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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

0.5.0 - 2023-07-18

Fixed

  • Properly handling Ns in the MSA, and in the denovo sequences (see PR #60 and PR #61 for more details);

Changed

  • scikit-learn, numpy and pytest dependencies updated;
  • The KMeans algorithm used is now elkan;

0.4.0 - 2022-11-22

Added

  • make_prg update command, that updates PRGs without requiring to rebuild MSAs and the PRG itself from scratch;
  • Trace (-vv) logging level, to track make_prg behaviour (intended for developers only);
  • Multithreading support (-t parameter);
  • A sample example;
  • 365 new tests (from 116 to 481 total tests), with test coverage >99% in non-argument parsing code;
  • Precompiled binary;

Changed

  • make_prg from_msa: input can now be a single file or a directory. If it is a single file, a <prefix>.prg.bin, a <prefix>.prg.fa, a <prefix>.prg.gfa and a <prefix>.update_DS.zip files are created. If it is a directory, all files in the directory are scanned and the same execution for a single file is done for each input file found. The output files are a collection of the single-input execution: a <prefix>.prg.bin.zip file will contain a collection of .prg.bin files, similar to <prefix>.prg.gfa.zip and <prefix>.update_DS.zip; <prefix>.prg.fa will be a multi fasta;

  • Other make_prg from_msa CLI changes (please run make_prg from_msa -h for a full description of the new parameters):

    • Parameters removed: --prg_name, --seqid, --no_overwrite;
    • Parameters added: -s, --suffix, -F, --force, -t, --threads, -g, --output-graphs;
    • Parameters changed: Replaced --outdir by --output_prefix;

  • The recursive clustering and collapse algorithm is now explicitly represented as a tree with internal data structures that remember the multiple sequence subalignment at any point of the recursion, as well as several other internal data, allowing the serialization and deserialization of the recursion tree at any point. Thus updates can be done avoiding any recomputation by firstly saving the state of the recursion tree to disk, and then loading this recursion tree, adding denovo sequences to some specific nodes, and triggering recomputation of the modified nodes. Any preorder traversal of the recursion tree yields the same order of recursive calls of the previous algorithm, thus allowing us to translate the algorithms in the previous version as preorder traversals with custom visit operations.

  • Moved from setup.py to pyproject.toml

Fixed

  • Several minor bugs;
  • Heavy refactoring of almost the whole codebase;

Removed

  • Dropped support for python 3.7, supported python versions are: 3.8, 3.9, 3.10, 3.11.
  • Dropped support for Mac OS X;

0.2.0 - 2021-10-27

Added

  • New CLI:
    • -S, --seqid option to name the PRG sequence, which by default uses the file name.
    • -N shortcut for max nesting
    • -L shortcut for min match length
    • --log to enable specifying log file should go to path. Default behaviour is now that log goes to stderr by default
    • -O, --output-type option to specify what output files are required. Defaults to all
  • Integration test for nested variation

Removed

  • summary file

Changed

  • New CLI:
    • --prefix CLI parameter of from_msa subcommand removed in favor of CLI parameters --outdir and --prg_name, with sensible defaults (current working directory and MSA file name stem respectively). This allows finer control over where to place output files.
  • Output files:
    • No longer contain 'max_nesting' and 'min_match_length' in their names; these appear in the log files, and in the .prg fasta header.
    • .bin file now stores even integer markers at site ends; this is the format used by gramtools.
    • Summary file not written by default

Fixed

  • Bugfix (#27)- Part 1: clustering termination was not properly detected, causing spurious site production
  • Bugfix (#27)- Part 2: added criteria for not clustering, to reduce construction of ambiguous graphs

0.1.1 - 2021-01-22

Added

  • Dockerfile
  • -V option to get version

Changed

  • A test that was clustering all unique 5-mers was reduced to all 4-mers as the memory usage of all 5-mers was causing a segfault when trying to run the tests during the docker image build.

Removed

  • Singularity file as it is redundant with the new Dockerfile (that will be hosted on quay.io)
  • scipy dependency. We never actually explicitly use scipy.

0.1.0 - 2021-01-20

Added

  • This CHANGELOG file to hopefully serve as an evolving example of a standardized open source project CHANGELOG.