a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef
lrnassar
  Tue Jul 16 17:13:07 2024 -0700
Nesting OMIM into a single superTrack, refs #25682

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 825f835..3f15a07 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -3695,66 +3695,30 @@
     shortLabel Stan Jurkat NRSF/REST/Upstate
     longLabel Stanford ChIP-chip (Jurkat cells, NRSF/REST/Upstate ChIP)
     priority 12
 
 track rgdQtl override
 shortLabel RGD Human QTL
 
 track nibbImageProbes override
 group expression
 
 track allenBrainAli override
 group expression
 
 track eponine override
 
-track omimLocation
-shortLabel OMIM Cyto Loci
-longLabel OMIM Cytogenetic Loci Phenotypes - Gene Unknown
-group phenDis
-visibility hide
-color 0, 80, 0
-type bed 4
-hgsid on
-url http://www.omim.org/entry/
-tableBrowser noGenome
-noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org
-
-track omimGene2
-shortLabel OMIM Genes
-longLabel OMIM Gene Phenotypes - Dark Green Can Be Disease-causing
-group phenDis
-visibility dense
-color 0, 80, 0
-type bed 4
-hgsid on
-url http://www.omim.org/entry/
-tableBrowser noGenome omimGeneMap omimGeneMap2 omimPhenotype omimGeneSymbol omim2gene
-noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org
-
-track omimAvSnp
-shortLabel OMIM Alleles
-longLabel OMIM Allelic Variant Phenotypes
-group phenDis
-visibility hide
-color 0, 80, 0
-type bed 4
-hgsid on
-url http://www.omim.org/entry/
-tableBrowser noGenome omimAv omimAvRepl
-noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org
-
 track cosmic
 shortLabel COSMIC
 longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer
 group phenDis
 visibility hide
 color 200, 0, 0
 type bed 4
 hgsid on
 url http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=
 release alpha
 
 track cosmicNew
 shortLabel COSMIC
 longLabel COSMIC: Catalogue Of Somatic Mutations In Cancer
 group phenDis
@@ -4358,68 +4322,30 @@
 searchMethod exact
 query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%"
 xrefTable kiddEichlerToNcbi
 xrefQuery select name, cloneAcc from %s where cloneAcc = '%s'
 termRegex AC[0-9]{6}
 searchPriority 52
 
 searchTable kiddEichlerDiscG248
 searchMethod exact
 query select chrom,chromStart,chromEnd,name from %s where name like "%s,%%"
 xrefTable kiddEichlerToNcbi
 xrefQuery select name, cloneAcc from %s where cloneAcc = '%s'
 termRegex AC[0-9]{6}
 searchPriority 52
 
-searchName omimAvSnpAcc
-searchTable omimAvSnp
-searchMethod exact
-searchType bed
-shortCircuit 1
-semiShortCircuit 1
-termRegex ([0-9]{6})\.([0-9]{4})
-searchPriority 10
-padding 50
-
-searchName omimGene2Acc
-searchTable omimGene2
-searchMethod exact
-searchType bed
-shortCircuit 1
-semiShortCircuit 1
-termRegex ([0-9]{6})
-searchPriority 10
-#release beta,public
-
-#searchName omimGene2AccBb
-#searchTable omimGene2bb
-#searchMethod exact
-#searchType bigBed
-#shortCircuit 1
-#semiShortCircuit 1
-#termRegex ([0-9]{6})
-#searchPriority 10
-#release alpha
-
-searchName omimGeneLocAcc
-searchTable omimLocation
-searchMethod exact
-searchType bed
-semiShortCircuit 1
-termRegex ([0-9]{6})
-searchPriority 10
-
 track fox2ClipSeqComp
 compositeTrack on
 shortLabel FOX2 CLIP-seq
 longLabel FOX2 Adaptor-trimmed CLIP-seq reads
 subGroup1	view Tracks reads=Reads density=Density clusters=Clusters
 group regulation
 visibility hide
 type bed 3 .
 dataVersion January 2009
 
     track fox2ClipSeqCompViewreads
     shortLabel Reads
     view reads
     visibility pack
     parent fox2ClipSeqComp
@@ -4935,30 +4861,33 @@
         subGroups view=dose class=path level=cur
 
         track clinGenTriploSensitivity
         parent doseSensitivity
         shortLabel Triplo Sensitivity
         longLabel ClinGen Triplo Sensitivity
         visibility dense
         priority 2
         type bigBed 9 +
         bigDataUrl /gbdb/$D/doseSensitivity/clinGenTriploSensitivity.bb
         mouseOverField mouseOver
         subGroups view=dose class=path level=cur
 
 include phastBias.ra
 
+include omim.ra beta,public
+include omim.alpha.ra alpha
+
 searchName decipherId
 searchTable decipher
 termRegex [0-9]+
 searchType bed
 searchPriority 50
 release public
 
 searchName decipherSnvsId
 searchTable decipherSnvs
 termRegex [0-9]+
 searchType bed
 searchPriority 50
 
 searchTable ensGene
 searchType genePred