Snpio

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.

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.

Bug Fixes

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

Bug Fixes

- Fixed copy method for use with pysam VariantHeader objects.

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.

Bug Fixes

- Fix for VCF FORMAT field being in the wrong order.