ ├── mimeDecodeTest.txt │ │ │ ├── sacCerTest.gff3 │ │ │ ├── simple1.txt │ │ │ └── specialCasesTest.gff3 │ │ ├── jsonQueryTest.c │ │ ├── makefile │ │ ├── mimeDecodeTest.c │ │ ├── mimeTester.c │ │ ├── miniBlat.c │ │ ├── pipelineTester.c │ │ ├── safeTester.c │ │ ├── tabixFetch.c │ │ ├── testBase64.c │ │ ├── testDecodedString.c │ │ ├── testHash.c │ │ ├── testOutOfMem.c │ │ ├── testQuotedP.c │ │ ├── testQuotedString.c │ │ ├── testSumDoubles.c │ │ ├── udcCacheSizesCheck.c │ │ ├── udcTest.c │ │ ├── udcTrials.csh │ │ └── vcfParseTest.c │ ├── textOut.c │ ├── tokenizer.c │ ├── trix.c │ ├── twoBit.c │ ├── udc.c │ ├── uuid.c │ ├── vGfx.c │ ├── vGfxPrivate.h │ ├── vPng.c │ ├── valgrind.suppress │ ├── vcf.c │ ├── vcfBits.c │ ├── verbose.c │ ├── wildcmp.c │ ├── windowsToAscii.c │ ├── wormdna.c │ ├── x86_64 │ │ └── placeHolder.c │ ├── xAli.as │ ├── xAli.c │ ├── xAli.sql │ ├── xa.c │ ├── xap.c │ ├── xenshow.c │ ├── xmlEscape.c │ ├── xp.c │ └── zlibFace.c │ ├── machTest.sh │ ├── makefile │ └── optimalLeaf │ 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