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onavx2

Commits on May 27, 2026
- r352: heuristic to lower bs-seq mapq
  lh3
  committed
  2757adb
Commits on May 26, 2026
- extension in the 4-base space
  lh3
  committed
  c8ae227
- 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 9, 2026
- r310: support bs-seq in public API
  lh3
  committed
  e1ebe92
- r309: support bs-seq in mb_map public API
  lh3
  committed
  38077ab
- r308: is_pe is redundant in mb_map_batch
  lh3
  committed
  bd09926
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
- side work: reduce kalloc fragmentation
  lh3
  committed
  c11ccb9
- 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 Apr 26, 2026
- r271: tuned mapQ for long reads
  lh3
  committed
  5292ce4
- r270: fixed unintended chain sorting
  lh3
  committed
  74f77fb
Commits on Apr 24, 2026
- r269: fix inconsistent subchain selection
  lh3
  committed
  5f5edb6
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
- r247: reduce pri_ratio to 0.5 and simplify
  lh3
  committed
  f5bb6cf
- r246: ported mm2 part for recal dp_max
  lh3
  committed
  a024b67
- r243: fixed a bug in the last commit
  lh3
  committed
  5d57c68
Commits on Apr 14, 2026
- r242: adaptive pri_ratio; sr batch size to 100m
  lh3
  committed
  613dd1f
- fix memory leak when no seeds are found
  
  lh3
  and
  claude
  committed
  61213d7
Commits on Apr 13, 2026
- r239: reset kalloc pool when it is too large
  lh3
  committed
  7ff6eaa
Commits on Apr 12, 2026
- fix memory leak in mb_select_sub: free r->p for discarded hits
  
  lh3
  and
  claude
  committed
  2ee5fa5
- 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
- skip some alignment on long anchors
  lh3
  committed
  ae26e8b
Commits on Apr 6, 2026
- prepare for SAM output
  lh3
  committed
  c6f8488
Commits on Feb 9, 2026
- r193: changed the set parent logic
  lh3
  committed
  b8534ea
- r191: min_dp_max should be scaled by matching sc
  lh3
  committed
  da25618
Commits on Jan 26, 2026
- fixed a bug that removes rescued hits
  lh3
  committed
  565cf3a

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Commits on May 27, 2026

Commits on May 26, 2026

Commits on May 10, 2026

Commits on May 9, 2026

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Commits on May 3, 2026

Commits on Apr 26, 2026

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Commits on Apr 17, 2026

Commits on Apr 15, 2026

Commits on Apr 14, 2026

Commits on Apr 13, 2026

Commits on Apr 12, 2026

Commits on Apr 11, 2026

Commits on Apr 6, 2026

Commits on Feb 9, 2026

Commits on Jan 26, 2026