abbbd616fe0c3203b35cae02fc2f8b063c3b1d9c
max
  Wed Feb 19 14:12:44 2020 -0800
converting clinvar to two files that are included, refs #24850

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 23a7eef..ee7869d 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -8,30 +8,34 @@
 # Neandertal tracks
 include trackDb.nt.ra
 
 # Denisova tracks
 include trackDb.denisova.ra
 
 # Genome variants aka pgSnp aka personal genomes
 include trackDb.pgSnp.ra
 
 # Genotype Tissue Expresssion (GTEx)
 include trackDb.gtex.ra
 
 # GeneHancer from Weizmann labs
 include trackDb.geneHancer.ra
 
+# NCBI ClinVar
+include trackDb.clinvar.ra public,beta
+include trackDb.clinvarTest.ra alpha
+
 track cytoBandIdeo
 shortLabel Chromosome Band (Ideogram)
 longLabel Chromosome Bands Localized by FISH Mapping Clones (for Ideogram)
 group map
 visibility dense
 type bed 4 +
 
 track cytoBand
 shortLabel Chromosome Band
 longLabel Chromosome Bands Localized by FISH Mapping Clones
 group map
 visibility hide
 type bed 4 +
 
 track hiSeqDepth
@@ -3722,73 +3726,30 @@
 searchMethod exact
 searchType bigBed
 termRegex rs[0-9]+
 searchPriority 1
 padding 50
 semiShortCircuit 1
 
 searchTable snpediaText
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 11.001
 padding 50
 
-track clinvar
-compositeTrack on
-shortLabel ClinVar Variants
-longLabel ClinVar Variants
-group phenDis
-visibility hide
-type bed 12 +
-itemRgb on
-urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/"
-scoreLabel ClinVar Star-Rating (0-4)
-
-    track clinvarMain
-    shortLabel ClinVar Short Variants
-    longLabel ClinVar Short Variants <= 100bp
-    visibility pack
-    parent clinvar
-    priority 1
-    type bigBed 12 +
-    #filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other
-    #filterType._clinSign singleList
-    #filterValues.origin not-reported,uniparental,tested-inconclusive,biparental,not applicable,paternal,maternal,inherited,de novo,somatic,not provided,unknown,germline
-    #filterType.origin multipleListOr
-    #filterByRange._valLen on
-    mouseOverField _mouseOver
-    bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb
-
-    track clinvarCnv
-    shortLabel ClinVar Long Variants
-    longLabel ClinVar Long Variants > 100bp (mostly Copy-Number Variants)
-    visibility pack
-    type bigBed 12 +
-    parent clinvar
-    priority 2
-    #filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other
-    #filterType._clinSign singleList
-    #filterValues.origin not-reported,uniparental,tested-inconclusive,biparental,not applicable,paternal,maternal,inherited,de novo,somatic,not provided,unknown,germline
-    #filterType.origin multipleListOr
-    #filter._varLen 0
-    #filterByRange._varLen on
-    #filterByRange.bullshit on
-    mouseOverField _mouseOver
-    bigDataUrl /gbdb/$D/bbi/clinvar/clinvarCnv.bb
-
 track interactions
 shortLabel Gene Interactions
 longLabel Protein Interactions from Curated Databases and Text-Mining
 group phenDis
 visibility hide
 type bigBed 9
 itemRgb on
 exonNumbers off
 noScoreFilter on
 #release alpha,beta
 # draw the name field directly over the feature
 labelOnFeature on
 # linkIdInName means that the first part of the "name" field (space-separated) is the ID used for the %s parameter in directUrl
 directUrl hgGeneGraph?db=hg19&gene=%s
 # split off everything after the first space for the directUrl linkout