aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe
angie
  Mon Aug 8 14:12:39 2016 -0700
Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
and protein (p.) simple substitutions relative to NP_.
Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
out-of-bounds coordinates and mismatching reference alleles.
refs #15071, #15554

diff --git src/hg/lib/makefile src/hg/lib/makefile
index a3d2b9e..6757fbc 100644
--- src/hg/lib/makefile
+++ src/hg/lib/makefile
@@ -54,31 +54,31 @@
     flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o \
     genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o \
     geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o \
     geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o \
     genomeRangeTreeFile.o genomicDups.o \
     genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o \
     ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o \
     growthCondition.o grp.o \
     gtexAse.o gtexBoxplot.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o \
     gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o \
     gwasCatalog.o hAnno.o haplotypes.o \
     hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o \
     hapmapSnps.o hapmapSnpsCombined.o \
     hashJoin.o hCommon.o \
     hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o \
-    hgFindSpec.o hgFindSpecCustom.o \
+    hgFindSpec.o hgFindSpecCustom.o hgHgvs.o \
     hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o \
     HInv.o hubConnect.o hui.o humanParalog.o \
     imageClone.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o \
     jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o \
     jgiGene.o joinMixer.o \
     kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o \
     lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o \
     llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o \
     makeItemsItem.o mammalPsg.o mapSts.o \
     mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o \
     minChromSize.o minGeneInfo.o mrnaMisMatch.o \
     mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o \
     ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o \
     orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o \
     peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o \