9a63ecfed718d4ad0b2c5212c7ad8844c9d23531
lrnassar
  Mon Jun 29 14:21:07 2026 -0700
lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258

Per the updated qa-track standard, link the track's UCSC source artifacts on
github.com/ucscGenomeBrowser/kent from every lrSv description page:
- Add the missing links to the lrSv supertrack page and colorsDbSv.
- Backfill the trackDb.ra link (third artifact) across the subtrack pages that
already linked the makedoc + scripts dir.
lrSv1kLin is left as its placeholder (staged, not released).

diff --git src/hg/makeDb/trackDb/human/lrSvAll.html src/hg/makeDb/trackDb/human/lrSvAll.html
index 29ef4d56918..1b97f6518c6 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
 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 preliminary or unpublished subtracks (e.g. the Kim PD brain, 1000 Genomes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>.
+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>