Changelog

0.8.1 - 2023-05-17

This is a major release.

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.

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).

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).

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).