67db2dd6a07c07db8c564893e590ef2e1628fb05 max Tue Jun 3 08:25:19 2025 -0700 adding a label field to the clinvar track, must have a unique name field, refs #35750 diff --git src/hg/makeDb/trackDb/human/clinvar.alpha.ra src/hg/makeDb/trackDb/human/clinvar.alpha.ra index 632ee0c1cce..0ce588d503b 100644 --- src/hg/makeDb/trackDb/human/clinvar.alpha.ra +++ src/hg/makeDb/trackDb/human/clinvar.alpha.ra @@ -19,31 +19,32 @@ group phenDis itemRgb on priority 1 type bigBed 12 + showCfg on # note that you cannot change these values. Old carts will contain them. If you must change these, you'll have to rename # the field, which will reset the cart variables. Or use the cart rewrite mechanism. You can add more values, though filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,RF|risk factor,OT|other,VUS|vus filterType._clinSignCode multiple filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,UNK|unknown filterType._originCode multiple filterLabel._originCode Alelle Origin filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN filterType._allTypeCode multiple filter._varLen 0 - skipFields rcvAcc + #skipFields rcvAcc + labelFields _label 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,initiator codon variant|initiator codon variant mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/clinvarAlpha/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/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId maxWindowCoverage 10000000 decorator.default.bigDataUrl /gbdb/$D/bbi/clinvarAlpha/clinvarMainDecor.bb track clinvarCnvAlpha parent clinvarAlpha shortLabel ClinVar CNVs ALPHA longLabel ClinVar ALPHA Copy Number Variants >= 50bp