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 \