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ondist

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 3, 2026
- merge alt-liftgroup (feat/alt-aware-liftgroup)
  web-flow
  committed
  895fb2e
- merge submem-ablation (feat/submem-ablation)
  web-flow
  committed
  11872f1
- merge soft-clip-penalty (feat/soft-clip-penalty)
  web-flow
  committed
  a991796
- feat(meth): add --meth-tags to select which Bismark tags --meth emits
  nh13
  committed
  e1ab15c
Commits on Jul 24, 2026
- r412: renamed --xa-ratio to --outs
  lh3
  committed
  bb39631
Commits on Jun 25, 2026
- feat: enable --pe-pair-primary by default under .alt
  nh13
  committed
  93d0e9a
- r385: output secondary aligments to XA
  lh3
  committed
  3970d06
- feat: ALT-aware mapping via liftover groups
  nh13
  committed
  fa30992
Commits on Jun 15, 2026
- feat(align): 5'/3' soft-clip penalty (-L)
  nh13
  committed
  0655e32
- feat(map): expose --max-sub-occ and --min-sub-occ CLI ablation flags
  nh13
  committed
  8fb79a9
Commits on Apr 21, 2026
- r265: added Usage
  lh3
  committed
  6030fcf
Commits on Apr 20, 2026
- r262: trade accuracy for performance
  lh3
  committed
  d8e9226
Commits on Apr 19, 2026
- r260: adaptive batch size
  lh3
  committed
  d01698d
Commits on Apr 18, 2026
- allow user-provided mimalloc.o
  lh3
  committed
  65c82d1
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
- r245: further rediuce pri_ratio to 0.7
  lh3
  committed
  ca6af22
- r244: reduced long-read pri_ratio to 0.75
  lh3
  committed
  7836dc6
Commits on Apr 14, 2026
- r242: adaptive pri_ratio; sr batch size to 100m
  lh3
  committed
  613dd1f
Commits on Apr 13, 2026
- r239: reset kalloc pool when it is too large
  lh3
  committed
  7ff6eaa
Commits on Apr 12, 2026
- improve manpage and option help message
  lh3
  committed
  ac20cc2
- r234: separate sr and adap; more manpage
  lh3
  committed
  d84b1df
- expose bandwidth to CLI
  lh3
  committed
  b6ca052
- re-chaining: fix best-chain selection and related fixes
  
  lh3
  and
  claude
  committed
  6b11c1d
- r227: merged sr:adap to sr. More documentation
  lh3
  committed
  c9980fe
Commits on Apr 11, 2026
- set is_sr based on read length
  lh3
  committed
  9cd0f2c
- backup; not working properly yet
  lh3
  committed
  07ddce0
Commits on Jan 26, 2026
- select better hits for rescue
  lh3
  committed
  e9ac401
Commits on Jan 25, 2026
- implemented the full PE logic
  lh3
  committed
  c50daa0
- fixed a bug in is_rev and is_larger
  lh3
  committed
  ef7cc9f
- allow predefined PE stats
  lh3
  committed
  0168176
- backup
  lh3
  committed
  b4fc4ff

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Commits on Jan 26, 2026

Commits on Jan 25, 2026