bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/srSv.ra src/hg/makeDb/trackDb/human/srSv.ra index 31780b2f3b1..993874ac099 100644 --- src/hg/makeDb/trackDb/human/srSv.ra +++ src/hg/makeDb/trackDb/human/srSv.ra @@ -1,137 +1,137 @@ track srSv superTrack on shortLabel Short-read SVs longLabel Structural Variants from Short-read Sequencing (comparators for the long-read SV supertrack) group varRep visibility hide # Supertrack-level filters, mirroring the lrSv structure so users moving # between long- and short-read SV tracks get the same UI. Cart values # stored under "srSv.filter.<field>.min/max" are inherited by every # subtrack via cartOptionalStringClosestToHome() walking tdb->parent. -filterValues.svType DEL,INS,INV,CPX,DUP,CNV,CTX,INSDEL,MIXED,BND,MEI,TRA +filterValues.svType DEL|DEL (Deletion),INS|INS (Insertion),INV|INV (Inversion),CPX|CPX (Complex rearrangement),DUP|DUP (Duplication),CNV|CNV (Copy-number variant),CTX|CTX (Chromosomal translocation),INSDEL|INSDEL (Insertion-deletion),MIXED|MIXED (multi-allele snarl),BND|BND (Breakend / translocation),MEI|MEI (Mobile element insertion),TRA|TRA (Translocation) filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:250000000 filterByRange.svLen on filterLabel.svLen SV Length (bp) filter.insLen 0:1000000 filterByRange.insLen on filterLabel.insLen Insertion Length (bp) filter.AC 0:30000 filterByRange.AC on filterLabel.AC Allele Count noScoreFilter on track abelSv parent srSv bigDataUrl /gbdb/$D/srSv/abelSv.bb shortLabel CCDG 17795 SR SVs longLabel Structural Variants from 17,795 Genomes - Illumina SHORT-READ CCDG callset (Abel et al. 2020) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$af AC=$AC/$an callset=$callset MSQ=$msq skipEmptyFields on skipFields mateChrom,matePos filterValues.svType DEL|deletion,DUP|duplication,INV|inversion,MEI|mobile element insertion,BND|breakend/translocation filterType.svType multipleListOr filterLabel.svType SV Type filterValues.callset B38|Native GRCh38 callset (14623 samples),B37lift|Lifted from GRCh37 callset (8417 samples) filterType.callset multipleListOr filterLabel.callset Source Callset filterValues.filter PASS|High confidence,LOW|Low confidence filterType.filter multipleListOr filterLabel.filter Filter Status filterByRange.af on filter.af 0:1 filterLimits.af 0:1 filterLabel.af Allele Frequency (AF) filterByRange.svLen on filter.svLen 0:250000000 filterLimits.svLen -1:250000000 filterLabel.svLen SV Length (bp; -1 for BND) filter.insLen 0:8545 filterByRange.insLen on filterLabel.insLen Insertion Length filterByRange.msq on filter.msq 0:500 filterLimits.msq 0:500 filterLabel.msq Mean Sample Quality (MSQ) filterByRange.AC on filter.AC 0:30000 filterLimits.AC 0:30000 filterLabel.AC Allele Count (AC) url https://www.nature.com/articles/s41586-020-2371-0 urlLabel Abel et al, Nature 2020: track onekg3202Sr parent srSv bigDataUrl /gbdb/$D/srSv/onekg3202sr.bb shortLabel 1KG 3202 SR SVs longLabel 1000 Genomes 3202-sample Illumina SHORT-READ GATK-SV callset (Byrska-Bishop 2022) type bigBed 9 + itemRgb on visibility dense mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber popMax=$popmaxAf filterValues.svType DEL,INS,DUP,INV,CPX,CTX,CNV filterType.svType multipleListOr filterLabel.svType SV Type filter.svLen 0:154807729 filterByRange.svLen on filterLabel.svLen SV Length filter.insLen 0:178243 filterByRange.insLen on filterLabel.insLen Insertion Length filter.AC 0:6404 filterByRange.AC on filterLabel.AC Allele Count filter.alleleFreq 0:1 filterByRange.alleleFreq on filterLimits.alleleFreq 0:1 filterLabel.alleleFreq Allele Frequency (all) filter.popmaxAf 0:1 filterByRange.popmaxAf on filterLimits.popmaxAf 0:1 filterLabel.popmaxAf Population Max AF filter.afAfr 0:1 filterByRange.afAfr on filterLimits.afAfr 0:1 filterLabel.afAfr AF African filter.afEur 0:1 filterByRange.afEur on filterLimits.afEur 0:1 filterLabel.afEur AF European skipEmptyFields on track tommoJpCnv parent srSv container multiWig aggregate transparentOverlay showSubtrackColorOnUi on shortLabel ToMMo 48K CNV SR longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) type bigWig 0 48874 autoScale on viewLimits 0:1000 viewLimitsMax 0:48874 maxHeightPixels 100:32:8 visibility full priority 2.5 track tommoJpCnvLoss parent tommoJpCnv bigDataUrl /gbdb/$D/srSv/tommoJpCnvLoss.bw shortLabel ToMMo CNV Loss longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV type bigWig 0 48874 color 200,0,0 altColor 200,0,0 track tommoJpCnvGain parent tommoJpCnv bigDataUrl /gbdb/$D/srSv/tommoJpCnvGain.bw shortLabel ToMMo CNV Gain longLabel Samples with copy-number gain (CN>2) per 1 kb bin, ToMMo 48KJPN-CNV type bigWig 0 48874 color 0,160,0 altColor 0,160,0