75e232bbeda2dd0d3a81e927e7c5c1dde9d6d9df
braney
  Fri Jun 7 12:08:22 2024 -0700
dropping assocations to hg19 knownGene that aren't applicable anymore

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 985712f..2959eb1 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -685,32 +685,32 @@
 "Link together Ucsc Retrogenes and class"
     $hg.encodePseudogeneUcsc.name dupeOk
     $hg.encodePseudogeneClass.name minCheck=0.22 unique
 
 identifier refGeneRetro dependency
 "Link refGene to ucscRetroInfo"
     $ucscRetroDb.refGene.name dupeOk
     hg19.ucscRetroInfo4.refSeq minCheck=0.96 exclude=noRefSeq
     hg19.ucscRetroInfo5.refSeq minCheck=0.96 exclude=noRefSeq
     hg38.ucscRetroInfo9.refSeq minCheck=0.96 exclude=noRefSeq
     mm9.ucscRetroInfo1.refSeq minCheck=0.96 exclude=noRefSeq
 
 identifier knownGeneRetro dependency
 "Link knownGene to ucscRetroInfo"
     $ucscRetroDb.knownGene.name dupeOk chopAfter=.
-    hg19.ucscRetroInfo4.kgName minCheck=0.96 exclude=noKg chopAfter=.
-    hg19.ucscRetroInfo5.kgName minCheck=0.96 exclude=noKg chopAfter=.
+    #hg19.ucscRetroInfo4.kgName minCheck=0.96 exclude=noKg chopAfter=.
+    #hg19.ucscRetroInfo5.kgName minCheck=0.96 exclude=noKg chopAfter=.
     hg38.ucscRetroInfo9.kgName minCheck=0.96 exclude=noKg chopAfter=.
     mm9.ucscRetroInfo1.kgName minCheck=0.94 exclude=noKg chopAfter=.
 
 identifier ucscRetroInfo[1,2,4,5,6,9] dependency
 "Link together Ucsc Retrogenes and ucsc retroGene alignments"
     $ucscRetroDb.ucscRetroInfo[].name unique
     $ucscRetroDb.ucscRetroAli[].qName
     $ucscRetroDb.ucscRetroOrtho[].name
     $ucscRetroDb.ucscRetroExpressed[].name
 
 identifier ucscRetroOrtho[1,2,4,5,6,9] dependency
 "Link together Ucsc Retrogenes and ucsc retro orthology"
     $ucscRetroDb.ucscRetroAli[].qName dupeOk
     $ucscRetroDb.ucscRetroOrtho[].name
 
@@ -9299,39 +9299,39 @@
     $ccdsDb.ccdsGene.name dupeOk
     $ccdsDb.ccdsInfo.ccds full
     $ccdsDb.ccdsKgMap.ccdsId
     $ccdsDb.ccdsNotes.ccds
 
 identifier ctdGeneSymbol
 "CTD Gene Symbol"
     hgFixed.ctdSorted.GeneSymbol dupeOk
     $hg.kgXref.geneSymbol minCheck=0.30
 
 identifier rdmrGene
 "R-DMR Gene"
     $hg.rdmr.name dupeOk
     $hg.rdmrRaw.gene minCheck=0.95
 
-identifier gadId
-"GAD Gene ID"
-    $hg.kgXref.geneSymbol dupeOk
-    $hg.gad.name minCheck=0.94
+#identifier gadId
+#"GAD Gene ID"
+    #$hg.kgXref.geneSymbol dupeOk
+    #$hg.gad.name minCheck=0.94
 
-identifier gadAllId
-"GAD Gene Symbol in raw input"
-    $hg.kgXref.geneSymbol dupeOk
-    $hg.gadAll.geneSymbol minCheck=0.95
+#identifier gadAllId
+#"GAD Gene Symbol in raw input"
+    #$hg.kgXref.geneSymbol dupeOk
+    #$hg.gadAll.geneSymbol minCheck=0.95
 
 identifier hugeId
 "HuGE Gene ID"
     $hg.kgXref.geneSymbol dupeOk
     $hg.huge.geneSymbol minCheck=0.89
 
 # Fields parsed out of a Genbank flat file, associated with mRNA records
 
 identifier metaGbCdnas
 "Connect metaGbd gbCdnaInfo with mRNA/EST"
     hgFixed.gbCdnaInfo.acc
     $metaGbd.all_mrna.qName
     $metaGbd.all_est.qName
     $metaGbd.refGene.name
     $metaGbd.xenoRefGene.name
@@ -10943,34 +10943,34 @@
     $sacCer.growthCondition.name
     $sacCer.transRegCodeCondition.growthCondition
 
 identifier transRegCode
 "Harbison, Gordon et al regulatory motifs and CHIP/CHIP data"
     $sacCer.transRegCodeCondition.name dupeOk
     $sacCer.transRegCodeMotif.name
     $sacCer.transRegCode.name
     $sacCer.transRegCodeProbe.tfList comma chopAfter=_
 
 identifier anoEstTclId
 "AnoEST TCL* ID -- joins track and aux. table of expressed IDs"
     $anoGam.anoEstTcl.name
     $anoGam.anoEstExpressed.name minCheck=0.30
 
-identifier allenBrainGene
-"KG link to Allen Brain Institute: Gene Expression in the Human Cortex"
-    $gbd.kgXref.geneSymbol dupeOk
-    $gbd.allenBrainGene.geneSymbol minCheck=0.95
+#identifier allenBrainGene
+#"KG link to Allen Brain Institute: Gene Expression in the Human Cortex"
+    #$gbd.kgXref.geneSymbol dupeOk
+    #$gbd.allenBrainGene.geneSymbol minCheck=0.95
 
 identifier allenBrainProbe
 "A probe used in the Allen Brain Atlas"
     $gbd.allenBrainUrl.name
     $gbd.allenBrainAli.qName
 
 identifier jaxRepTranscriptName external=MGI
 "Jackson Labs/MGI Allele name: representative transcript ID"
     $mm.jaxRepTranscript.name dupeOk
     $mm.jaxRepTranscriptAlias.name
 
 identifier jaxAlleleName external=MGI
 "Jackson Labs/MGI Allele name: concatenated representative transcript ID and allele ID"
     # Using dupeOk here because there are some case-sensitive allele name diffs (ugh)
     $mm.jaxAllele.name dupeOk
@@ -11061,34 +11061,34 @@
 "contig difference track"
     hg19.gold.frag dupeOk
     hg19.hg19ContigDiff.name
 
 identifier ContigDiff
 "contig difference track"
     hg19,hg38.gold.frag dupeOk
     hg19,hg38.hg38ContigDiff.name
 
 # lsSnpPdb tables
 identifier lsSnpPdbProtId
 "lsSnpPdb table protId field"
     uniProt.extDbRef.acc dupeOk
     $lsSnpDb.lsSnpPdb.protId
 
-identifier lsSnpPdbKgId
-"lsSnpPdb table protId field"
-    $lsSnpDb.kgXref.spID dupeOk
-    $lsSnpDb.lsSnpPdb.protId minCheck=0.99
+#identifier lsSnpPdbKgId
+#"lsSnpPdb table protId field"
+    #$lsSnpDb.kgXref.spID dupeOk
+    #$lsSnpDb.lsSnpPdb.protId minCheck=0.99
 
 identifier lsSnpPdbPdbId
 "lsSnpPdb table pdbId field"
     uniProt.extDbRef.extAcc1 dupeOk
     $lsSnpDb.lsSnpPdb.pdbId minCheck=0.99
 
 identifier lsSnpPdbSnpHg18
 "lsSnpPdb table snpId field"
     hg18.snp130.name dupeOk
     hg18.lsSnpPdb.snpId
 
 identifier lsSnpPdbSnpHg19
 "lsSnpPdb table snpId field"
     hg19.snp131.name dupeOk
     hg19.lsSnpPdb.snpId