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CHANGELOG.md

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Changelog

0.8.1 - 2023-05-19

This is a major release.

Added

  • Integrated congruency of SNVs within paired-end reads into contamination calculations (a1744a4).
  • Base cutoff values are now dynamically calculated based upon gene-specific quality score, length, and depth of coverage, with a starting cutoff of 3 which can be changed using --base_cutoff (880445d, 84b7d91, c06d438).
  • Option to download rMLST databases using -u/--unverified within the confindr_database_setup command, for downloading databases behind a firewall and/or have a self-signed certificate.

Changed

  • Refactored code by moving methods to methods.py (a7e9af6).
  • Improved README.md and MkDocs documentation with increased accuracy and readability.
  • Pytest tests now use downsampled samples from the originally published ConFindr benchmarking dataset, and instructions for running these tests have been added to the MkDocs (cc27c94).
  • Enforced Phred33 encoding for bbduk.sh calls to support future development with Nanopore reads (#39) (ac3b976).

Removed

  • Percentage contamination reporting; this was found to be unreliable and sometimes misleading (ec3ae7a).
  • --cross_details flag; analysis is now always continued after cross-genus contamination has been detected (ec3ae7a).

Fixed

  • TypeError that occurred when using an older version of BioPython (#27, #30, #38, #41) (19d0d1d, 96e1c7d).
  • Error in install.md which suggested that rMLST databases are freely available to all users (a1ce7dc).