8cf469a79d1071bd5aab4072ae0ded8ef3f418e8
lrnassar
  Thu Jun 6 17:48:00 2024 -0700
Staging the work to nest all covid tracks into a single superTrack, refs #32887

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 1ed4194..5e9044b 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -5588,46 +5588,34 @@
 track uniprot override
 hideEmptySubtracks off
 
 searchTable cnvDevDelayCase
 semiShortCircuit 1
 termRegex nssv[0-9]+
 searchType bed
 searchPriority 50
 
 searchTable cnvDevDelayControl
 semiShortCircuit 1
 termRegex nssv[0-9]+
 searchType bed
 searchPriority 50
 
-include covidHgiGwas.ra
-
-track covidMuts
-type bigBed 12 + 
-shortLabel COVID Rare Harmful Var
-longLabel Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort
-mouseOver $gene $name $rsId Genotype: $genotype; Zygosity: $zygo ; Inheritance: $inhMode
-labelFields gene, name
-defaultLabelFields gene, name
-noScoreFilter on
-priority 2.2
-group phenDis
-color 179,0,0
-visibility hide
-bigDataUrl /gbdb/$D/covidMuts/covidMuts.bb
-multiRegionsBedUrl /gbdb/$D/covidMuts/covidMuts.regions.bed
+include covidHgiGwas.ra beta,public
+include covidHgiGwas.alpha.ra alpha
+include covidTracks.ra beta,public
+include covidTracks.alpha.ra alpha
  
 track orphadata
 bigDataUrl /gbdb/$D/bbi/orphanet/orphadata.bb
 shortLabel Orphanet
 longLabel Orphadata: Aggregated Data From Orphanet
 group phenDis
 type bigBed 9 +
 bedNameLabel OrphaCode
 url http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$
 urlLabel OrphaNet Phenotype Link:
 urls ensemblID="https://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=$$" pmid="https://pubmed.ncbi.nlm.nih.gov/$$" orphaCode="http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=$$" omim="https://www.omim.org/entry/$$?search=$$&highlight=$$" hgnc="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$"
 skipEmptyFields on
 skipFields name,score,itemRgb
 mouseOver Gene: $geneSymbol, Disorder: $disorder, Inheritance(s): $inheritance, Onset: $onsetList
 filterValues.assnType Biomarker tested in,Candidate gene tested in,Disease-causing germline mutation(s) (gain of function) in,Disease-causing germline mutation(s) (loss of function) in,Disease-causing germline mutation(s) in,Disease-causing somatic mutation(s) in,Major susceptibility factor in,Modifying germline mutation in,Part of a fusion gene in,Role in the phenotype of