Miniprot-0.3 (r137)

Notable changes:

• Improvement: fine tune parameters and heuristics: higher non-GT-AG penalty,
  higher frameshift penalty, higher penalty on in-frame stop codons and a
  small penalty on long terminal introns. Miniprot is a little more sensitive
  and a little more accurate, at a minor cost of performance.

• New feature: richer GFF output. Miniprot now reports per-exon alignment
  score, number of frameshifts, number of in-frame stop codons and
  non-canonical donor/acceptor sequences.

• New feature: added option --outn to control the number of alignments per
  protein to output.

• New feature: added option -P to change the ID prefix in GFF output (#6).

• Bug fix: fixed a segmentation fault when there are no k-mers on a reference
  sequence (#4).

(0.3: 22 September 2022, r137)

Miniprot-0.2 (r116)

Notable changes:

• New feature: output GFF3 with option --gff. PAF alignments are embedded in
  ##PAF lines in the output GFF3.

• Improvement: give a bonus score -B if extension reaches the end of a protein.
  BWA-MEM and minimap2 both have this heuristic.

• Improvement: pay more effort to the first and the last exons. This increases
  the sensitivity at the cost of performance.

• Improvement: increased non-canonical splicing penalty -C from 6 to 11. This
  increases overall specificity.

• Improvement: rank an alignment with the DP score disregarding introns. This
  is to reduce the effect pseudogenes. Minimap2 uses the same strategy.

• Bug fixes: fixed incorrect CIGAR in corner cases and patched a minor memory
  leak.

This version works on several real datasets to decent accuracy without crashing
or memory leaks. It is ready for more users.

(0.2: 12 September 2022, r116)

Miniprot-0.1 (r97)

This is the first public release of miniprot, a mapper for aligning proteins to a large genome. This release has a few issues and is generally not recommended for production uses.

(0.1: 9 September 2022, r97)