798b37017a4e1b95f3ccdf7c8b477dfb5446a324
lrnassar
  Fri Jul 24 15:22:34 2026 -0700
lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888

Add BND to filterValues.svType on the longReadVariants supertrack and the merged
lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that
noyvertSv contributes are filterable. Correct a stale makedoc comment that said
CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and
hgdownload links in cardSv.html and noyvertSv.html.

diff --git src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
index 87989070980..4f4b507ef44 100644
--- src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
+++ src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
@@ -502,31 +502,31 @@
         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
         f.write("    filterValues.svType DEL,INS,DUP,INV,CPX,MIXED,INSDEL,"
-                "TRA\n")
+                "TRA,BND\n")
         f.write("    filterType.svType multipleListOr\n")
         f.write("    filterLabel.svType SV Type\n")
         # Range filters
         f.write("    filter.svLen 0:30000000\n")
         f.write("    filterByRange.svLen on\n")
         f.write("    filterLabel.svLen SV Length (bp)\n")
         f.write("    filter.insLen 0:600000\n")
         f.write("    filterByRange.insLen on\n")
         f.write("    filterLabel.insLen Insertion Length (bp)\n")
         f.write("    filter.maxAF 0:1\n")
         f.write("    filterByRange.maxAF on\n")
         f.write("    filterLimits.maxAF 0:1\n")
         f.write("    filterLabel.maxAF Max Allele Frequency (across DBs)\n")
         f.write("    filter.minAF 0:1\n")
         f.write("    filterByRange.minAF on\n")