haptk 0.3.2

A small release fixing an HST construction regression when data ran out on both sides

haptk version 0.3.2

• Regression: Bhst and uhst got stuck in a loop if genotyping data ran out on both sides
• Python: Recombination rates not mandatory for ancestral segment lengths python plots
• Python: Fixed HST construction for --all, published new version py-haptk 0.0.8

v0.3.1

haptk version 0.3.1

Features:

- Added sharded VCF reading to mrca
- Refactored a much faster haplotype comparison
- Faster longest-haplotype reading for compare-to-haplotype and compare-to-hst.
- Added sharded longest-haplotype selection to list-haplotypes
- Compare-to-haplotype speed up optimizations and sharded only-longest reading
- Added a circular visualization for match HSTs. Also, added a longest-leafs-only parameter to compare to HSTs
- Support reading ids from a hst scan
- --no-alt paramater now diregards all non-contradictory genotypes to save memory and compute

Enhancements:

- Changed tracing::error into a warning when duplicate genotypes are present
- Better error message for mrca gamma distribution failure
- Better logging

Fixes:

- Fixed marker listing from HSTs
- Fixed a hst comparison regression
- Fixed a regression on longest-haplotype selection for comparing to haplotypes

v0.3.0

HAPTK v0.3.0

This is a big release.

• HSTs can now be constructed by reading VCFs in smaller segments with the --window parameter, which defines a window in basepairs e.g. 2_000_000 bp around the starting locus. This can save significant amounts of RAM and speeds up processing of large VCFs.
• Node start_idx and stop_idx have now been replaced with Coords
• When constructing bidirectional HSTs, if the starting variant has contradictory genotypes, the first two child nodes have always just the starting variant SNP
• Haplotype comparison tools updated to support multihaplotype files and calculate frequencies
• Fasta-to-haplotype conversion added
• Coverage subcommand deprecated
• Rust based graphs deprecated except for MatrixGraph
• Experimental genome-wide methods outlined
• Polars dependency was moved to the experimental side only, which results in much faster compile times
• The experimental py-haptk library was bumped to v0.0.6 with a lot of still disorganized additions to HST analyses

Version 0.2.4

v0.2.4

readme updated