8e1de594b0f580652a3a7b4f1d1a3865356077fc
lrnassar
  Fri Sep 11 11:47:29 2020 -0700
Removing test.ra for clinVar track improvements refs #24850

diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
index c4be9d9..14cac1c 100644
--- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
+++ src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
@@ -1,30 +1,72 @@
 track clinvar
 compositeTrack on
 shortLabel ClinVar Variants
 longLabel ClinVar Variants
 group phenDis
 visibility hide
 type bed 12 +
+noParentConfig on
 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 < 50bp
-    visibility pack
         parent clinvar
+        shortLabel ClinVar SNVs
+        longLabel ClinVar Short Variants < 50bp
+        visibility hide
+        group phenDis
+        itemRgb on
         priority 1
         type bigBed 12 +
+        showCfg on
+        filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other
+        filterType._clinSignCode singleList
+        filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown
+        filterType._originCode singleList
+        filterLabel._originCode Alelle Origin
+        filterValues._allTypeCode SNV|single nucleotide variant - SNV,INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH
+        filterType._allTypeCode singleList
+        filter._varLen 0
+        filterByRange._varLen on
+        filterLimits._varLen 0:49
+        filterValues.molConseq genic downstream transcript variant|genic downstream transcript variant,no sequence alteration|no sequence alteration,inframe indel|inframe indel,stop lost|stop lost,genic upstream transcript variant|genic upstream transcript variant,initiatior codon variant|initiatior codon variant,inframe insertion|inframe insertion,inframe deletion|inframe deletion,splice acceptor variant|splice acceptor variant,splice donor variant|splice donor variant,5 prime UTR variant|5 prime UTR variant,nonsense|nonsense,non-coding transcript variant|non-coding transcript variant,3 prime UTR variant|3 prime UTR variant,frameshift variant|frameshift variant,intron variant|intron variant,synonymous variant|synonymous variant,missense variant|missense variant,|unknown
         mouseOverField _mouseOver
         bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMain.bb
+        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/$$/"
+        noScoreFilter on
+        searchIndex _dbVarSsvId
 
         track clinvarCnv
-    shortLabel ClinVar Long Variants
-    longLabel ClinVar Long Variants >= 50bp (mostly Copy-Number Variants)
-    visibility pack
-    type bigBed 12 +
         parent clinvar
+        shortLabel ClinVar CNVs
+        longLabel ClinVar Copy Number Variants > 50bp
+        visibility hide
+        type bigBed 12 +
+        itemRgb on
+        group phenDis
         priority 2
+        filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown
+        filterType._originCode singleList
+        filterLabel._originCode Alelle Origin
+        filterValues._allTypeCode INS|insertion - INS,DEL|deletion - DEL,INDEL|insertion-deletion - INDEL,dupl|duplication - DUPL,OTH|other - OTH
+        filterType._allTypeCode singleList
+        filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other
+        filterType._clinSign singleList
+        filter._varLen 50:999999999
+        filterByRange._varLen on
+        filterLimits._varLen 50:999999999
         mouseOverField _mouseOver
         bigDataUrl /gbdb/$D/bbi/clinvar/clinvarCnv.bb
+        mergeSpannedItems 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/$$/"
+        noScoreFilter on
+        searchIndex _dbVarSsvId
+
+searchTable clinvarCnv
+searchType bigBed
+searchDescription ClinVar Copy Number Variants 
+
+searchTable clinvarMain
+searchType bigBed
+searchDescription ClinVar Copy Number Variants