f2ef97844c0973a30cbbc1afcdd01b4096143a69 lrnassar Wed Jun 3 10:56:07 2026 -0700 Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen). diff --git src/hg/makeDb/trackDb/human/trackDb.dbVar.ra src/hg/makeDb/trackDb/human/trackDb.dbVar.ra index e007b39c523..625eef01bc6 100644 --- src/hg/makeDb/trackDb/human/trackDb.dbVar.ra +++ src/hg/makeDb/trackDb/human/trackDb.dbVar.ra @@ -1,382 +1,383 @@ track dbVarSv superTrack on group varRep html dbVarCurated shortLabel dbVar Struct Var longLabel NCBI dbVar Structural Variants +dataVersion /gbdb/$D/bbi/dbVar/version.txt track dbVar_common superTrack dbVarSv pack compositeTrack on visibility pack itemRgb on type bigBed 9 + . html dbVarCommon shortLabel dbVar Common SV longLabel NCBI dbVar Curated Common Structural Variants mouseOverField label searchIndex name hideEmptySubtracks on filterLabel.type Variant Type filterValues.type alu deletion,alu insertion,copy number gain,copy number loss,copy number variation,deletion,duplication,herv deletion,insertion,line1 deletion,line1 insertion,mobile element deletion,mobile element insertion,sva deletion,sva insertion filterLabel.length Variant Size filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB filterLabel.freq_range Frequency Range filterValues.freq_range Under 0.02,0.02 to 0.05,0.05 to 0.1,0.1 to 0.2,0.2 to 0.5,Over 0.5 track dbVar_common_gnomad parent dbVar_common on shortLabel dbVar Curated gnomAD SVs longLabel NCBI dbVar Curated Common SVs: all populations from gnomAD bigDataUrl /gbdb/$D/bbi/dbVar/common_gnomad.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 1 track dbVar_common_1000g parent dbVar_common on shortLabel dbVar Curated 1000 Genomes SVs longLabel NCBI dbVar Curated Common SVs: all populations from 1000 Genomes bigDataUrl /gbdb/$D/bbi/dbVar/common_1000g.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 2 track dbVar_common_decipher parent dbVar_common on shortLabel dbVar Curated DECIPHER SVs longLabel NCBI dbVar Curated Common SVs: all populations from DECIPHER bigDataUrl /gbdb/$D/bbi/dbVar/common_decipher.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 3 track dbVar_common_lee parent dbVar_common off shortLabel dbVar Curated Lee SVs longLabel NCBI dbVar Curated Common SVs: all populations from Lee bigDataUrl /gbdb/$D/bbi/dbVar/common_lee.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 4 track dbVar_common_abel parent dbVar_common off shortLabel dbVar Curated Abel SVs longLabel NCBI dbVar Curated Common SVs: all populations from Abel bigDataUrl /gbdb/$D/bbi/dbVar/common_abel.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 5 track dbVar_common_byrska_bishop parent dbVar_common off shortLabel dbVar Curated Byrska-Bishop SVs longLabel NCBI dbVar Curated Common SVs: all populations from Byrska-Bishop bigDataUrl /gbdb/$D/bbi/dbVar/common_byrska_bishop.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 6 track dbVar_common_global parent dbVar_common on shortLabel dbVar Curated All Populations longLabel NCBI dbVar Curated Common SVs: all populations bigDataUrl /gbdb/$D/bbi/dbVar/common_global.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 10 track dbVar_common_african parent dbVar_common on shortLabel dbVar Curated African SVs longLabel NCBI dbVar Curated Common SVs: African bigDataUrl /gbdb/$D/bbi/dbVar/common_african.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 11 track dbVar_common_american parent dbVar_common off shortLabel dbVar Curated American SVs longLabel NCBI dbVar Curated Common SVs: American bigDataUrl /gbdb/$D/bbi/dbVar/common_american.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 12 track dbVar_common_east_asian parent dbVar_common off shortLabel dbVar Curated East Asian SVs longLabel NCBI dbVar Curated Common SVs: East Asian bigDataUrl /gbdb/$D/bbi/dbVar/common_east_asian.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 13 track dbVar_common_european parent dbVar_common on shortLabel dbVar Curated European SVs longLabel NCBI dbVar Curated Common SVs: European bigDataUrl /gbdb/$D/bbi/dbVar/common_european.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 14 track dbVar_common_south_asian parent dbVar_common off shortLabel dbVar Curated South Asian SVs longLabel NCBI dbVar Curated Common SVs: South Asian bigDataUrl /gbdb/$D/bbi/dbVar/common_south_asian.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 15 track dbVar_common_other parent dbVar_common off shortLabel dbVar Curated Other Pop SVs longLabel NCBI dbVar Curated Common SVs: Other bigDataUrl /gbdb/$D/bbi/dbVar/common_other.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: priority 16 track dbVar_conflict superTrack dbVarSv pack compositeTrack on visibility pack itemRgb on type bigBed 9 + . html dbVarConflict shortLabel dbVar Conflict SV longLabel NCBI dbVar Curated Conflict Variants mouseOverField label searchIndex name filterLabel.overlap Variant Overlap filterValues.overlap 10 to 25,25 to 50,50 to 75,75 to 90,90 to 100 filterLabel.type Variant Type filterValues.type copy number gain,copy number loss,copy number variation,deletion,duplication filterLabel.length Variant Size filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB track dbVar_conflict_pathogenic parent dbVar_conflict on shortLabel dbVar Curated Conflict SVs longLabel NCBI dbVar Common SVs in Conflict with Pathogenic Variants bigDataUrl /gbdb/$D/bbi/dbVar/conflict_pathogenic.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: track dbVarNr superTrack dbVarSv pack shortLabel dbVar NR all SV ALPHA longLabel dbVar Non-redundant Structural Variants (DEL+DUP+INS merged, 4.6M) - ALPHA only type bigBed 9 + itemRgb on release alpha visibility hide bigDataUrl /gbdb/$D/bbi/dbVar/nr.bb searchIndex name mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen $binSize, count=$variantCount subsets=$subsets study=$study filterValues.svType DEL|DEL (Deletion),DUP|DUP (Duplication),INS|INS (Insertion) filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:248886400 filterByRange.svLen on filterLabel.svLen SV Length on reference (bp) filter.insLen 0:21714506 filterByRange.insLen on filterLabel.insLen Insertion sequence length (bp; INS only) filterValues.binSize small,medium,large filterType.binSize multipleListOr filterLabel.binSize Bin size (small <50bp, medium <1Mb, large >=1Mb) filterValues.subsets common|in common subset,pathogenic|in pathogenic subset,somatic|in somatic subset filterType.subsets multipleListOr filterLabel.subsets Subset membership filterValuesDefault.subsets common,pathogenic,somatic filter.variantCount 1:10000 filterByRange.variantCount on filterLabel.variantCount Merged subvariants (number of submitted SVs at this exact placement) url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: skipEmptyFields on searchTable dbVarNr searchMethod exact searchType bigBed termRegex ^[ne]ssv[0-9]+ track dbVar_somatic superTrack dbVarSv compositeTrack on visibility hide itemRgb on type bigBed 9 + . html dbVarSomatic shortLabel dbVar Somatic SV longLabel NCBI dbVar Somatic Structural Variants mouseOverField label searchIndex name filterLabel.type Variant Type filterValues.type complex substitution,copy number gain,copy number loss,copy-neutral loss of heterozygosity,deletion,duplication,insertion,inversion,mobile element insertion,tandem duplication filterLabel.length Variant Size filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB filterLabel.method Discovery Method filterValues.method Curated,Multiple,SNP array,Sequencing filterLabel.overlap Pathogenic Reciprocal Overlap filterValues.overlap none,10 to 25,25 to 50,50 to 75,75 to 90,90 to 100 track dbVar_somatic_sv parent dbVar_somatic off shortLabel dbVar Somatic SVs visibility pack longLabel NCBI dbVar Somatic Structural Variants bigDataUrl /gbdb/$D/bbi/dbVar/somatic_sv.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: mergeSpannedItems on track dbVar_other superTrack dbVarSv compositeTrack on visibility hide itemRgb on type bigBed 9 + . html dbVarOther shortLabel dbVar Other SV longLabel NCBI dbVar Other Structural Variants mouseOverField label searchIndex name hideEmptySubtracks on filterLabel.type Variant Type filterValues.type alu deletion,alu insertion,complex substitution,copy-neutral loss of heterozygosity,copy number gain,copy number loss,copy number variation,deletion,delins,duplication,herv deletion,herv insertion,insertion,inversion,line1 deletion,line1 insertion,mobile element deletion,mobile element insertion,novel sequence insertion,sequence alteration,sva deletion,sva insertion,tandem duplication filterLabel.length Variant Size filterValues.length Under 10KB,10KB to 100KB,100KB to 1MB,Over 1MB filterLabel.method Discovery Method filterValues.method Curated,Merging,Multiple,Oligo aCGH,Optical mapping,SNP array,Sequencing,other filterLabel.overlap Pathogenic Reciprocal Overlap filterValues.overlap none,10 to 25,25 to 50,50 to 75,75 to 90,90 to 100 filterLabel.population Population Code filterValues.population AFR,AMR,EAS,EUR,OTH,SAS,mixed,multiple,none,unknown track dbVar_other_healthy parent dbVar_other on visibility pack shortLabel dbVar Healthy SVs longLabel NCBI dbVar SVs with no reported phenotype bigDataUrl /gbdb/$D/bbi/dbVar/normal_healthy.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: mergeSpannedItems on track dbVar_other_phenotype parent dbVar_other on visibility pack shortLabel dbVar Phenotype SVs longLabel NCBI dbVar SVs with Phenotype (excluding clinical and somatic) bigDataUrl /gbdb/$D/bbi/dbVar/normal_phenotype.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/dbvar/variants/$$ urlLabel NCBI Variant Page: mergeSpannedItems on searchTable dbVar_common_gnomad searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_1000g searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_decipher searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_lee searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_abel searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_byrska_bishop searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_global searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_african searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_american searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_east_asian searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_european searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_south_asian searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_common_other searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_conflict_pathogenic searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_somatic_sv searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_other_healthy searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+ searchTable dbVar_other_phenotype searchMethod exact searchType bigBed termRegex ^[den]ssv[0-9]+