f665d4cc3b02924a8507b2f910eaf85eab54d433
braney
  Sat Jul 18 14:12:24 2026 -0700
hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts

Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to
test left-shifting indel placement and to measure how the deletions correspond
to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded
left-normalizer, the aggregation and subsampling drivers, the stability and
cross-release carryover analyses, and the dbSNP rs cross-reference prototype.
See README.txt for the manifest; full results and cached data live in
/hive/data/genomes/hg38/bed/hprc2X.

refs #37891

diff --git src/hg/makeDb/scripts/hprc2X/hprc2XIndelsAll.sh src/hg/makeDb/scripts/hprc2X/hprc2XIndelsAll.sh
new file mode 100755
index 00000000000..9309718c285
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2X/hprc2XIndelsAll.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+# Run hprc2XIndelsOne.sh over all HPRC2 assemblies in parallel to rebuild the
+# left-normalized indel intermediates for the hprc2X track set.
+# Redmine #35415
+# Usage: hprc2XIndelsAll.sh <hprc2Dir> <hprc2XDir> [jobs]
+
+set -beEu -o pipefail
+export PATH=/usr/bin:/bin:$HOME/bin/x86_64:/cluster/bin/x86_64:/cluster/bin/scripts:$PATH
+
+SRC="${1}"
+BED="${2}"
+jobs="${3:-16}"
+SC="$HOME/kent/src/hg/makeDb/scripts/hprc2X"
+
+mkdir -p "${BED}/procLogs"
+# assembly short names come from the chains already processed in the hprc2 workdir
+ls "${SRC}"/chain/*.chain | xargs -n1 basename | sed 's/\.chain$//' > "${BED}/names.txt"
+
+parallel -j "${jobs}" --bar --joblog "${BED}/procLogs/joblog.txt" \
+  "bash ${SC}/hprc2XIndelsOne.sh {} ${SRC} ${BED} > ${BED}/procLogs/{}.log 2>&1" \
+  :::: "${BED}/names.txt"
+
+echo "regenerated indels for $(ls ${BED}/arr/*.indel.txt | wc -l) assemblies"