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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.

[Unreleased]

Added

  • Coverage information is added to the merged_mutations_nt.csv file.
  • Add reference positions to mutations file mutations_nt_pos_ref_aa.csv, to be used for runControl package.

Fixed

  • Update drug resistance interpretation table.
  • Fix headers of reports

[v2.2.1] - 2018-10-17

Changed

  • Ambiguity score is now computed on PRRT up to aa 335.

Fixed

  • Bugfix: unannotated mutations were not always reported in the tables (issue #25).
  • Reference and consensus protein sequences having the same end would make annotate.py fail, fixed.

[v2.2] - 2017-02-05

Added

  • Report now includes ambiguity score derived from ambiguous consensus sequence.
  • Consensus sequence with ambiguous bases is saved into cns_ambiguous.fasta.
  • Cells of drug resistance report are colour coded.
  • The report includes levels of drug resistance inferred by HIVdb.

Changed

  • Recombinant sequences are checked for also with HIV data.
  • Threshold for sierra is read from the INI file ~/.minvar/runpars.ini
  • Minor changes in final report.
  • masterComments files with DRMs lists are updated to version 8.4
  • Both full drug name and abbreviation are written.
  • Subtype inference only reports top hit, subtype names are now clearer.

[v2.1.3] - 2017-01-18

  • Date added on every page of the report, major mutations are in bold.
  • Bugfix: minvar now works evene when neither HCV nor HIV reads are present.
  • Bugfix: find_subtype failed when reads from both HIV and HCV were present.
  • Bugfix: when no RAS mutation is found, reportdrm failed.
  • Bugfix: when the frequency of a mutation is 0.5/0.5, cns_max_freq was longer than the reference.
  • Problems with an assert when all reads have indels: removed the assert, phase_mutations has limitations.

[v2.1.2] - 2017-12-19

  • More information on the run included in the report.

[v2.1.1] - 2017-12-19

  • Fixed a bug showing up when sample consensus starts with a stop codon.

[v2.1] - 2017-12-18

Added

  • Support for non-overlapping amplicons.

[v2.0] - 2017-12-13

Added

  • Support for HCV.
  • Report in pdf now styled as article with information on footer of each page.
  • Contact information and a logo can be specified with a INI file in ~/.minvar
  • minvar can be called as a module or as command line program.

Changed

  • Improved generation of sample consensus.
  • Widespread use of shlex, i.e. processes are not called via shell.
  • Reorganization of the package structure:
    • code is now in src/minvar;
    • data are now in src/minvar/db;
    • data now include plenty of resources for HCV.
  • Import system has been changed.
  • Tests have been adapted (coverage is still very low).
  • Code quality via flake8, pep8, isort and pep257.

[v1.2b] - 2017-07-08

Changed

  • sort in pandas has been replaced by sort_values.
  • Latex template needs to define \highlight.

[v1.2a3] - 2017-06-13

Added

  • MinVar is now on bioconda.

[v1.2alpha] - 2017-06-07

Added

  • minvar -v now returns version

[v1.1] - 2017-03-08

Added

  • Switch -r added to turn on/off the calibration with GATK.
  • Documentation.
  • Ansible instructions.

[v1.0.1] - 2016-09-20

Production version, tested on 454 and Miseq and used in the manuscript.