v0.4.0

0.4.0 (2024-01-14)

This new version incorporates a number of bug fixes and exciting new features! Notably, it adds support for python 3.11 (whilst keeping support for python 3.7 for @TaraMirmira). And per a recent request by @XimeiWulilyy (and @s041629 a while ago), the haptools transform command now accepts multiallelic variants. Also, a quick shoutout to @RJDan for pointing out issues with the example script for converting .blocks.det files into .hap files.

Features

• a new GenotypesPLINKTR class for reading TRs from PGEN files (#222) (3c7abe6)
  This brings us one giant step closer to being able to analyze TRs in PLINK2! See #221 for the remaining work that is needed. Credit for this work belongs to the awesome @gonzalogc1
• allow multiallelic variants in transform (#232) (371415c)
• support for python 3.11 (#207) (8e01ed4)

Bug Fixes

• UnboundLocalError arising from headerless .hap files (#229) (a499b0c)
• bug where Phenotypes.subset(inplace=True) would raise an AttributeError (#226) (cff6d9b)
• convert samples argument in Genotypes.read into a set and fix tr_harmonizer bug arising when TRTools is also installed (#225) (06cc273)
• Not having 23 chromosomes in genotype blocks when 23 chromosomes listed in centromere file resulted in Value Error (#234) (ef36798)

Documentation

• fix example of .blocks.det to .hap conversion in API docs (#236) (1ed9139)
• handle whitespace in blocks2hap example (#237) (bbdacf8)