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History for

onaltlg-hygiene

Commits on Aug 8, 2026
- feat(alt): drop --pe-pair-primary; upstream r417 does this now
  nh13
  committed
  67a1c85
Commits on Aug 7, 2026
- feat: enable --pe-pair-primary by default under .alt
  nh13
  committed
  64e5878
- feat: opt-in PE-pair-primary SAM selection (--pe-pair-primary)
  nh13
  committed
  5bf2e52
- feat: ALT-aware mapping via liftover groups
  nh13
  committed
  c33be9c
Commits on Aug 6, 2026
- Release minibwa-0.7 (r421)
  lh3
  committed
  d6d9f87
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 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 16, 2026
- r405: support bs-seq in APIs
  lh3
  committed
  317a3bb
- r404: improve paired-end mapq
  lh3
  committed
  98e89de
Commits on Jul 12, 2026
- Release minibwa-0.4 (r400)
  lh3
  committed
  b2dcea9
Commits on Jul 5, 2026
- r399: penalize clipping during rescoring
  lh3
  committed
  870ce8e
Commits on Jun 30, 2026
- r396: fixed a few typos in CLI help messages
  lh3
  committed
  84d4135
Commits on Jun 29, 2026
- r392: CL in SAM missing subcommand name
  lh3
  committed
  fdd33dd
Commits on Jun 28, 2026
- Release minibwa-0.3 (r391)
  lh3
  committed
  a679d17
- r390: output number of secondary hits to n2 tag
  lh3
  committed
  981a711
- r389: added --xa
  lh3
  committed
  9fb8672
Commits on Jun 25, 2026
- r387: more bwa-mem options exposed to 'mem'
  lh3
  committed
  a8cf4d3
- r386: add "mem" subcommand, bwa-mem compatible CLI
  lh3
  committed
  bf37862
- r385: output secondary aligments to XA
  lh3
  committed
  3970d06
Commits on Jun 24, 2026
- r384: added -H to insert arbitrary header lines
  lh3
  committed
  f441349
Commits on Jun 23, 2026
- r383: fixed a crash caused by #39
  lh3
  committed
  27f2821
- r382: check SA size on index reading
  lh3
  committed
  35bd906
Commits on Jun 21, 2026
- r379: added getref to get the reference from .l2b
  lh3
  committed
  a125bfd
Commits on Jun 18, 2026
- Release minibwa-0.2 (r370)
  lh3
  committed
  f3dc746
- r369: fixed incorrect comment len in index
  lh3
  committed
  da10239
- r368: fixed double TAB ahead of MD
  lh3
  committed
  a2ca463

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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 20, 2026

Commits on Jul 19, 2026

Commits on Jul 16, 2026

Commits on Jul 12, 2026

Commits on Jul 5, 2026

Commits on Jun 30, 2026

Commits on Jun 29, 2026

Commits on Jun 28, 2026

Commits on Jun 25, 2026

Commits on Jun 24, 2026

Commits on Jun 23, 2026

Commits on Jun 21, 2026

Commits on Jun 18, 2026