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Changelog

v1.2.3 (2024-11-12)

  • :pr:`141`: Allow chunked reading of uBAM.
  • Added support for Python 3.13
  • Dropped support for Python 3.8

v1.2.2 (2024-10-04)

  • :pr:`139`: Fix an error that occurred when decoding BAM records with missing quality values. These are now converted to None.

v1.2.1 (2024-06-17)

  • Make macOS ARM64 wheels available.

v1.2.0 (2023-12-11)

  • :pr:`124`: Added support for chunking FASTA reads to read_paired_chunks. Previously, only FASTQ was supported.

v1.1.0 (2023-11-20)

  • :pr:`116`: Added experimental support for reading unaligned BAM files (single-end only at the moment). This uses a custom, highly efficient BAM parser, making dnaio faster than htslib in this particular case.

v1.0.1 (2023-10-06)

  • :pr:`120`: Improved type annotations.
  • Dropped support for Python 3.7
  • Added support for Python 3.12

v1.0.0 (2023-09-06)

  • :pr:`110`: Added id and comment properties to SequenceRecord.

v0.10.0 (2022-12-05)

  • :pr:`99`: SequenceRecord initialization is now faster, which also provides a speed boost to FASTQ iteration. SequenceRecord.__new__ cannot be used anymore to initialize SequenceRecord objects.
  • :pr:`96`: open_threads and compression_level are now added to ~dnaio.open as arguments. By default dnaio now uses compression level 1 and does not utilize external programs to speed up gzip (de)compression.
  • :pr:`87`: ~dnaio.open can now open more than two files. The file1 and file2 arguments are now deprecated.

v0.9.1 (2022-08-01)

  • :pr:`85`: macOS wheels are now also built as part of the release procedure.
  • :pr:`81`: API documentation improvements and minor code refactors for readability.

v0.9.0 (2022-05-17)

  • :pr:`79`: Added a ~dnaio.records_are_mates function to be used for checking whether three or more records are mates of each other (by checking the ID).
  • :pr:`74`, :pr:`68`: Made FASTQ parsing faster by implementing the check for ASCII using SSE vector instructions.
  • :pr:`72`: Added a tutorial.

v0.8.0 (2022-03-26)

  • Preliminary documentation is available at <https://dnaio.readthedocs.io/>.
  • :pr:`53`: Renamed Sequence to ~dnaio.SequenceRecord. The previous name is still available as an alias so that existing code will continue to work.
  • When reading a FASTQ file, there is now a check that ensures that all characters are ASCII.
  • Function record_names_match is deprecated, use ~dnaio.SequenceRecord.is_mate instead.
  • Added ~dnaio.SequenceRecord.reverse_complement.
  • Dropped Python 3.6 support as it is end-of-life.

v0.7.1 (2022-01-26)

  • :pr:`34`: Fix parsing of FASTA files that just contain a comment and no reads

v0.7.0 (2022-01-17)

  • @rhpvorderman contributed many performance improvements in :pr:`15`, :pr:`17`, :pr:`18`, :pr:`20`, :pr:`21`, :pr:`22`, :pr:`23`. Reading and writing FASTQ files and reading of paired-end FASTQ files was sped up significantly. For example, reading uncompressed FASTQ is 50% faster (!) than before.
  • :pr:`28`: Windows support added

v0.6.0 (2021-09-28)

  • :pr:`12`: Improve FASTQ writing speed twofold (thanks to @rhpvorderman)

v0.5.2 (2021-09-07)

  • :issue:`7`: Ignore a trailing "3" in the read id