v1.1.0.1

• Added UserManual.pdf via pandoc
• tidied up API docs

v1.1.0

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 1.0.4

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.

Bug Fixes

• Fix spacing between printed STDOUT.

Version 1.0.3.3

• Fix bug where VCF file CHROM strings were cut off after 10 characters.

Version 1.0.3.1

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 1.0.1.0.0

Update docs

Version 1.0.1.0

Update docs

Version 1.0.1

• Switched to cyvcf2 instead of scikit-allel because scikit-allel wouldn't compile on Mac.
• Updated documentation

v1.0.0

Merge pull request #3 from tkchafin/master

add check to validate q matrix from iqtree