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onaltlg-hygiene

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Commits on Aug 8, 2026
- feat(alt): drop --pe-pair-primary; upstream r417 does this now
  nh13
  committed
  67a1c85
Commits on Aug 7, 2026
- 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: ALT-aware mapping via liftover groups
  nh13
  committed
  c33be9c
Commits on Aug 4, 2026
- r417: fixed inconsistent 0x2 flag
  lh3
  committed
  54fb387
Commits on Jun 25, 2026
- 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 May 27, 2026
- r352: heuristic to lower bs-seq mapq
  lh3
  committed
  2757adb
Commits on May 26, 2026
- in the meth mode, split at disallowed mismatches
  lh3
  committed
  0f53506
Commits on May 10, 2026
- r318: revert; also disable pairing in ex-batch
  lh3
  committed
  20ed35f
- a failed experiment; will revert soon
  lh3
  committed
  a04eb42
- r316: move meth conversion into inner functions
  lh3
  committed
  1496158
Commits on May 8, 2026
- wip: base alignment works for tiny test dataset
  lh3
  committed
  1c58d90
- wip: --meth chaining done on tiny test datasets
  lh3
  committed
  cb74f4c
- wip: implement meth anchor filtering in process_batch
  
  lh3
  and
  claude
  committed
  d50b37b
- wip: add is_meth param to mb_idx_load, rename ex-sgl to ex-one
  
  lh3
  and
  claude
  committed
  7f008a1
Commits on May 3, 2026
- r285: added mb_map_batch() for batch alignment
  
  lh3
  and
  claude
  committed
  3f9fb44
- r284: finished the simple API
  lh3
  committed
  b119f58
Commits on May 1, 2026
- feat(sam): add MC and MQ tags to PE SAM output
  nh13
  committed
  d7168f1
Commits on Apr 26, 2026
- r270: fixed unintended chain sorting
  lh3
  committed
  74f77fb
Commits on Apr 19, 2026
- r259: mix short- and long-read mapq
  lh3
  committed
  cf61e30
Commits on Apr 17, 2026
- r250: implement -5; testing on Hi-C needed
  lh3
  committed
  0c2e3dd
Commits on Apr 15, 2026
- r246: ported mm2 part for recal dp_max
  lh3
  committed
  a024b67
Commits on Apr 12, 2026
- re-chaining: fix best-chain selection and related fixes
  
  lh3
  and
  claude
  committed
  6b11c1d
Commits on Apr 11, 2026
- set is_sr based on read length
  lh3
  committed
  9cd0f2c
Commits on Apr 10, 2026
- removed MB_SEED_SELF
  lh3
  committed
  11da67c
Commits on Apr 6, 2026
- use unified format API for output
  lh3
  committed
  4af03af
- sam header and read group
  lh3
  committed
  4ec2d62
- prepare for SAM output
  lh3
  committed
  c6f8488
- support --MD
  lh3
  committed
  9cbda7e
Commits on Apr 5, 2026
- cleanup PAF output (unifinished)
  lh3
  committed
  9259c95
- write cs/ds tag; not tested
  lh3
  committed
  f901352
Commits on Feb 17, 2026
- moved matrix gen to ksw2.h
  lh3
  committed
  d3a2cce
Commits on Feb 9, 2026
- r192: option to debug anchor positions
  lh3
  committed
  c3ec3e5
Commits on Jan 26, 2026
- fixed a bug that removes rescued hits
  lh3
  committed
  565cf3a

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Commits on Jan 26, 2026