42cfa7cdcf1157a9f9cffa92967ae49df2b42b64
max
  Fri Jan 31 01:56:25 2020 -0800
adding clinvar filters, refs #24850

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index 52f7026..e69c4e8 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -3726,49 +3726,66 @@
 
 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 bigBed 12 .
+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/$$/"
-mouseOverField _mouseOver
 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