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CHANGELOG.md

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Taranys 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.

[3.0.1] - 202X-XX-XX : https://github.com/BU-ISCIII/relecov-tools/releases/tag/

Same version as before for proper publish to pip.

Credits

Code contributions to the release:

Sara Monzon - saramonzon

Modules

Added enhancements

Fixes

Changed

Removed

Requirements

[3.0.0] - 2025-01-02 : https://github.com/BU-ISCIII/taranys/releases/tag/3.0.0

  • Code refactor to create a proper python package
  • Implementation of parallel computation for execution speed.
  • New implementation of reference-alleles module using leiden algorithm for allele clustering.
  • New param defaults based on empirical testing.
  • Distance matrix is rewritten with more params available.

[2.0.1beta] - 2021-07-14 : https://github.com/BU-ISCIII/taranys/releases/tag/2.0.1

New features

  • New default missing values threshold imposed for samples in distance matrix creation
  • New default perc_identity_ref value for loci search in allele calling analysis
  • Github actions for testing and docker generation.

Bug fixes

  • multiple statistic modes bug fixed
  • BLAST database creation bug due to punctuation signs in file name fixed
  • ST profile identification bug fixed
  • Python modules installed from conda-forge in environment.yml

Documentation

  • Channel order in conda installation command

[2.0.0beta] - 2021-06-24 : https://github.com/BU-ISCIII/taranys/releases/tag/2.0.0edge

Pre-release

[0.3.3beta] - 2018-11-05 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.3

BUG FIX:

  • Fix num_threads in blast commands

[0.3.2beta] - 2018-11-02 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.2

BUG FIX:

  • Added ERROR posibility to allele classification, when the allele is not PLOT but is too near to contig end, and protein codification finishes without finding a stop codon.

[0.3.1beta] - 2018-10-27 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.1

  • Added cpus as parameter.

[0.3.0beta] - 2018-10-25 : https://github.com/BU-ISCIII/taranys/releases/tag/0.3.0

Bug fixes:

  • Allow dependency check for versions greater than needed.

Features:

  • Added graphics for schema evaluation(beta)
  • Added SNP calling (beta)

[0.0.1beta] - 2018-10-22 : https://github.com/BU-ISCIII/taranys/releases/tag/0.1

  • cg/wgMLST analysis using assembled contigs as input using a defined schema. Comparison matrix is generated for phyloviz visualization. Blast hit are classified as Exact match , new allele, etc.
  • cg/wgMLST statistics.
  • beta: SNP analysis.
  • Insertions, deletions and paralogues detection.