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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[0.7.0] - 2025-04-18

Added

  • Add the phred_quality_score method to the Python Record class (#98)
  • Add Phred decoding functionality (#102)

[0.4.1] - 2020-03-12

Added

  • ParseErrorKind::EmptyFile variant to handle cases where there are less than two bytes in a file [#51]

[0.4.0] - 2020-07-08

Changed

  • Added parse_fastx_file which replaces parse_sequence_reader and offers an iterator like usage and is faster than 0.3. Also adds parse_fastx_reader and parse_fastx_stdin.
  • SequenceRecord now offers more information about the file such as line ending, which allows writing a file identical to the input one.

[0.3.0] - 2019-09-12

Added

  • Improved error reporting (i.e., a parse failure now gives the record it failed on).
  • Significant code cleanup and additional linting (cargo clippy).
  • Significant additional test coverage, including via fuzzing.
  • Significant improvements to library documentation.

Changed

  • The .kmers method has been simplified and a new .canonical_kmers method has been introduced with much of the original's functionality.
  • Added parse_sequence_reader, which replaces fastx_stream and fastx_bytes.
  • fastx_cli updated and renamed to parse_sequence_path.
  • SeqRecord is now SequenceRecord and many of its methods are now in the Sequence trait (e.g., working on byte slices).
  • Automatic decompression now takes Read instead of Read + Seek so we can handle e.g. gzip files piped in through stdin.
  • See this link for additional details on updating code to v0.3.0.

Removed

  • Single-file zip handling (zip requires Seek) 😞

[0.3.1] - 2019-09-18

Fixed

  • Needletail no longer runs out of memory when parsing large, compressed files.