Use minigraph with the large-inversion patch#1948
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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) <noreply@anthropic.com>
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Point to minigraph fork with vibe-coded inversion scope increase. Will see about merging it upstream but in the meantime it seems to help Cactus, both in a few little test cases as well as chm13-hg002-t2t-giab evaluation for hprc-v2.1. brings F1 from 0.9927 to 0.9933 (with vcfwave).