9d3d295f183b11cd6c6c7f45292b66114ac27b5a
braney
  Fri Sep 27 12:56:37 2019 -0700
more Gencode V32 changes

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 75b239d..03e6092 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -5486,30 +5486,31 @@
     $kgDb.knownIsoforms.transcript full
     $kgDb.knownToAllenBrain.name
     $kgDb.knownToCdsSnp.name
     $kgDb.knownToEnsembl.name
     $kgDb.knownToLynx.name
     $kgDb.ucscScop.ucscId
     $kgDb.knownToMrna.name
     $kgDb.knownToMrnaSingle.name
     $kgDb.knownToNextProt.name
     $kgDb.knownToGnf1h.name
     $kgDb.knownToGnfAtlas2.name
     $kgDb.knownToHInv.name
     $kgDb.knownToHprd.name
     $kgDb.knownToLocusLink.name
     $kgDb.knownToPfam.name
+    $kgDb.knownToMupit.name
     $kgDb.knownToSuper.gene
     $kgDb.knownToTag.name
     $kgDb.knownToTreefam.name
     $kgDb.knownToU133.name
     $kgDb.knownToU133Plus2.name
     $kgDb.knownToU95.name
     $kgDb.knownToVisiGene.name
     $kgDb.knownToWikipedia.name
     $kgDb.refSeqKg.kgId minCheck=0.50
     $kgDb.rankProp.query
     $kgDb.rankProp.target
     $kgDb.pPsiBlast.kgId1
     $kgDb.pPsiBlast.kgId2
     $ccdsDb.ccdsKgMap.geneId
     $kgDb2,!rn4.knownGenePep.name full
@@ -5527,30 +5528,37 @@
     $kgDb.kg2ToKg3.newId minCheck=0.5 exclude=
     $kgDb.kg3ToKg4.oldId minCheck=0.5 exclude=
     $kgDb.kg3ToKg4.newId minCheck=0.5 exclude=
     $kgDb,!hg19.kg4ToKg5.newId minCheck=0.5 exclude=
     $kgDb,!mm10.kg5ToKg6.newId exclude=
     $kgDb,!mm10.kg6ToKg7.newId exclude=
     $kgDb,!mm10.kg7ToKg8.newId exclude=
     $kgDb,!mm10.kg8ToKg9.newId exclude=
     $kgDb,!hg38,!mm10.kg9ToKg10.newId exclude=
     $kgDb.kg10ToKg11.newId exclude=
     $kgDb,!hg16.kgTargetAli.qName full
     hg19.knownGeneTxMrna.name
     hg19.knownGeneTxPep.name
     $kgDb.kg11ToKg12.newId exclude=
     $kgDb.knownAttrs.kgID
+    $kgDb.knownCds.name
+
+identifier knownGeneOld11Id dependency
+"Previous UCSC Gene build"
+    $kgDb.knownGeneOld11.name
+    $kgDb.kg10ToKg11.oldId full
+    $kgDb.kgXrefOld11.kgID full
     
 identifier knownGeneOld10Id dependency
 "Previous UCSC Gene build"
     $kgDb.knownGeneOld10.name
     $kgDb.kg10ToKg11.oldId full
     $kgDb.kgXrefOld10.kgID full
     
 identifier knownGeneOld9Id dependency
 "Previous UCSC Gene build"
     $kgDb.knownGeneOld9.name
     $kgDb.kg9ToKg10.oldId full
     $kgDb.kgXrefOld9.kgID full
 
 identifier knownGeneOld8Id dependency
 "Previous UCSC Gene build"
@@ -6462,31 +6470,31 @@
 identifier cgapId
 "NCI Cancer Genome Annotation Project Gene ID"
     $gbd.cgapAlias.cgapID dupeOk
     $gbd.cgapBiocPathway.cgapID
 
 identifier cgapMapId
 "NCI Cancer Genome Annotation Project Map ID"
     $gbd.cgapBiocDesc.mapID
     $gbd.cgapBiocPathway.mapID
 
 identifier cgapAlias
 "NCI Cancer Genome Annotation Project Alias"
     $gbd.cgapAlias.alias dupeOk
     $gbd,!hg16,!hg18,!hg19,!mm9,!mm10,!hg38.knownGene.name minCheck=0.50
     hg16.knownGene.name minCheck=0.05
-    hg18,hg19,hg38,mm9,mm10.kgXref.geneSymbol minCheck=0.70
+    hg18,hg19,hg38,mm9,mm10.kgXref.geneSymbol minCheck=0.65
 
 # SNP (Simple Nucleotide Polymorphism) Stuff
 
 identifier affySnp10KId external=Affymetrix
 "Affymetrix 10K SNP Identifier"
     hgFixed.affy10KDetails.affyId
     $hg.affy10K.name
 
 identifier affySnp120KId external=Affymetrix
 "Affymetrix 120K SNP Identifier"
     hgFixed.affy120KDetails.affyId
     $hg.affy120K.name
 
 identifier dbSnpId external=dbSNP fuzzy
 "NCBI dbSNP ID"