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/scripts/abelSv/build.sh src/hg/makeDb/scripts/srSv/abelSvBuild.sh
similarity index 76%
rename from src/hg/makeDb/scripts/abelSv/build.sh
rename to src/hg/makeDb/scripts/srSv/abelSvBuild.sh
index 0b7c7c7a1bd..f2ba59d357b 100755
--- src/hg/makeDb/scripts/abelSv/build.sh
+++ src/hg/makeDb/scripts/srSv/abelSvBuild.sh
@@ -1,51 +1,51 @@
 #!/usr/bin/env bash
 # Build the abelSv bigBed for hg38 from the public Abel et al. 2020 CCDG
 # structural-variant VCFs (B38 native + B37 lifted to hg38).
 #
-# Expects to be run from /hive/data/genomes/hg38/bed/abelSv/ (cwd) with
-# Build38.public.v2.vcf.gz and Build37.public.v2.vcf.gz already downloaded
-# (see makeDoc for download URLs).
+# Expects to be run from /hive/data/genomes/hg38/bed/srSv/abelSv/ (cwd)
+# with Build38.public.v2.vcf.gz and Build37.public.v2.vcf.gz already
+# downloaded (see makeDoc for download URLs).
 
 set -euo pipefail
 
-SCRIPTS=/cluster/home/max/kent/src/hg/makeDb/scripts/abelSv
+SCRIPTS=/cluster/home/max/kent/src/hg/makeDb/scripts/srSv
 CHAIN=/gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz
 CHROMSIZES=/hive/data/genomes/hg38/chrom.sizes
 NTHREADS=8
 
 # --- B38: native GRCh38 ---
 echo "[$(date +%T)] processing B38 VCF..."
 zcat Build38.public.v2.vcf.gz \
-    | "$SCRIPTS/vcfToBed.py" B38 \
+    | "$SCRIPTS/abelSvVcfToBed.py" B38 \
     > B38.bed
 
 # --- B37: lift to hg38 ---
 echo "[$(date +%T)] processing B37 VCF..."
 zcat Build37.public.v2.vcf.gz \
-    | "$SCRIPTS/vcfToBed.py" B37 \
+    | "$SCRIPTS/abelSvVcfToBed.py" B37 \
     > B37.prelift.bed
 
 echo "[$(date +%T)] lifting B37 to hg38..."
 # bed has 35 columns; we use -bedPlus=9 -tab so liftOver passes extra
 # columns through unchanged.
 liftOver -tab -bedPlus=9 B37.prelift.bed "$CHAIN" \
     B37lift.bed B37.unmapped.bed
 
 echo "  B37 mapped:    $(wc -l < B37lift.bed)"
 echo "  B37 unmapped:  $(grep -c -v '^#' B37.unmapped.bed || true)"
 
 # --- merge + sort ---
 echo "[$(date +%T)] merging and sorting..."
 cat B38.bed B37lift.bed \
     | sort -k1,1 -k2,2n --parallel="$NTHREADS" \
     > abelSv.bed
 
 echo "  total variants: $(wc -l < abelSv.bed)"
 
 # --- bigBed ---
 echo "[$(date +%T)] building bigBed..."
-bedToBigBed -type=bed9+26 -tab -as="$SCRIPTS/abelSv.as" \
+bedToBigBed -type=bed9+29 -tab -as="$SCRIPTS/abelSv.as" \
     abelSv.bed "$CHROMSIZES" abelSv.bb
 
 ls -lh abelSv.bb
 echo "[$(date +%T)] done."