b9a59376d126a820a58fc0d0f239adc9347cf7b0
lrnassar
  Thu Jul 9 12:05:41 2026 -0700
lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258

- Remove the alpha release gating from the lrSv include (human/trackDb.ra and
hs1/trackDb.ra) so the supertrack can graduate past dev/alpha.
- Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two
preliminary/unpublished subtracks stay dev-only when the container is
promoted (now valid, since the include no longer supplies a release override).
- Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a
T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built
datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the
hg38 track.
- hs1 override: default colorsDbSv to visibility pack so it is shown when the
(off-by-default) supertrack is first enabled, since hs1 has no merged track.
- hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the
deduped data.

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index bbf9433b952..2873d0e21c5 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -383,30 +383,31 @@
     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
 
     # NOT FOR RELEASE: preliminary and unpublished (Kim et al. 2026 not out yet),
     # and the callset has breakend artifacts up to 190 Mb (e.g. a single "INV"
     # spanning all of chr4). Held on dev/alpha and kept out of the lrSvAll merge
     # (removed from databases.tsv) until the data is published and cleaned.
     track kwanhoSv
     parent lrSv
+    release alpha
     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>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC<br><b>AF (PD)</b>: $afPd<br><b>AF (HC)</b>: $afHc<br><b>Case-control diff</b>: $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
@@ -502,30 +503,31 @@
     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 hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $NS
     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