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Releases: althonos/pyrodigal

v3.5.2

04 Sep 12:30
v3.5.2
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Added

  • Warning in CLI when given sequences with empty identifiers.

Fixed

  • FASTA parser used in CLI crashing on empty header lines (#61).

v3.5.1

17 Jul 20:48
v3.5.1
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Fixed

  • Outdated code in pyrodigal.cli breaking the CLI.

v3.5.0

17 Jul 15:30
v3.5.0
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Added

  • Support for reading from stdin in CLI (#35).
  • Flag for changing parallel computation to use Pool instead of ThreadPool (#57).
  • Better documentation of command line interface (#56).
  • Allow changing the formatter class in pyrodigal.cli.argument_parser.

Changed

  • Migrate documentation to pydata-sphinx-theme.

Fixed

  • Cython warnings with unused except * statements in MetagenomicBins.
  • Signatures of __init__ methods missing from all Cython types after the v3.0 update.
  • Small typos in documentation.

v3.4.1

23 May 14:57
v3.4.1
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Changed

  • Refactor SIMD code to reduce number of required registers, and improve SSE2 performance.
  • Refactor Prodigal initialization functions into sparse initializer code to reduce library size.

v3.4.0

19 May 09:36
v3.4.0
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Added

  • strict argument to Gene.translate to control translation of ambiguous codons with unambiguous translation (#54).
  • strict_translation argument to Genes.write_genbank and Genes.write_translation.
  • Support for translation tables 26 to 33 in Gene.translate.
  • Support for translation tables 26, 29, 30, 32 and 33 in GeneFinder.train.
  • Genes.score property to count the total score of all extracted genes.
  • full_id parameter to Genes.write_gff, Genes.write_translation and Genes.write_genes to control the ID field written for each gene (#53).

Changed

  • Gene.translate now raises a warning when called with a translation table incompatible with the training info.

Fixed

  • Bug in code for masking trailing nucleotides (#55).

v3.3.0

24 Jan 20:01
v3.3.0
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Added

  • CLI option to disable translation of stop codons (#51, by @zclaas).

Changed

  • Scorer internal API to separate connection scoring and overlap disentangling.

Fixed

  • Bug with computation of minimum node in connection scoring loop (hyattpd/Prodigal#108).
  • Out-of-bounds sequence access in _shine_dalgarno_exact and _shine_dalgarno_mm methods of Sequence.
  • Memory leak in Nodes.__setstate__ caused by incorrect reallocation.

v3.2.2

21 Jan 01:44
v3.2.2
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Fixed

  • Always mark SSE2 support on x86-64 CPUs independently of archspec-detected features (#49).

v3.2.1

27 Nov 15:14
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Added

  • Option to change argument parser in pyrodigal.cli.main.

v3.2.0

27 Nov 13:16
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Added

  • AVX-512 implementation of the SIMD pre-filter.
  • Additional support for reading lz4 and xz and zstd-compressed input in the CLI.
  • Option to change gene finder type in pyrodigal.cli.main.

v3.1.1

06 Nov 01:04
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Fixed

  • Incorrect unpickling of GeneFinder causing crashes with multiprocessing (#46).