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