04c67a0e7bcb65c217598e5e44084bf4c5c0674d angie Tue Mar 5 12:16:10 2013 -0800 Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output. diff --git src/hg/lib/makefile src/hg/lib/makefile index 36453f8..4eea116 100644 --- src/hg/lib/makefile +++ src/hg/lib/makefile @@ -1,21 +1,22 @@ include ../../inc/common.mk XINC = -I$(MYSQLINC) O = acemblyClass.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o \ affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o \ - altGraphX.o ancientRref.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamWig.o \ + altGraphX.o ancientRref.o \ + annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamWig.o \ api.o atomDb.o axtInfo.o \ axtLib.o bactigPos.o hgBam.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o \ bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o \ bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bioImage.o \ blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o\ cart.o cartDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o \ ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o \ celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o \ chainDb.o chainLink.o chainNet.o chainNetDbLoad.o \ chicken13kInfo.o chromBins.o chr18deletions.o \ chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o \ clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o \ contigAcc.o coordConv.o \ cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o \ cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o \ @@ -73,31 +74,31 @@ pal.o pbStamp.o pcrResult.o pepPred.o plasEndPairs.o \ polyGenotype.o protFeat.o pscreen.o \ pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o \ rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o \ refLink.o refSeqStatus.o \ rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o rgdQtl.o \ rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o \ rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o \ rnaSecStr.o tfbsConsFactors.o \ roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o \ sage.o sageCounts.o sageExp.o samAlignment.o sample.o \ sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o \ scopDes.o scoredRef.o search.o sgdAbundance.o \ sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o \ snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o \ - snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o \ + snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o \ spDb.o splignAlign.o stanMad.o stsAlias.o \ stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o \ stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o \ switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o \ sqlProg.o tfbsCons.o tfbsConsSites.o \ tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o \ taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o \ tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o \ trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o \ transRegCode.o transRegCodeCondition.o \ transRegCodeProbe.o txCluster.o txCommon.o txEdgeBed.o \ txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o \ validateGisaid.o variant.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o \ wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o \ wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o \