All pull requests

Pull requests

• perf(aln): plain aln no-hit proof with a cost gate, and an in-place radix pairing sort

  #790·nh13 opened Nov 12, 2026·

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  5

• feat(aln): --known-snvs-cache keeps the ALT-window index in a file across runs

  #789·nh13 opened Nov 12, 2026·

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  6

• perf(aln): faster --meth search pops and row resolution (byte-identical)

  #788·nh13 opened Nov 12, 2026·

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  5

• perf(aln): end --meth searches on a pigeonhole proof that a read has no hit

  #787·nh13 opened Nov 12, 2026·

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  5

• feat(aln): end --meth single-end reads on saturation certificates

  #786·nh13 opened Nov 12, 2026·

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  5

• perf(aln): take stock aln's cuts from the verified --meth best cost

  #785·nh13 opened Nov 12, 2026·

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  5

• feat(aln): score --meth rows along their search path

  #784·nh13 opened Nov 12, 2026·

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  5

• perf(aln): score equal-span --meth windows with 64-bit words

  #783·nh13 opened Nov 12, 2026·

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  5

• fix(aln): drop --meth windows over the read's -n limit

  #782·nh13 opened Nov 11, 2026·

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  5

• feat(aln): add --exact-rescue-window, on by default under --meth

  #779·nh13 opened Nov 10, 2026·

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  5

• perf(aln): let seeded --meth reads use the certified stratum stop

  #778·nh13 opened Nov 10, 2026·

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  5

• perf(aln): stop resolving --meth rows once the lookup budget is bound

  #777·nh13 opened Nov 10, 2026·

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  5

• perf(aln): skip the --meth window DP when the ungapped alignment provably wins

  #776·nh13 opened Nov 10, 2026·

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  5

• feat(mem): add --alt-project to let ALT haplotypes decide placement

  #775·nh13 opened Nov 10, 2026·

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  12

• feat(aln): build the --known-snvs window index in memory

  #773·nh13 opened Nov 10, 2026·

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  6

• fix(pair): compute mem_pair's tie key without signed shift overflow

  #771·nh13 opened Nov 9, 2026·

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  9

• feat(aln): --known-snvs credits known SNV ALT alleles to remove reference bias in short reads

  #770·nh13 opened Nov 9, 2026·

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  3

• chore(main): release 0.18.0

  autorelease: pending
  #769·fg-labs-bot[bot] opened Nov 9, 2026Bot·

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  3

• feat(aln): add opt-in --ref-span-insert to measure inserts from alignment spans

  #765·nh13 opened Nov 8, 2026·

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  5

• perf(aln): store a finished --meth read's loci in a compact record

  #764·nh13 opened Nov 8, 2026·

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  5

• perf(aln): release --meth search memory once a read is finished

  #761·nh13 opened Nov 7, 2026·

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  5

• feat(aln): add opt-in --short-insert calibration

  #752·nh13 opened Nov 6, 2026·

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  5

• feat(aln): complete --meth strata and bound the candidate search

  #751·nh13 opened Nov 6, 2026·

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  44

• feat(aln): pair --meth reads and enable CpG context

  #750·nh13 opened Nov 6, 2026·

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  69

• feat(aln): align single-end --meth reads with stock cost accounting

  #749·nh13 opened Nov 6, 2026·

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  102