f058c8fe4601b223ff47468eb3525c05ccd03850
max
  Wed Apr 22 09:17:17 2026 -0700
srSv: new short-read SV supertrack, split out of lrSv

Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr,
tommoJpCnv) out of the Long-read SV supertrack into a new sibling
supertrack srSv (Short-read SVs), so the lrSv collection contains
only long-read callsets. Filter fields (svType, svLen, insLen, AC)
are mirrored at the srSv supertrack level to keep the UX parallel
to lrSv.

- trackDb: new human/srSv.ra with the three subtrack stanzas and
updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas
removed from human/lrSv.ra. human/trackDb.ra now includes
srSv.ra. Also a new human/srSv.html overview page; the SR rows
and SR-specific paragraphs removed from human/lrSv.html.
- Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/
{lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to
scripts/srSv/ with git mv (history preserved) and renamed to
drop the "lrSv" prefix. Internal path references in abelSvBuild.sh
and abelSvVcfToBed.py updated.
- makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and
extended with the onekg3202Sr and tommoJpCnv sections moved from
lrSv.txt. lrSv.txt leaves a pointer.
- Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr,
lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*.
/gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and
/gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/.

refs #36258

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index a9344786817..8ac801b5d81 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -1,16 +1,17 @@
 include lrSv.ra alpha
+include srSv.ra alpha
 
 include predictionScoresSuper.ra
 
 #PanelApp
 include panelApp.ra
 
 # ENCODE tracks
 include trackDb.encode.ra
 
 # chainNet tracks
 include trackDb.chainNet.ra
 
 # Neandertal tracks
 include trackDb.nt.ra