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/mei.html src/hg/makeDb/trackDb/human/mei.html
index e708a6d62a3..0d9f2a04f42 100644
--- src/hg/makeDb/trackDb/human/mei.html
+++ src/hg/makeDb/trackDb/human/mei.html
@@ -32,31 +32,31 @@
   <li><a href="hgTrackUi?g=meiHmeid">HMEID 5675 MEIs</a> -
       36,699 mobile element insertions called by MELT on 5,675 samples
       from the NyuWa Chinese cohort and the 1000 Genomes Project,
       with per-cohort and per-super-population allele frequencies
       (Niu et al. 2022, <em>Nucleic Acids Res</em>). hg38 only.</li>
   <li><a href="hgTrackUi?g=meiSwegen">SweGen 1000 MEIs</a> -
       18,090 mobile element insertions called by MELT v2.0.2 on the
       1,000 SweGen Swedish whole-genome samples (Ameur et al. 2017,
       <em>Eur J Hum Genet</em>), lifted from GRCh37 to hg38. The
       short-variant frequencies for the same cohort are in the
       <a href="hgTrackUi?g=swegen">SweGen</a> subtrack of
       <a href="hgTrackUi?g=varFreqs">SNV Frequencies</a>.</li>
 </ul>
 
 <p>
-Related: <a href="hgTrackUi?g=lrSv">Long-read Structural Variants</a>
+Related: <a href="hgTrackUi?g=longReadVariants">Long-read Structural Variants</a>
 contains the parent SV callsets from which several of these MEI tracks
 are derived. <a href="hgTrackUi?g=rmsk">RepeatMasker</a> shows
 all annotated mobile elements in the reference genome (regardless of
 whether they are polymorphic).
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Each MEI is shown as a 1-bp anchor block at the position where the
 insertion attaches to the reference. Items are colored by element class:
 </p>
 <ul>
   <li><span style="display:inline-block;background-color:#0072B2;width:18px;height:12px;vertical-align:middle;"></span> <b>Alu</b> &mdash; SINE (Short INterspersed Element)</li>
   <li><span style="display:inline-block;background-color:#D55E00;width:18px;height:12px;vertical-align:middle;"></span> <b>L1</b> &mdash; LINE-1 (Long INterspersed Element-1)</li>
   <li><span style="display:inline-block;background-color:#009E73;width:18px;height:12px;vertical-align:middle;"></span> <b>SVA</b> (SINE-VNTR-Alu) &mdash; composite retrotransposon</li>