748b06ac95ff2a3957be3845bd3594984e3cc3cf chmalee Wed Aug 17 19:21:48 2022 -0700 Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind diff --git src/hg/makeDb/trackDb/human/trackDb.clinvar.ra src/hg/makeDb/trackDb/human/trackDb.clinvar.ra index 7c61f94..2257514 100644 --- src/hg/makeDb/trackDb/human/trackDb.clinvar.ra +++ src/hg/makeDb/trackDb/human/trackDb.clinvar.ra @@ -1,99 +1,101 @@ 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/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) track clinvarMain parent clinvar 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 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 parent clinvar shortLabel ClinVar CNVs longLabel ClinVar Copy Number Variants >= 50bp visibility hide type bigBed 12 + itemRgb on group phenDis priority 2 # 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/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/$$/" noScoreFilter on searchIndex _dbVarSsvId track clinvarSubLolly parent clinvar shortLabel ClinVar interp longLabel ClinVar SNVs submitted interpretations and evidence bigDataUrl /gbdb/$D/clinvarSubLolly/clinvarSubLolly.bb xrefDataUrl /gbdb/$D/clinvarSubLolly/clinvarSub.bb type bigLolly group phenDis lollySizeField 10 yAxisNumLabels off lollyNoStems on configurable off yAxisLabel.0 0 on 150,150,150 OTH yAxisLabel.1 1 on 150,150,150 B yAxisLabel.2 2 on 150,150,150 LB yAxisLabel.3 3 on 150,150,150 VUS yAxisLabel.4 4 on 150,150,150 LP yAxisLabel.5 5 on 150,150,150 P lollyMaxSize 10 viewLimits 0:5 mouseOverField _mouseOver urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" searchTable clinvarCnv searchType bigBed searchDescription ClinVar Copy Number Variants +termRegex ^[ne]ssv[0-9]+ searchTable clinvarMain searchType bigBed searchDescription ClinVar Copy Number Variants +termRegex ^[ne]ssv[0-9]+