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@quwubin quwubin released this 17 Jul 04:38
v4.4.0
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MFEprimer v4.4.0

Faster --bind on large genomes: amplicon-scoped binding reports and a fully parallel binding path.

Highlights

  • New --bind-amp-only (implies -b / --bind)
    Compute and report binding sites only within the predicted amplicons, instead of running the full thermodynamic workup on every genome-wide k-mer hit. On multi-Gbp, repeat-rich genomes this turns spec -b runs that previously never finished into seconds. Background and benchmarks: issue #33.

  • Parallel binding path
    The k-mer binding query, the amplicon search, and the binding-detail workup now all run in the worker pool, so -c finally scales spec -b (previously the -b path was single-threaded).

  • Fix: duplicated binding entries on multi-record references
    Binding entries were appended once per record, so *.bind.txt grew quadratically and contained duplicated sites on multi-chromosome/contig databases. The reported site set is unchanged; the duplicates are gone.

  • Consistent counts with --bind-amp-only
    The per-primer header now shows both the genome-wide hit count and the reported subset, e.g. has [ 2/plus + 1/minus ] binding sites genome-wide, showing [ 1/plus + 0/minus ] within predicted amplicons.

Notes

  • Default -b output is unchanged except that duplicated entries are removed (byte-identical on single-record references).
  • With --bind-amp-only, the reported sites are exactly the full -b sites overlapping the predicted amplicons; with zero predicted amplicons it returns instantly.

Quick start

mfeprimer spec -i primers.fa -d huge_genome.fa -o out --bind-amp-only -c 16
Assets 10
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