6ec6c29454ddc661b78710d1bb6de040cafaa66d
lrnassar
  Sat Jun 13 09:39:33 2026 -0700
lrSv: remove premature per-track release tags that broke tdbQuery -strict. refs #36258

The hprc2JasmineSv and lrSv1kLin stanzas carried "release alpha", but the file
is pulled in via "include lrSv.ra alpha", and tdbQuery -check -strict rejects a
stanza-level release tag when the include line already supplies a release
override ("Release tag in stanza with include release override"). The
include-level alpha already keeps the entire supertrack on dev/alpha, so these
two unpublished subtracks do not graduate regardless. Per-track release tags
for the do-not-release subtracks should be added when the include line is later
changed past alpha.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 1a2afbf596e..e66a29dacc5 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -1,558 +1,556 @@
 track lrSv
 superTrack on
 shortLabel Long-read SVs
 longLabel Structural Variants from Long-read Sequencing
 group varRep
 visibility hide
 # Supertrack-level filters. These are rendered on the supertrack's own
 # hgTrackUi page (superTrackUi in hgTrackUi.c). Cart values stored under
 # "lrSv.filter.<field>.min/max" are inherited at read time by every
 # subtrack via cartOptionalStringClosestToHome() walking tdb->parent. A
 # subtrack-level filter always wins over the supertrack-level one.
 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 0:30176500
 filterByRange.insLen on
 filterLabel.insLen Insertion Length (bp)
 filter.AC 0:30000
 filterByRange.AC on
 filterLabel.AC Allele Count
 noScoreFilter on
 
     include lrSvAll.ra
 
     track colorsDbSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1427 SVs
     longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     dataVersion v1.2.0
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$AF AC=$AC/$AN (Hom:$acHom Het:$acHet Hemi:$acHemi) samples=$NS
     searchIndex name
     filterValues.svType DEL,INS,INV,DUP
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:101381
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:18724
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.AC 0:2854
     filterByRange.AC on
     filterLabel.AC Alt Allele Count (AC)
     filter.AF 0:1
     filterByRange.AF on
     filterLimits.AF 0:1
     filterLabel.AF Allele Frequency (AF)
     skipEmptyFields on
     priority 1
 
     track lrSv1kgOnt
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/1kgOnt.bb
     shortLabel 1KG ONT 1019 SVs
     longLabel Structural Variants from 1,019 Diverse Humans (Vienna ONT, Schloissnig et al. 2025)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen type=$insType family=$family AC=$AC AF=$alleleFreq
     filterValues.svType DEL,INS,CPX
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterValues.insType COMPLEX_DUP,DUP,DUP_INTERSPERSED,INV_DUP,NUMT,PSD,VNTR,chimera,orphan,partnered,solo
     filterType.insType multipleListOr
     filterLabel.insType Insertion/Deletion Type
     filterValues.family Alu,HERVK,L1,LTR5_Hs,SVA
     filterType.family multipleListOr
     filterLabel.family Transposon Family
     filter.svLen 0:49171
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:48091
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.AC 0:1816
     filterByRange.AC on
     filterLabel.AC Allele Count
     skipEmptyFields on
     dataVersion 1.1
     priority 2
 
     track gustafsonSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/gustafson.bb
     shortLabel 1KG ONT 100 SVs
     longLabel Structural Variants from 100 1000 Genomes ONT Samples (Gustafson et al. 2024)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC samples=$sampleCount
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:98289
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:25094
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:200
     filterByRange.AC on
     filterLabel.AC Allele Count (placeholder)
     filter.sampleCount 1:100
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Carrier Samples
     skipEmptyFields on
     priority 3
 
     track aou1kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/aou1k.bb
     shortLabel AoU 1027 SVs
     longLabel Structural Variants from 1,027 AoU Individuals (PacBio HiFi Long-read)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC AF_AFR=$afAfr AF_EUR=$afEur
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:9905
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:9998
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:2054
     filterByRange.AC on
     filterLabel.AC Allele Count (approx)
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
     filterLabel.afAfr AF African
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     filterByRange.afEas on
     filterLimits.afEas 0:1
     filterLabel.afEas AF East Asian
     skipEmptyFields on
 
     track han945Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/han945.bb
     shortLabel Han 945 SVs
     longLabel Structural Variants from 945 Han Chinese (Long-read Sequencing)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC samples=$sampleCount
     filterValues.svType DEL,INS,DUP,INV,TRA
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99743
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:27242
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:1890
     filterByRange.AC on
     filterLabel.AC Allele Count (approx 2*SUPP)
     filter.sampleCount 1:945
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Supporting Samples
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
     urls chr2="hgTracks?position=$$"
 
     track tommoJpSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/tommoJp.bb
     shortLabel ToMMo 333 SVs
     longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99985
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:30649
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.AC 0:444
     filterByRange.AC on
     filterLabel.AC Allele Count
 
     track ga4kSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/ga4kSv.bb
     shortLabel GA4K 502 SVs
     longLabel Structural Variants from 502 Children's Mercy GA4K Probands (PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC~$AC AF=$alleleFreq carriers=$carrierCount/$sampleTotal
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:809711
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:14923
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:996
     filterByRange.AC on
     filterLabel.AC Allele Count (approx)
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.carrierCount 1:498
     filterByRange.carrierCount on
     filterLabel.carrierCount Number of Carrier Samples
 
     track decodeSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/decodeSv.bb
     shortLabel deCODE 3622 SVs
     longLabel High-confidence Structural Variants from 3,622 Icelanders (deCODE, Oxford Nanopore)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC (placeholder)
     filterValues.svType DEL,INS,INSDEL
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:861080
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:22130
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:50
     filterByRange.AC on
     filterLabel.AC Allele Count (placeholder 50)
     skipEmptyFields on
 
     track hprc2v21Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hprc2v21.bb
     shortLabel HPRC v2.1 233 SVs
     longLabel Structural Variants from HPRC v2.1 Pangenome Graph (233 samples, minigraph-cactus)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples
     filterValues.svType INS,DEL
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99835
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:1064897
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:463
     filterByRange.AC on
     filterLabel.AC Allele Count
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filter.snarlLevel 0:7
     filterByRange.snarlLevel on
     filterLabel.snarlLevel Snarl Level
     skipEmptyFields on
 
     track hprc2JasmineSv
     parent lrSv
-    release alpha
     bigDataUrl /gbdb/$D/lrSv/hprc2Jasmine.bb
     shortLabel HPRC2 Jasmine 231 SVs
     longLabel Structural Variants from 231 HPRC v2 Assemblies (Jasmine merge of 14 SV callers)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$nSamples/$alleleNumber AF=$alleleFreq callers=$nCallers ($callers)
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30176500
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:30176500
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:231
     filterByRange.AC on
     filterLabel.AC Carrier Sample Count
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Carrier Frequency
     filter.nCallers 1:14
     filterByRange.nCallers on
     filterLabel.nCallers Number of Supporting Callers
     filterValues.callers DELLY,DeBreak,DeepVariant,PAV,SVDSS,SVIM,SVIM-asm,Sniffles2,cuteSV,cuteSV-asm,dipcall,longcallD,pbsv,sawfish
     filterType.callers multipleListAnd
     filterLabel.callers Supporting Callers
     filterValues.sources PAV,dipcall,longcallD
     filterType.sources multipleListAnd
     filterLabel.sources Source Pipeline
     skipEmptyFields on
 
     track hgsvc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb
     shortLabel HGSVC2 32 SVs
     longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC AF=$popAllAf
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:57207414
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:108546
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 1:35
     filterByRange.AC on
     filterLabel.AC Allele Count (carrier haplotypes)
     filter.sampleCount 1:35
     filterByRange.sampleCount on
     filterLabel.sampleCount Sample Count
     filterValues.refTrf True,False
     filterType.refTrf multipleListOr
     filterLabel.refTrf In Tandem Repeat
     filter.refSd 0:1
     filterByRange.refSd on
     filterLimits.refSd 0:1
     filterLabel.refSd Segmental Duplication Overlap
     skipEmptyFields on
 
     track hgsvc3Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc3.bb
     shortLabel HGSVC3 65 SVs
     longLabel Structural Variants from 65 Diverse Samples (HGSVC3 ONT+HIFI)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen samples=$sampleCount AC=$AC
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30176500
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:30176500
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 1:136
     filterByRange.AC on
     filterLabel.AC Allele Count (carrier haplotypes)
     filter.sampleCount 1:65
     filterByRange.sampleCount on
     filterLabel.sampleCount Sample Count
     filterValues.refTrf True,False
     filterType.refTrf multipleListOr
     filterLabel.refTrf In Tandem Repeat
     filter.refSd 0:1
     filterByRange.refSd on
     filterLimits.refSd 0:1
     filterLabel.refSd Segmental Duplication Overlap
     skipEmptyFields on
 
     track kwanhoSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/kwanho.bb
     shortLabel Kim PD 100 prelim
     longLabel Structural Variants from 100 Post-mortem Brains (Parkinson's disease, ILBD, Control; Kim et al. 2026, PacBio HiFi) - PRELIMINARY, data to be updated, contact the authors before using
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC AF_PD=$afPd AF_HC=$afHc diff=$differentialRate
     filterValues.svType DEL,INS,DUP,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:200000000
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:20145
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:200
     filterByRange.AC on
     filterLabel.AC Allele Count (PD+HC+ILBD)
     filter.qual 0:100
     filterByRange.qual on
     filterLabel.qual Quality
     filter.afPd 0:1
     filterByRange.afPd on
     filterLimits.afPd 0:1
     filterLabel.afPd Allele Frequency (PD)
     filter.afHc 0:1
     filterByRange.afHc on
     filterLimits.afHc 0:1
     filterLabel.afHc Allele Frequency (HC)
     filter.afIlbd 0:1
     filterByRange.afIlbd on
     filterLimits.afIlbd 0:1
     filterLabel.afIlbd Allele Frequency (ILBD)
     filter.differentialRate -1:1
     filterByRange.differentialRate on
     filterLimits.differentialRate -1:1
     filterLabel.differentialRate Case-Control Differential (case - control)
     skipEmptyFields on
 
     track aprSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
     longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99885
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:584016
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:107
     filterByRange.AC on
     filterLabel.AC Allele Count
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
 
     track cpc1Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/cpc1.bb
     shortLabel CPC 58 SVs
     longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:8998096
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:376583
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.AC 0:116
     filterByRange.AC on
     filterLabel.AC Allele Count
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
 
     track chirmade101Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/chirmade101.bb
     shortLabel SVatalog 101 SVs
     longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 2026)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen genes=$geneCount
     filterValues.svType DEL,INS,DUP,INV,CPX
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:1321484
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:31711
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.geneCount 0:200
     filterByRange.geneCount on
     filterLabel.geneCount Gene Count
     skipEmptyFields on
 
     # NOT FOR RELEASE: data received from Eichler lab via email, not yet published.
     # Do not add to lrSvAll merged track until a preprint or paper is available.
     track lrSv1kLin
     parent lrSv
-    release alpha
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Linear 1218 SVs
     longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AC=$AC/$AN AF=$AF AF_AFR=$afAfr AF_EUR=$afEur samples=$NS
     searchIndex name
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99565
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:99968
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.AC 0:2436
     filterByRange.AC on
     filterLabel.AC Allele Count
     filter.AF 0:1
     filterByRange.AF on
     filterLimits.AF 0:1
     filterLabel.AF Allele Frequency
     filterByRange.afAfr on
     filterLimits.afAfr 0:1
     filterLabel.afAfr AF African
     filterByRange.afAmr on
     filterLimits.afAmr 0:1
     filterLabel.afAmr AF Admixed American
     filterByRange.afEas on
     filterLimits.afEas 0:1
     filterLabel.afEas AF East Asian
     filterByRange.afEur on
     filterLimits.afEur 0:1
     filterLabel.afEur AF European
     filterByRange.afSas on
     filterLimits.afSas 0:1
     filterLabel.afSas AF South Asian
     filter.NS 1:1218
     filterByRange.NS on
     filterLabel.NS Samples with Genotype Data
     skipEmptyFields on