[0.4.0](https://github.com/CAST-genomics/haptools/compare/v0.3.0...v0.4.0) (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](https://github.com/CAST-genomics/haptools/issues/222)) ([3c7abe6](https://github.com/CAST-genomics/haptools/commit/3c7abe6922e8d6953debf3b0d6a02dee9610bbda))
This brings us one giant step closer to being able to analyze TRs in PLINK2! See 221 for the remaining work that is needed.
* allow multiallelic variants in `transform` ([232](https://github.com/CAST-genomics/haptools/issues/232)) ([371415c](https://github.com/CAST-genomics/haptools/commit/371415cb9007522221ee800ab0c9570703aae6d4))
* support for python 3.11 ([207](https://github.com/CAST-genomics/haptools/issues/207)) ([8e01ed4](https://github.com/CAST-genomics/haptools/commit/8e01ed449e47eda6cf032504c9536b053f97d588))
Bug Fixes
* `UnboundLocalError` arising from headerless `.hap` files ([229](https://github.com/CAST-genomics/haptools/issues/229)) ([a499b0c](https://github.com/CAST-genomics/haptools/commit/a499b0cd294c7709f866c330f7ce7431320acfbd))
* bug where `Phenotypes.subset(inplace=True)` would raise an AttributeError ([226](https://github.com/CAST-genomics/haptools/issues/226)) ([cff6d9b](https://github.com/CAST-genomics/haptools/commit/cff6d9b0082a6170c7b0873b25445fd0915f9aab))
* convert `samples` argument in `Genotypes.read` into a set and fix `tr_harmonizer` bug arising when TRTools is also installed ([225](https://github.com/CAST-genomics/haptools/issues/225)) ([06cc273](https://github.com/CAST-genomics/haptools/commit/06cc273fb063d73ec65071c3807c76bf63f0d448))
* Not having 23 chromosomes in genotype blocks when 23 chromosomes listed in centromere file resulted in Value Error ([234](https://github.com/CAST-genomics/haptools/issues/234)) ([ef36798](https://github.com/CAST-genomics/haptools/commit/ef3679838e0e0193eefad2cacc37fc4d1b26715d))
Documentation
* fix example of `.blocks.det` to `.hap` conversion in API docs ([236](https://github.com/CAST-genomics/haptools/issues/236)) ([1ed9139](https://github.com/CAST-genomics/haptools/commit/1ed9139b5425c754256e1fc981259efbbde35d62))
* handle whitespace in blocks2hap example ([237](https://github.com/CAST-genomics/haptools/issues/237)) ([bbdacf8](https://github.com/CAST-genomics/haptools/commit/bbdacf8f53522237ea846ca1a8f2c59c978a1d7d))