ALT-aware mapping via post-extension liftover groups - #7

Draft

nh13 wants to merge 25 commits into

feat/alt-aware-liftgroup

Commits on Aug 7, 2026

feat: ALT-aware mapping via liftover groups
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c33be9c
feat: fold displaced/unliftable ALT twins into their primary group
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4867f27
feat: opt-in PE-pair-primary SAM selection (--pe-pair-primary)
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5bf2e52
chore: idiomatic debug flags and comment clarity
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a09cb7f
feat: enable --pe-pair-primary by default under .alt
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64e5878
feat: damp MAPQ for rescue-manufactured coin-flip pairs
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595dec8
build(api-test): pass $(LIBS) when linking the ALT example programs
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7c9f393
fix: gate the two non-ALT-safe PE behaviours on ALT presence
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6e4c3d2
chore(alt): run the ALT suite, and make its baseline checks mean something
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79304ae

Commits on Aug 8, 2026

test(alt): drive the suite through `map`, not the bwa-compat `mem`
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6ca77f2
chore: ignore the ALT suite's build artifacts
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f4e04e5
feat(alt): drop --pe-pair-primary; upstream r417 does this now
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67a1c85

Commits on Aug 20, 2026

Commits on Aug 22, 2026

Commits on Aug 23, 2026