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/scripts/lrSv/lrSvMergeAll.py src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
index 642c037945f..907d37e57b6 100644
--- src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
+++ src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
@@ -485,31 +485,32 @@
 
 def write_trackdb_stanza(out_path, dbs):
     """Auto-generated full trackDb stanza for the lrSvAll track.
 
     Written directly into the trackDb dir and pulled in via
     `include lrSvAll.ra` from lrSv.ra.
     """
     # Commas are the separator in filterValues, so strip them from labels.
     # The original label (with commas) still appears on the detail page via
     # the autoSql field descriptions.
     src_parts = [f"{db['key']}|{db['label'].replace(',', '')}" for db in dbs]
     with open(out_path, "w") as f:
         f.write("# AUTO-GENERATED by ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py\n")
         f.write("# Do not edit by hand - re-run the merge script and re-commit.\n\n")
         f.write("    track lrSvAll\n")
-        f.write("    parent lrSv\n")
+        f.write("    parent longReadVariants
+")
         f.write("    bigDataUrl /gbdb/$D/lrSv/lrSvAll.bb\n")
         f.write("    shortLabel All LR SVs merged\n")
         f.write("    longLabel All long-read SVs merged across subtracks "
                 "by exact position, with per-database AC\n")
         f.write("    type bigBed 9 +\n")
         f.write("    itemRgb on\n")
         f.write("    visibility pack\n")
         f.write("    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\n")
         # Source filter
         f.write("    filterValues.sources " + ",".join(src_parts) + "\n")
         f.write("    filterType.sources multipleListOr\n")
         f.write("    filterLabel.sources Source Database\n")
         # SV type