feat: add streaming sequence reader and superkmer iterator

Introduce the `obiread` crate with a streaming byte normalizer that processes FASTA, FASTQ, and GenBank files using a 64 KiB ring buffer for O(1) memory usage. Integrate this crate into `obiskbuilder` to provide `SuperKmerStreamIter`, enabling memory-efficient superkmer traversal with rolling entropy and minimizer-based cut conditions.

This commit is contained in:

Eric Coissac

2026-05-27 00:09:12 +02:00

parent 0d9be53d1f

commit a4b57a96de

8 changed files with 671 additions and 1 deletions

src/Cargo.lock

Generated

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@@ -1637,6 +1637,7 @@ dependencies = [
  "lazy_static",
  "obikrope",
  "obikseq",
  "obiread",
 ]
 [[package]]