3258e4421c0a95ef8ca84445b077c77faaf04970 braney Mon Aug 10 18:14:37 2026 -0700 clinvar: give clinvarSubLolly a maxHeightPixels ceiling, refs #38072 A bigLolly row is a fixed pixel height, so neither pix nor textSize reaches it. A figure rendered at three times the normal width left the ClinVar submitted interpretations row at 128 pixels while the tracks around it grew with the font, so it came out a sliver with unreadable y-axis labels. Docent asks for a taller row for a print render (see 140e29ae689, refs #37892), but each track's own maxHeightPixels clamps that request, and this track had no setting, so the ceiling fell back to the 128 default and the request was clamped straight back. Raise the ceiling to 512. The default stays at 128, so an ordinary view is unchanged and only a render that asks for more can get it. The two files are kept in step because the alpha stanza carries its own copy. diff --git src/hg/makeDb/trackDb/human/clinvar.ra src/hg/makeDb/trackDb/human/clinvar.ra index 59d67f140e6..e8ff37358d4 100644 --- src/hg/makeDb/trackDb/human/clinvar.ra +++ src/hg/makeDb/trackDb/human/clinvar.ra @@ -1,114 +1,119 @@ 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) dataVersion /gbdb/$D/bbi/clinvar/version.txt track clinvarMain parent clinvar shortLabel ClinVar SNVs longLabel ClinVar Short Nucleotide 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 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/clinvar/clinvarMain.bb urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" geneId="https://www.ncbi.nlm.nih.gov/gene/$$" snpId="https://www.ncbi.nlm.nih.gov/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId,snpId,vcvId maxWindowCoverage 10000000 decorator.default.bigDataUrl /gbdb/$D/bbi/clinvar/clinvarMainDecor.bb decorator.default.blockMode hide decorator.default.glyphMode hide track clinvarCnv parent clinvar shortLabel ClinVar CNVs longLabel ClinVar Copy Number Variants >= 50bp visibility hide type bigBed 12 + itemRgb on group phenDis priority 2 skipFields rcvAcc # note that you cannot change these values. Old carts will contain them. If you must change these, you'll have to rename # the field, which will reset the cart variables. Or use the cart rewrite mechanism. You can add more values, though filterValues._originCode GERM|germline,SOM|somatic,GERMSOM|germline/somatic,NOVO|de novo,UNK|unknown filterType._originCode multiple filterLabel._originCode Alelle Origin filterValues._allTypeCode SUBST|single nucleotide variant - SUBST,STRUCT|translocation and fusion - STRUCT,LOSS|deletion and copy loss - LOSS,GAIN|duplication and copy gain - GAIN,INS|indel and insertion - INS,INV|inversion - INV,SEQALT|undetermined - SEQALT,SEQLEN|repeat change - SEQLEN filterType._allTypeCode multiple filterValues._clinSignCode BN|benign,LB|likely benign,CF|conflicting,PG|pathogenic,LP|likely pathogenic,UC|uncertain,OT|other filterType._clinSignCode multiple filter._varLen 50:999999999 filterByRange._varLen on filterLimits._varLen 50:999999999 mouseOverField _mouseOver bigDataUrl /gbdb/$D/bbi/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/snp/$$" nsvId="https://www.ncbi.nlm.nih.gov/dbvar/variants/$$/" origName="https://www.ncbi.nlm.nih.gov/clinvar/variation/$$/" noScoreFilter on searchIndex _dbVarSsvId,snpId,vcvId track clinvarSubLolly parent clinvar shortLabel ClinVar interp longLabel ClinVar SNVs submitted interpretations and evidence bigDataUrl /gbdb/$D/clinvarSubLolly/clinvarSubLolly.bb xrefDataUrl /gbdb/$D/clinvarSubLolly/clinvarSub.bb type bigLolly group phenDis lollySizeField 10 yAxisNumLabels off lollyNoStems on configurable off skipFields reviewStatus yAxisLabel.0 0 on 150,150,150 OTH yAxisLabel.1 1 on 150,150,150 B yAxisLabel.2 2 on 150,150,150 LB yAxisLabel.3 3 on 150,150,150 VUS yAxisLabel.4 4 on 150,150,150 LP yAxisLabel.5 5 on 150,150,150 P lollyMaxSize 10 + # Default stays the bigLolly default of 128; the ceiling is raised so a print/figure + # render can ask for a taller row (clinvarSubLolly.heightPer). Without this, + # cartTdbFetchMinMaxPixels clamps any request back to 128 and the lollipop row is a + # sliver in a 3x-wide image. + maxHeightPixels 512:128:11 viewLimits 0:5 mouseOverField _mouseOver filterValues.score 5|Pathogenic,4|Likely Pathogenic,3|Variant of Unknown Significance,2|Likely Benign,1|Benign,0|Others filterType.score multiple filterLabel.score Filter by variant classification urls rcvAcc="https://www.ncbi.nlm.nih.gov/clinvar/$$/" 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 searchType bigBed searchDescription ClinVar Copy Number Variants termRegex ^([ne]ssv.*)|(rs[0-9]+)|(VCV.*) searchMethod prefix searchTable clinvarMain searchType bigBed searchDescription ClinVar Short Nucleotide Variants termRegex ^([ne]ssv.*)|(rs[0-9]+)|(VCV.*) searchMethod prefix