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v0.39.0

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@d-laub d-laub released this 17 Jul 21:28
· 182 commits to main since this release

Feat

  • flat-variants: accept str/bytes/NucleotideAlphabet for VarWindowOpt.token_alphabet
  • svar2: support spliced variant records
  • svar2: scatter-write FFI entry for read-bound haplotypes
  • reverse: rc_bounded_rows_inplace for scattered rows

Fix

  • svar2: deterministic tie-break for scatter-write bounds sort
  • svar2: validate out_bounds and to_rc in scatter-write FFI entry
  • reference: reject in_memory=False with reordered/subset contigs (#285)

Refactor

  • svar2: per-row destination bounds in the reconstruct core

Perf

  • svar2: vectorize build_splice_plan permutation
  • svar2: scatter-write spliced haplotypes, no Python re-order