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@mr-eyes mr-eyes released this 10 Sep 19:56
· 3 commits to main since this release
cbcf02d

Fix paired-end output, rename fragments to segments, expand the digest report

Fixes #3 #2

Fixed

  • --gzip silently dropped records over ~8KB, leaving R1 and R2 different lengths. Only
    0.23% of pairs were correctly mated; hifiasm was reading mismatched pairs.
  • The default uncompressed writer had the same unchecked-write bug.
  • R1 and R2 carried /1 and /2, so the two files disagreed on every pair name.
  • -l was not honored for R2, which came out shorter than asked for. Low values of -l
    produced 1bp reads.
  • R2 was never reverse-complemented on the default path.
  • Report sections were missing under --fast.
  • Yield figures ignored reads that failed the filters, so the bases did not add up.
  • reads_in counted BAM records the statistics never saw.
  • Out-of-range cut_offset in process_reads_custom caused an underflow and overlapping segments.

Added to the digest report

  • Input reads: length distribution, total bases, GC, enzyme sites.
  • Yield: bases in against bases written, and where the rest went.
  • Filtering breakdown by cause.
  • Segments and pairs per read as distributions.

Changed

  • -l default is now 60, was 20. hifiasm drops a pair outright if either mate is under
    31bp, so shorter mates were written and then discarded.
  • --revcomp-r2 is now off by default. R2 keeps the orientation it was sequenced in.

Breaking

  • --min-fragments and --min-frag-len are now --min-segments and --min-segment-len.
    Short -m and -l are unchanged.
  • Python keyword arguments and _stats.json keys renamed to match.
  • --revcomp-r2 no longer implies --no-strip-overhang; the two options are independent.