9fbdfa3416ffde377072fafd2de44059155c3b44
max
  Thu Apr 30 06:57:35 2026 -0700
lrSv: add lrSvAll merged track combining all long-read SV subtracks

Variants are merged on exact (chrom, start, end, svType, svLen, insLen).
Per-database AC columns are stored as strings; "unknown" is used where
the source dataset has only placeholder AC values (deCODE, SVatalog 101,
1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy
(HC) AC columns. Gustafson contributes sampleCount instead of AC.

Output: 2,694,871 unique SVs from 3,706,100 input rows across 15
subtracks (27% dedup). The merged track sits as the first subtrack of
the lrSv supertrack with filters on sources, svType, svLen, insLen,
maxAF/minAF, AC, and sourceCount.

The trackDb stanza is generated by the build script directly into
human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra,
so labels in databases.tsv stay the single source of truth.

lrSv.html: add a "Disease cases" column to the dataset summary,
strip parenthesized internal track names from the section headers,
and shorten exact SV counts to ~Nk / ~N.NM in the prose.

refs #36642

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 60cf45acf71..9244f30c19c 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -11,30 +11,32 @@
 # 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