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/doc/hg38/abelSv.txt src/hg/makeDb/doc/hg38/abelSv.txt
deleted file mode 100644
index 5766ef07c7f..00000000000
--- src/hg/makeDb/doc/hg38/abelSv.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-# 2026-04-20: Abel et al 2020 CCDG structural-variant track (Claude)
-#
-# Paper:  Abel HJ et al., Nature 583:83-89 (2020), doi 10.1038/s41586-020-2371-0
-# Data :  https://github.com/hall-lab/sv_paper_042020
-#          Supplementary_File_1.zip  (B38 native callset,  14,623 samples)
-#          Supplementary_File_2.zip  (B37 callset,          8,417 samples)
-#
-# The two public callsets are non-overlapping in SVs but share 5,245 samples.
-# For the hg38 track we display B38 natively and lift B37 coordinates to
-# hg38 with the standard UCSC liftOver chain. B37 variants that do not lift
-# (626 of 280,518 primary records) are dropped.
-
-mkdir -p /hive/data/genomes/hg38/bed/abelSv
-cd /hive/data/genomes/hg38/bed/abelSv
-
-# Fetch site-frequency callsets
-wget -c https://raw.githubusercontent.com/hall-lab/sv_paper_042020/master/Supplementary_File_1.zip
-wget -c https://raw.githubusercontent.com/hall-lab/sv_paper_042020/master/Supplementary_File_2.zip
-unzip -o Supplementary_File_1.zip   # -> Build38.public.v2.{vcf,bedpe}.gz
-unzip -o Supplementary_File_2.zip   # -> Build37.public.v2.{vcf,bedpe}.gz
-
-# Convert, lift B37, merge, build bigBed.
-# The script parses each VCF, collapses detailed MEI subtypes
-# (e.g. <DEL:ME:LINE|L1|L1HS>) to SVTYPE=MEI, drops SECONDARY BND records
-# so each translocation pair appears only once, and emits one bed14+
-# line per variant with per-population AC/AN, MSQ, etc.
-bash ~/kent/src/hg/makeDb/scripts/abelSv/build.sh
-
-# Result:
-#   B38 bed      :  458,106 records
-#   B37 bed      :  280,518 records (before lift)
-#   B37 lifted   :  279,892 records (626 unmapped)
-#   abelSv.bb    :  737,998 records, 31 MB
-
-# Symlink for trackDb
-mkdir -p /gbdb/hg38/abelSv
-ln -sf /hive/data/genomes/hg38/bed/abelSv/abelSv.bb /gbdb/hg38/abelSv/abelSv.bb