v1.1.0

What's Changed

• Add unique segment output and native contact reconstruction by @mr-eyes in #7

Full Changelog: v1.0.0...v1.1.0

v1.0.0

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.

v0.2.3

Full Changelog: v0.2.2...v0.2.3

v0.2.2

Full Changelog: v0.2.1...v0.2.2

v0.2.1

Full Changelog: v0.2.0...v0.2.1

v0.2.0

Full Changelog: https://github.com/mr-eyes/cifi-toolkit/commits/v0.2.0