20a0cbcc777f9a5360b8f096a932bf95735c435c
tdreszer
  Wed Apr 24 10:50:29 2013 -0700
First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section.  This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes.  Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results.  Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
diff --git src/hg/lib/makefile src/hg/lib/makefile
index 45e0666..fb0e49a 100644
--- src/hg/lib/makefile
+++ src/hg/lib/makefile
@@ -41,31 +41,31 @@
     encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o \
     encode/encodeExp.o \
     encode3/encode2Manifest.o encode3/encode3Valid.o \
     ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o \
     est3.o estOrientInfo.o \
     estPair.o exoFish.o expData.o expRecord.o exprBed.o \
     fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o \
     flyBase2004Xref.o \
     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 gwasCatalog.o \
+    growthCondition.o grp.o gwasCatalog.o haplotypes.o \
     hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o \
     hapmapSnps.o hapmapSnpsCombined.o \
     hCommon.o \
     hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o \
     hgFindSpec.o hgFindSpecCustom.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 \
     kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o \
     ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o \
     llaInfo.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 \