04456b0be37a7d7b57551e0d9596e3ef0b8f0393
max
  Thu Jul 16 00:34:37 2026 -0700
Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415

#Preview2 week - bugs introduced now will need a build patch to fix
New pan-genome track container (group hprc) derived from the HPRC Release 2
per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the
existing HPRC release 1 tracks:
- hprc2Coverage: fraction of assemblies aligning across GRCh38
- hprc2Breaks:   alignment breaks, colored by prevalence
- hprc2Rearr:    insertions/deletions/inversions/duplications/complex indels,
lrSv color palette, numeric size field, 50 bp default filter
- hprc2Chains:   per-haplotype bigChain composite, grouped by superpopulation
Container hidden by default. Scripts, autoSql, and makeDoc included.

diff --git src/hg/makeDb/scripts/hprc2/hprc2ProcessAll.sh src/hg/makeDb/scripts/hprc2/hprc2ProcessAll.sh
new file mode 100755
index 00000000000..86272071bc9
--- /dev/null
+++ src/hg/makeDb/scripts/hprc2/hprc2ProcessAll.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+# Run hprc2ProcessOne.sh over all HPRC2 assemblies in parallel.
+# Redmine #35415
+# Usage: hprc2ProcessAll.sh <jobs.tsv> <bedDir> [jobs]
+#   jobs.tsv: rawChainPath <TAB> shortName  (one per line)
+
+set -beEu -o pipefail
+export PATH=/usr/bin:/bin:/cluster/bin/x86_64:/cluster/bin/scripts:$PATH
+
+jobsTsv="${1}"
+BED="${2}"
+jobs="${3:-16}"
+SC="$HOME/kent/src/hg/makeDb/scripts/hprc2"
+
+mkdir -p "${BED}/procLogs"
+parallel -j "${jobs}" --colsep '\t' --bar --joblog "${BED}/procLogs/joblog.txt" \
+  "bash ${SC}/hprc2ProcessOne.sh {1} {2} ${BED} > ${BED}/procLogs/{2}.log 2>&1" \
+  :::: "${jobsTsv}"
+
+echo "processed $(ls ${BED}/chain/*.chain | wc -l) assemblies"