e6bcec351aa8f5bc7218e8862e15c149aadb3479
lrnassar
  Fri Jul 10 12:18:40 2026 -0700
lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258

Completes the previous rename commit (which carried only the colorsDbLegacy file
moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds
"html lrSv" to keep the existing description page), reparents all subtracks plus
the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1
override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links.
Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the
internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the
lrSv.ra filename are unchanged.

diff --git src/hg/makeDb/trackDb/human/lrSvAll.ra src/hg/makeDb/trackDb/human/lrSvAll.ra
index bf2c5bd32fa..cfeb912dee1 100644
--- src/hg/makeDb/trackDb/human/lrSvAll.ra
+++ src/hg/makeDb/trackDb/human/lrSvAll.ra
@@ -1,40 +1,40 @@
 # AUTO-GENERATED by ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
 # Do not edit by hand - re-run the merge script and re-commit.
 
     track lrSvAll
-    parent lrSv
+    parent longReadVariants
     bigDataUrl /gbdb/$D/lrSv/lrSvAll.bb
     shortLabel All LR SVs merged
     longLabel All long-read SVs merged across subtracks by exact position, with per-database AC
     type bigBed 9 +
     itemRgb on
     visibility pack
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Sources</b>: $sources<br><b>AF range</b>: $minAF-$maxAF<br><b>AC</b>: $AC
     filterValues.sources CoLoRSdb|CoLoRSdb 1427 (PacBio),1000G-ONT-Vienna|1KG ONT Vienna 1019,1000G-ONT|1KG ONT 100 (Gustafson),AoU1K|All of Us 1027 (PacBio),Han945|Han Chinese 945,TommoJapan|ToMMo 333 (Japanese),GA4K|GA4K 502 (rare disease),deCODE|deCODE 3622 (Icelandic),HPRCv2.1|HPRC v2.1 233,HGSVC2|HGSVC2 32,HGSVC3|HGSVC3 65,ArabUAE53|Arab APR 53,China58|CPC 58 (Chinese),Svatalog101|SVatalog 101
     filterType.sources multipleListOr
     filterLabel.sources Source Database
     filterValues.svType DEL,INS,DUP,INV,CPX,MIXED,INSDEL,TRA
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:30000000
     filterByRange.svLen on
     filterLabel.svLen SV Length (bp)
     filter.insLen 0:600000
     filterByRange.insLen on
     filterLabel.insLen Insertion Length (bp)
     filter.maxAF 0:1
     filterByRange.maxAF on
     filterLimits.maxAF 0:1
     filterLabel.maxAF Max Allele Frequency (across DBs)
     filter.minAF 0:1
     filterByRange.minAF on
     filterLimits.minAF 0:1
     filterLabel.minAF Min Allele Frequency (across DBs)
     filter.AC 0:30000
     filterByRange.AC on
     filterLabel.AC Total AC (across DBs)
     filter.sourceCount 1:14
     filterByRange.sourceCount on
     filterLabel.sourceCount Number of Source Databases
     skipEmptyFields on
     priority 0