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.html src/hg/makeDb/trackDb/human/lrSvAll.html
index 1b97f6518c6..b12c1a8b655 100644
--- src/hg/makeDb/trackDb/human/lrSvAll.html
+++ src/hg/makeDb/trackDb/human/lrSvAll.html
@@ -1,81 +1,81 @@
 <h2>Description</h2>
 <p>
 This track combines the structural-variant (SV) callsets from the individual
-subtracks of the <a href="hgTrackUi?g=lrSv">Long-read SVs</a> supertrack into a
+subtracks of the <a href="hgTrackUi?g=longReadVariants">Long-read SVs</a> supertrack into a
 single, position-merged overview. Each item is an SV locus seen in one or more
 of the contributing long-read databases. For every merged locus the track
 records which databases report it, the summed allele count across those
 databases, and the range of allele frequencies observed, making it useful for
 quickly seeing how widely an SV has been reported across cohorts.
 </p>
 <p>
 This is a summary view. For cohort-specific genotypes, per-population allele
 frequencies, and dataset-specific annotations, use the individual subtracks of
 the supertrack. The merge includes the released long-read callsets only;
 preliminary or unpublished subtracks (e.g. the Kim PD brain, 1000 Genomes
 linear, and HPRC Jasmine sets) are <b>not</b> part of this merged track.
 </p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Items are colored by SV type, matching the individual subtracks:
 <ul>
 <li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
 <li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
 <li><span style="color: rgb(0,160,0);">Duplications (DUP)</span> - green</li>
 <li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li>
 <li><span style="color: rgb(140,0,200);">Complex and other multi-allele events</span> - purple</li>
 </ul>
 </p>
 <p>
 The mouseover shows the variant name, SV type, reference and insertion lengths,
 the list of contributing source databases, the allele-frequency range across
 those databases, and the total allele count. Filters are available for the
 <b>source database</b>, <b>SV type</b>, <b>SV length</b>, <b>insertion
 length</b>, <b>total allele count</b>, <b>minimum and maximum allele
 frequency</b>, and the <b>number of source databases</b> reporting each locus.
 The detail page lists the per-database allele counts.
 </p>
 
 <h2>Methods</h2>
 <p>
 The merged track is built by the <tt>lrSvMergeAll.py</tt> script, which reads
 the bigBed of each contributing subtrack (configured in
 <tt>databases.tsv</tt>) and groups records that share an identical
 <tt>(chromosome, start, end)</tt> position and SV type. For each merged locus
 the script records the set of contributing databases (<tt>sources</tt>), the
 number of those databases (<tt>sourceCount</tt>), the sum of their allele counts
 (<tt>AC</tt>), and the minimum and maximum allele frequency across databases
 that report one (<tt>minAF</tt>, <tt>maxAF</tt>). The per-database allele counts
 are carried as additional columns.
 </p>
 <p>
 The step-by-step build commands are recorded in the UCSC makeDoc for this track
 collection:
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank">
 doc/hg38/lrSv.txt</a>. The merge script and autoSql schema live in
 <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">
 makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSvAll.ra" target="_blank">trackDb/human/lrSvAll.ra</a>.
 </p>
 
 <h2>Data Access</h2>
 <p>
 The data can be explored interactively with the
 <a href="../cgi-bin/hgTables">Table Browser</a> or the
 <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed
 programmatically through our <a href="https://api.genome.ucsc.edu">API</a>,
 track=<i>lrSvAll</i>.
 </p>
 <p>
 The bigBed is available from
 <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/lrSv/" target="_blank">our
 download server</a> as <tt>lrSvAll.bb</tt>. Example:
 <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/lrSv/lrSvAll.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
 </p>
 
 <h2>Credits</h2>
 <p>
 This merged view is derived entirely from the contributing long-read SV
 callsets; please see the individual subtrack description pages for the data
 producers and citations for each cohort.
 </p>