16f9dcdc9a1ed10c08aae7908039627e194488a6 max Fri Jan 12 01:00:29 2024 -0800 trying a new thing: making clinvar ALPHA track appear on hgwdev and also the public release track, at the same time. Also activating version.txt now that the file has made it to the RR through the autopusher change and autopusher update, emails with QA and cluster-admin diff --git src/hg/makeDb/trackDb/human/clinvar.alpha.ra src/hg/makeDb/trackDb/human/clinvar.alpha.ra index c67ef78..ae0c30f 100644 --- src/hg/makeDb/trackDb/human/clinvar.alpha.ra +++ src/hg/makeDb/trackDb/human/clinvar.alpha.ra @@ -1,106 +1,106 @@ -track clinvar +track clinvarAlpha compositeTrack on shortLabel ClinVar Variants ALPHA longLabel ClinVar Variants ALPHA 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/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" scoreLabel ClinVar Star-Rating (0-4) dataVersion /gbdb/$D/bbi/clinvarAlpha/version.txt - track clinvarMain - parent clinvar + track clinvarMainAlpha + parent clinvarAlpha shortLabel ClinVar SNVs longLabel ClinVar Short Variants < 50bp visibility hide 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 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 - track clinvarCnv - parent clinvar + track clinvarCnvAlpha + parent clinvarAlpha shortLabel ClinVar CNVs longLabel ClinVar Copy Number Variants >= 50bp visibility hide type bigBed 12 + itemRgb on group phenDis priority 2 skipFields rcvAcc # 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._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,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 filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other filterType._clinSignCode multiple filter._varLen 50:999999999 filterByRange._varLen on filterLimits._varLen 50:999999999 mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/clinvarAlpha/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/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId - track clinvarSubLolly - parent clinvar + track clinvarSubLollyAlpha + parent clinvarAlpha shortLabel ClinVar interp longLabel ClinVar SNVs submitted interpretations and evidence bigDataUrl /gbdb/$D/clinvarSubLollyAlpha/clinvarSubLolly.bb xrefDataUrl /gbdb/$D/clinvarSubLollyAlph/clinvarSub.bb type bigLolly group phenDis lollySizeField 10 yAxisNumLabels off lollyNoStems on configurable off skipFields reviewStatus yAxisLabel.0 0 on 150,150,150 OTH yAxisLabel.1 1 on 150,150,150 B yAxisLabel.2 2 on 150,150,150 LB yAxisLabel.3 3 on 150,150,150 VUS yAxisLabel.4 4 on 150,150,150 LP yAxisLabel.5 5 on 150,150,150 P lollyMaxSize 10 viewLimits 0:5 mouseOverField _mouseOver urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" 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/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" -searchTable clinvarCnv +searchTable clinvarCnvAlpha searchType bigBed searchDescription ClinVar Copy Number Variants termRegex ^[ne]ssv[0-9]+ -searchTable clinvarMain +searchTable clinvarMainAlpha searchType bigBed searchDescription ClinVar Copy Number Variants termRegex ^[ne]ssv[0-9]+