From d5343c75bbcf08e0dcd8592964bf225e2f591530 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Thu, 2 Jul 2026 11:52:48 -0400 Subject: [PATCH] Build minigraph with the large-inversion patch Point downloadPangenomeTools at glennhickey/minigraph commit 4636f2d (branch large-inversions-min) instead of upstream v0.21. That commit is v0.21's C source plus the ggsimple large-inversion patch: relax the inversion length gate to |pd-qd| < max(min_var_len, qd/10), scale the reverse-complement WFA cap to max(5000, qd/4), and bound WFA memory for large caps (max_pen>50000 -> checkpointed traceback, result-identical to exact). The intervening upstream commits r607-r613 change only misc/ JS tooling that cactus does not build, so this is functionally v0.21 plus the inversion patch. Confirmed a safe win on the full HPRC regen VCF eval: FP 33035->30337, FN 28101->25537, F-measure .9927->.9933 (precision and sensitivity both up). Co-Authored-By: Claude Opus 4.8 (1M context) --- build-tools/downloadPangenomeTools | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/build-tools/downloadPangenomeTools b/build-tools/downloadPangenomeTools index ecb340073..8cdb18070 100755 --- a/build-tools/downloadPangenomeTools +++ b/build-tools/downloadPangenomeTools @@ -71,9 +71,9 @@ fi # minigraph cd ${pangenomeBuildDir} -git clone https://github.com/lh3/minigraph.git +git clone https://github.com/glennhickey/minigraph.git pushd minigraph -git checkout v0.21 +git checkout 4636f2d42864ee7a32c082d23097fb226acd2a67 # hack in flags support sed -i Makefile -e 's/CFLAGS=/CFLAGS+=/' -e 's/LIBS=/LIBS+=/' LIBS="${jemallocLib}" make -j ${numcpu}