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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.

[v0.3.2]

Added

  • Update to dorado_stereo.sh, do not create directories when using -n flag (dry run).

[v0.3.1]

Added

  • wrapper for a prototype stereo-calling pipeline dorado_stereo.sh that does 2-stage stereo calling.

[v0.3.0]

Changed

  • update fastx iteration in split_pairs to be compatible with pyfastx>=0.9.0.

Fixed

  • Bug where split_pairs would raise a StopIteration if dataset has < 5k reads.

[v0.2.20]

Added

  • split_pairs, a tool to recover non-split reads into their template/complement parts.

[v0.2.19]

Fixed

  • Bug where approximate start times led to incorrectly rejecting candidate duplex pairs.

[v0.2.18]

Fixed

  • Bug where aligned BAMs would be used as inputs to filter_pairs. This meant running filter_pairs on a guppy directory would report an incorrect duplex rate

[v0.2.17]

Fixed

  • Bug where an incorrect tag was used to get sequence lengths from .bam files (for dorado)

Changed

  • ProcessPoolExecutor -> ThreadPoolExecutor in filter_pairs for faster filtering
  • Reporting duplex rate in duplex_tools pair

[v0.2.16]

Added

  • Ability to use an unmapped bam (output from dorado) as input to pairs_from_summary
  • Ability to use an unmapped bam (output from dorado) as input to filter_pairs
  • Convenience script (duplex_tools pair unmapped.bam) to call both pairs_from_summary and filter_pairs on a bam
    • usage: duplex_tools pair unmapped.bam

[v0.2.15]

Fixed

  • Bug where template/complement pairs with small negative time between them would not be chosen (rounding error).

Added

  • Option to set --no_end_penalties in filter_pairs. This option favours partial matches and avoids unbounded negative pairing scores

[v0.2.14]

Fixed

  • Bug where template/complement pairs with no time between them would not be chosen

[v0.2.13]

Added

  • Option to set --threads in filter_pairs

Updated

  • Updated defaults in readme for duplex basecalling (chunks_per_runner 16 -> 416)

[v0.2.12]

Fixed

  • Update defaults in pairs_from_summary to --min_qscore 7 --max_abs_seqlen_diff 1000

[v0.2.11]

Fixed

  • Passed --trim_start and --trim_end from cli to main function for split_on_adapter

[v0.2.10]

Added

[v0.2.9]

Added

  • Flag to allow splitting multiple times for reads with multiple adapters
  • Moving debug output and edited reads to the main output directory

[v0.2.8]

Changed

[v0.2.7]

Fixed

  • split_on_adapter also defaults to both .fastq and fastq.gz from cli

Added

  • Options --min_qscore and --max_abs_seqlen_diff to find duplex reads
  • Default filtering on min_qscore (12) and maximum length difference in pairs_from_summary for duplex reads

[v0.2.6]

Fixed

  • Surprising behaviour in split_on_adapter to only work on gzipped fastqs by default

[v0.2.5]

Added

  • Arguments --max_length and --min_length in filter_pairs

[v0.2.4]

Changed

  • Fixed argument bug in split_on_adapter. sample_type is now positional

[v0.2.3]

Changed

  • Corrected documentation for fillet.md.
  • Enabled multiprocessing for fastq extraction in filter_pairs.

[v0.2.2]

Changed

  • Fixed number formatting in number of pairs logging.

[v0.2.1]

Changed

  • Documentation for read splitting

[v0.2.0]

Changed

  • Project name to duplex tools.
  • Create single entry point program with subcommands.

Added

  • Duplex read pairing and filtering programs.

[v0.1.3]

Added

  • Integration test to run the main read_fillet entry point.

Fixed

  • Bug that caused compressed outputs to be missing the .gz extension.

[v0.1.2]

Fixed

  • Bug that caused setting trim=0 to return an empty sequence.

[v0.1.1]

Changed

  • Updated README.

[v0.1.0]

Added

  • First version.