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ondist

Commits on Oct 20, 2026
- sync: assemble 0.7-nh13.dev+f7d7f14 on upstream 74bdd48
  web-flow
  committed
  e79a76c
Commits on Sep 6, 2026
- sync: assemble 0.7-nh13.dev+7df2016 on upstream f0e1174
  web-flow
  committed
  c30023a
Commits on Aug 23, 2026
- sync: assemble 0.7-nh13.dev+3d10d42 on upstream f0e1174
  web-flow
  committed
  c887691
Commits on Aug 22, 2026
- sync: assemble 0.7-nh13.dev+6ca35d1 on upstream f0e1174
  web-flow
  committed
  b0eb65c
Commits on Aug 20, 2026
- sync: assemble 0.7-nh13.dev+1647092 on upstream f0e1174
  web-flow
  committed
  a708168
Commits on Aug 8, 2026
- sync: assemble 0.7-nh13.dev+32d519b on upstream c42d875
  web-flow
  committed
  0faa4fe
Commits on Aug 7, 2026
- sync: assemble 0.7-nh13.dev+6304587 on upstream d6d9f87
  web-flow
  committed
  23d2376
Commits on Aug 3, 2026
- merge alt-liftgroup (feat/alt-aware-liftgroup)
  web-flow
  committed
  895fb2e
- merge submem-ablation (feat/submem-ablation)
  web-flow
  committed
  11872f1
Commits on Jun 25, 2026
- chore: idiomatic debug flags and comment clarity
  nh13
  committed
  ddc1ddf
- feat: opt-in PE-pair-primary SAM selection (--pe-pair-primary)
  nh13
  committed
  fce781c
- r385: output secondary aligments to XA
  lh3
  committed
  3970d06
- feat: ALT-aware mapping via liftover groups
  nh13
  committed
  fa30992
Commits on Jun 24, 2026
- r384: added -H to insert arbitrary header lines
  lh3
  committed
  f441349
Commits on Jun 15, 2026
- feat(map): expose --max-sub-occ and --min-sub-occ CLI ablation flags
  nh13
  committed
  8fb79a9
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

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Commits on Apr 26, 2026

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Commits on Apr 11, 2026

Commits on Apr 10, 2026

Commits on Apr 6, 2026