c81011d4a8f57db347e15aa1248c501b2c8a6fea
lrnassar
  Mon Jun 1 13:16:15 2026 -0700
QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258

Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv,
chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the
lrSvMergeAll.py generator so a re-run reproduces it).
Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across
lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic"
and "UAE UPR").
lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1
native 161,332, each with its own type breakdown) and encode non-ASCII author
names as numeric entities.
hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231
DEL+INS, 176,531 total).
colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well
as hg38.
cpc1Sv.html: encode a Unicode minus sign as a numeric entity.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 9244f30c19c..51296503a68 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -197,31 +197,31 @@
     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/$D/lrSv/ga4kSv.bb
     shortLabel GA4K 502 SVs
-    longLabel Structural Variants from 502 Children's Mercy GA4K Probands and Families (PacBio HiFi)
+    longLabel Structural Variants from 502 Children's Mercy GA4K Probands (PacBio HiFi)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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
@@ -249,61 +249,61 @@
     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 hprc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hprc2.bb
     shortLabel HPRC v2 233 SVs
-    longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 Samples, minigraph-cactus + vcfwave)
+    longLabel Structural Variants from the HPRC v2 Pangenome Graph (233 samples, minigraph-cactus)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) svLen=$svLen insLen=$insLen AF=$alleleFreq AC=$AC/$alleleNumber samples=$nSamples
     filterValues.svType INS,DEL,CPX,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99113
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:97718
     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 0:10
     filterByRange.snarlLevel on
     filterLabel.snarlLevel Snarl Level
     skipEmptyFields on
 
     track hgsvc2Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/hgsvc2.bb
     shortLabel HGSVC2 32 SVs
-    longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert et al. 2021)
+    longLabel Structural Variants from 32 Haplotype-Resolved Genomes (HGSVC2 freeze 4, Ebert 2021)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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
@@ -387,83 +387,83 @@
     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/$D/lrSv/apr.bb
     shortLabel Arab APR 53 SVs
-    longLabel Structural Variants from Arabic Pangenome Reference (53 UAE-resident Arab samples)
+    longLabel Structural Variants from the Arab Pangenome Reference (53 UAE-resident Arab samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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/$D/lrSv/cpc1.bb
     shortLabel CPC 58 SVs
-    longLabel Structural Variants from Chinese Pangenome Consortium (58 samples, CPC portion of the CPC+HPRC graph; HPRC-specific SVs removed)
+    longLabel Structural Variants from the Chinese Pangenome Consortium (58 samples, CPC-only)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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/$D/lrSv/chirmade101.bb
     shortLabel SVatalog 101 SVs
-    longLabel Structural Variants from 101 Long-read Whole-Genome Sequences (GWAS SVatalog, Chirmade et al. 2026)
+    longLabel Structural Variants from 101 Long-read WGS (GWAS SVatalog, Chirmade 2026)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$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