Changelog

This document outlines the changes made to the project with each release.

Version 1.1.1 (2024-10-25)

Features

  • Updated tree parsing functionality and added it to the TreeParser class in the analysis/tree_parser.py module to conform to refactor, and added new functionality to parse, modify, draw, and save Newick and NEXUS tree files.

  • siterates and qmatrix files now dynamically determine if they are in IQ-TREE format or if they are just in a simple tab-delimited or comma-delimited format.

  • site_rates and qmat are now read in as pandas DataFrames with less complex logic.

  • Added unit test for tree parsing.

  • Added integration test for tree parsing.

  • Added documentation for tree parsing.

Bug Fixes

  • Fixed bug where the PhylipReader and StructureReader classes did not have the verbose and debug attributes.

Changes

  • q property is now called qmat for clarity and easier searching in files.

  • Removed redundant siterates_iqtree and qmatrix_iqtree arguments attributes from the GenotypeData, VCFReader, PhylipReader, StructureReader, and TreeParser classes.

  • Added error handling for tree parsing.

  • Added error handling for siterates and qmatrix files.

Version 1.1.0 (2024-10-08)

Features

  • Full refactor of the codebase to improve user-friendliness, maintainability and readability.

    • Method chaining: All functions now return the object itself, allowing for method chaining and custom filtering orders with NRemover2.

    • Most objects now just take a GenotypeData object as input, making the code more modular and easier to maintain.

    • Improved documentation and docstrings.

    • Improved error handling.

    • Improved logging. All logging is now done with the Python logging module via the custom LoggerManager class.

    • Improved testing.

    • Improved performance.

      • Reduced memory usage.

      • Reduced disk usage.

      • Reduced CPU usage.

      • Reduced execution time, particularly for reading, loading, filtering, and processing large VCF files.

    • Improved plotting.

    • Improved data handling.

    • Improved file handling. All filenames now use pathlib.Path objects.

    • Code modularity: Many functions are now in separate modules for better organization.

    • Full unit tests for all functions.

    • Full integration tests for all functions.

    • Full documentation for all functions.

Version 1.0.5 (2023-09-16)

Features

  • Added thin and random_subset options to nremover() function. thin removes loci within thin bases of the nearest locus. random_subset randomly subsets the loci using an integer or proportion.

Changes

  • Changed unlinked to unlinked_only option for clarity

Version 1.0.4 (2023-09-10)

Features

  • Added functionality to filter out linked SNPs using CHROM and POS fields from VCF file.

Performance

  • Made the Sankey plot function more modular and dynamic for easier maintainability.

Bug Fixes

  • Fix spacing between printed STDOUT.

Version 1.0.3.3 (2023-09-01)

Bug Fixes

  • Fixed bug where CHROM VCF field had strings cut off at 10 characters.

Version 1.0.3.2 (2023-08-28)

Bug Fixes

  • Fixed copy method for pysam.VariantHeader objects.

Version 1.0.3 (2023-08-27)

Features

  • Performance improvements for VCF files.

  • Load and write VCF file in chunks of loci to improve memory consumption.

  • New output directory structure for better organization.

  • VCF file attributes are now written to an HDF5 file instead of all being loaded into memory.

  • Increased usage of numpy to improve VCF IO.

  • Added AF INFO field when converting PHYLIP or STRUCTURE files to VCF format.

  • VCF file reading uses pysam instead of cyvcf2 now.

Bug Fixes

  • Fixed bug with search_threshold plots where the x-axis values would be sorted as strings instead of integers.

  • Fixed bugs where sampleIDs were out of order for VCF files.

  • Ensured correct order for all objects.

  • Fixed bugs when subsetting with popmaps files.

  • Fixed to documentation.

Version 1.0.2 (2023-08-13)

Bug Fixes

  • Fix for VCF FORMAT field being in wrong order.

Version 1.0.1 (2023-08-09)

Bug Fixes

  • Band-aid fix for incorrect order of sampleIDs in VCF files.

Initial Release

  • Reads and writes PHYLIP, STRUCTURE, and VCF files.

  • Loads data into GenotypeData object.

  • Filters DNA sequence alignments using NRemover2.

    • Filters by minor allele frequence, monomorphic, and non-billelic sites

    • Filters with global (whole columns) and per-population, per-locus missing data thresholds.

  • Makes informative plots.