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Commits

Commits on Aug 8, 2026
- feat(alt): drop --pe-pair-primary; upstream r417 does this now
  nh13
  committed
  67a1c85
- chore: ignore the ALT suite's build artifacts
  nh13
  committed
  f4e04e5
- test(alt): drive the suite through `map`, not the bwa-compat `mem`
  nh13
  committed
  6ca77f2
Commits on Aug 7, 2026
- chore(alt): run the ALT suite, and make its baseline checks mean something
  nh13
  committed
  79304ae
- fix: gate the two non-ALT-safe PE behaviours on ALT presence
  nh13
  committed
  6e4c3d2
- build(api-test): pass $(LIBS) when linking the ALT example programs
  nh13
  committed
  7c9f393
- feat: damp MAPQ for rescue-manufactured coin-flip pairs
  nh13
  committed
  595dec8
- feat: enable --pe-pair-primary by default under .alt
  nh13
  committed
  64e5878
- chore: idiomatic debug flags and comment clarity
  nh13
  committed
  a09cb7f
- feat: opt-in PE-pair-primary SAM selection (--pe-pair-primary)
  nh13
  committed
  5bf2e52
- feat: fold displaced/unliftable ALT twins into their primary group
  nh13
  committed
  4867f27
- feat: ALT-aware mapping via liftover groups
  nh13
  committed
  c33be9c
Commits on Aug 6, 2026
- Release minibwa-0.7 (r421)
  lh3
  committed
  d6d9f87
- reporting missing an option at the right place
  lh3
  committed
  4db24c4
Commits on Aug 4, 2026
- r419: revert to the bwa-mem 0x2 behavior
  lh3
  committed
  95a79d4
- r418: incorrect RNEXT for unmapped mates
  lh3
  committed
  6019322
- r417: fixed inconsistent 0x2 flag
  lh3
  committed
  54fb387
Commits on Jul 30, 2026
- Release minibwa-0.6 (r416)
  lh3
  committed
  ebc59ea
Commits on Jul 27, 2026
- r415: -I was not working
  lh3
  committed
  8ca238f
Commits on Jul 26, 2026
- Release minibwa-0.5 (r414)
  lh3
  committed
  3065ca8
Commits on Jul 24, 2026
- r412: renamed --xa-ratio to --outs
  lh3
  committed
  bb39631
Commits on Jul 23, 2026
- explain --mmap=lite
  lh3
  committed
  e798e94
Commits on Jul 20, 2026
- r411: added --xa-ratio and -I; document new opts
  lh3
  committed
  84019dc
- r410: refactored mmap
  lh3
  committed
  0e6367c
Commits on Jul 19, 2026
- r409: added --mmap=lite mode
  lh3
  committed
  f88db46
- add --mmap option to load the index via mmap()
  
  lh3
  and
  claude
  committed
  d46dd7b
Commits on Jul 17, 2026
- updated snp calling results to r404
  lh3
  committed
  27b1fef
Commits on Jul 16, 2026
- override compiler flags in Makefile
  lh3
  committed
  e367988
- r405: support bs-seq in APIs
  lh3
  committed
  317a3bb
- r404: improve paired-end mapq
  lh3
  committed
  98e89de
Commits on Jul 12, 2026
- changed the bioconda link
  lh3
  committed
  cf4e50c
- fixed the wrong badge
  lh3
  committed
  4925b35
- add github download badge
  lh3
  committed
  31ad22c
- Release minibwa-0.4 (r400)
  lh3
  committed
  b2dcea9
Commits on Jul 5, 2026
- r399: penalize clipping during rescoring
  lh3
  committed
  870ce8e

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Commits on Aug 8, 2026

Commits on Aug 7, 2026

Commits on Aug 6, 2026

Commits on Aug 4, 2026

Commits on Jul 30, 2026

Commits on Jul 27, 2026

Commits on Jul 26, 2026

Commits on Jul 24, 2026

Commits on Jul 23, 2026

Commits on Jul 20, 2026

Commits on Jul 19, 2026

Commits on Jul 17, 2026

Commits on Jul 16, 2026

Commits on Jul 12, 2026

Commits on Jul 5, 2026