Miniprot-0.18 (r281)

Older miniprot failed to count in-frame stop codons in deletions. This release
fixes the issue (#75).

(0.18: 11 July 2025, r281)

Miniprot-0.17 (r279)

Notable changes:

• Bugfix: older versions may output overlapping exons with --spsc.

(0.17: 15 June 2025, r279)

Miniprot-0.16 (r273)

Notable changes:

• Improvement: --spsc now works with and optimized for minisplice output.
  Note that depending on scoring in --spsc, miniprot may generate 1bp
  introns in extremely rare cases. This happens to 3 out of 4.6 million
  aligned introns with zebrafish minisplice scores.

This version produces alignment identical to v0.15 unless --spsc is used.

(0.16: 22 May 2025, r273)

Miniprot-0.15 (r270)

Notable change:

• Improvement: better alignment in tandem gene duplications (#35). This
  slightly improves overall junction accuracy on all test datasets in the
  miniprot paper. Thank the NCBI EGAPx team for providing test cases and
  explaining the relevance in gene annotation.

(0.15: 18 April 2025, r270)

Miniprot-0.14 (r265)

Notable changes:

• Bug fix: support chromosomes longer than 2Gbp (#59)

• EXPERIMENTAL feature: read splice scores from a file specified by --spsc
  and consider the scores during residue alignment. The feature makes it
  possible to apply advanced splice models and to improve miniprot alignment.

• Improvement: documented the C APIs and added an example program on using
  the APIs (#69).

This version produces alignment identical to v0.13, except for long chromosomes
or when the new feature is used.

(0.14: 7 March 2025, r265)

Miniprot-0.13 (r248)

Notable changes:

• New feature: added option -T to specify a non-standard NCBI translation
  table (#56 and #57). As this is an indexing option, the binary index format
  has to be changed accordingly. Miniprot will reject indices built with
  previous versions.

• Improvement: properly handle reference deletions involving in-frame stop
  codons (#58). Older versions would not penalize these stop codons. This
  change also improves junction accuracy especially for distant homologs.

• Bugfix: in the GFF3 output, CDS now includes stop codons (#55). Note that
  in GTF, CDS excludes stop codons.

• Bugfix: suppress an extra amino acid in the --trans or --aln output (#47).
  In rare cases, this may lead to memory violation.

(0.13: 6 March 2024, r248)

Miniprot-0.12 (r237)

Notable changes:

• New feature: added option --no-cs to disable the cs tag. This tag is not as
  useful as the cs tag for nucleotide alignment because it does not encode the
  matching amino acids.

• New feature: output the number of frameshifts and in-frame stop codons in
  the PAF output. It is non-trivial to parse in-frame stop codons.

• Bugfix: fixed malformatted protein sequences when --gtf and --trans are both
  specified (#45).

(0.12: 24 June 2023, r237)

Miniprot-0.11 (r234)

Notable changes:

• New feature: added option --trans to output translated protein sequences. It
  is possible to extract these sequences from the --aln output but the --trans
  output is smaller and more convenient.

• Bugfix: infinite error messages if a wrong option is in use.

• Improvement: better error messages given nonexisting query files (#40).

(0.11: 18 April 2023, r234)

Miniprot-0.10 (r225)

Notable change:

• Bugfix: rare segmentation fault (#38 and #39). This bug affected all
  previous versions of miniprot.

(0.10: 3 April 2023, r225)

Miniprot-0.9 (r223)

Notable change:

• Bugfix: not all query proteins were outputted with option -u.

(0.9: 9 March 2023, r223)