Haptools

[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))

[0.3.0](https://github.com/CAST-genomics/haptools/compare/v0.2.1...v0.3.0) (2023-06-02)


Features

* `.snplist` input to `simphenotype` ([217](https://github.com/CAST-genomics/haptools/issues/217)) ([cb18970](https://github.com/CAST-genomics/haptools/commit/cb18970ca65ff8ee85dc83ea68c63af3c65fda59))
* Added ability to read tandem repeats with GenotypesTR ([204](https://github.com/CAST-genomics/haptools/issues/204)) ([6257264](https://github.com/CAST-genomics/haptools/commit/6257264c655752cac1324ebdd0387f1207c433d6))
* Added ability to set vcftype for reading str files ([214](https://github.com/CAST-genomics/haptools/issues/214)) ([0d734cd](https://github.com/CAST-genomics/haptools/commit/0d734cdd9235dca128af6d53fbf043f0f17511ee))
* Clump ([211](https://github.com/CAST-genomics/haptools/issues/211)) ([3740ec1](https://github.com/CAST-genomics/haptools/commit/3740ec108075594d3b43c81840600ac59283a940))
* do not require sorting `.hap` lines by line type ([208](https://github.com/CAST-genomics/haptools/issues/208)) ([f221397](https://github.com/CAST-genomics/haptools/commit/f2213979f66b954fa21e4ed8b953426f1736d9f8))
* new `Phenotypes.subset()` method ([203](https://github.com/CAST-genomics/haptools/issues/203)) ([c5594d9](https://github.com/CAST-genomics/haptools/commit/c5594d9b5d6455bd9a231f218610153117b2eec7))
* simphenotype `--environment` option ([216](https://github.com/CAST-genomics/haptools/issues/216)) ([bf69147](https://github.com/CAST-genomics/haptools/commit/bf69147f1e149d07d52adb6d407e5ec8a5e91ed3))
* Simphenotype and Index Repeat Support ([209](https://github.com/CAST-genomics/haptools/issues/209)) ([9e2ffe1](https://github.com/CAST-genomics/haptools/commit/9e2ffe1f432459ae424bf3c2cb5cdf4f78fb98dc))


Bug Fixes

* `Covariates.__init__` after updates to parent class ([206](https://github.com/CAST-genomics/haptools/issues/206)) ([ce2337b](https://github.com/CAST-genomics/haptools/commit/ce2337bfb5f295942dfee2e6d1bd482a440c1d5e))
* Added logic to finding all coord files ([201](https://github.com/CAST-genomics/haptools/issues/201)) ([be1d992](https://github.com/CAST-genomics/haptools/commit/be1d992d9a3d7651b05f66c968df354c2f71747e))
* check missing to check for 254 ([213](https://github.com/CAST-genomics/haptools/issues/213)) ([afeab85](https://github.com/CAST-genomics/haptools/commit/afeab85bb9b70e95ca937c253a57e5fa98599b22))
* explicitly ignore repeats in the `ld` command ([218](https://github.com/CAST-genomics/haptools/issues/218)) ([b9d0da1](https://github.com/CAST-genomics/haptools/commit/b9d0da13b7ff089ca31b8101a3b79de6806db224))
* GenotypesTR to properly load repeat count instead of GT ([212](https://github.com/CAST-genomics/haptools/issues/212)) ([93a4eb2](https://github.com/CAST-genomics/haptools/commit/93a4eb285dc2d556cc47033750723b8313a17934))

[0.2.1](https://github.com/CAST-genomics/haptools/compare/v0.2.0...v0.2.1) (2023-03-22)


Bug Fixes

* NoneType error in `Haplotypes.__iter__` ([197](https://github.com/CAST-genomics/haptools/issues/197)) ([aade751](https://github.com/CAST-genomics/haptools/commit/aade751001fb7f008382d246663dfee68886d6c6))
* precision of phenotypes written to pheno file ([199](https://github.com/CAST-genomics/haptools/issues/199)) ([a397c96](https://github.com/CAST-genomics/haptools/commit/a397c964d80c6a1a947458a1f1b0393974ae7102))

[0.2.0](https://github.com/CAST-genomics/haptools/compare/v0.1.3...v0.2.0) (2023-03-06)


Features

* `Phenotypes.check missing()` method ([191](https://github.com/CAST-genomics/haptools/issues/191)) ([621fc62](https://github.com/CAST-genomics/haptools/commit/621fc624d8b58223349767139ddd93bab6d622d3))
* Sampling without replacement option for simgenotype ([194](https://github.com/CAST-genomics/haptools/issues/194)) ([85bd494](https://github.com/CAST-genomics/haptools/commit/85bd4946fe70e72d8e18175cc9b19acbd9e39299))


Bug Fixes

* Fixed faulty coord file parsing logic ([196](https://github.com/CAST-genomics/haptools/issues/196)) ([f9819b1](https://github.com/CAST-genomics/haptools/commit/f9819b15416eb1c596f8e84167f1336f6885fdd6))
* regression in multiallelic support for `simgenotype` ([195](https://github.com/CAST-genomics/haptools/issues/195)) ([b57f91f](https://github.com/CAST-genomics/haptools/commit/b57f91fcd519845de23ce731648278bec6e3d056))


Documentation

* describe how to add to our CLI ([193](https://github.com/CAST-genomics/haptools/issues/193)) ([2056c7e](https://github.com/CAST-genomics/haptools/commit/2056c7e8488fdb5b2c3e47c10b98e8428fa0f07a))

[0.1.3](https://github.com/CAST-genomics/haptools/compare/v0.1.2...v0.1.3) (2023-02-10)


Bug Fixes

* build workflow for comment bot ([186](https://github.com/CAST-genomics/haptools/issues/186)) ([ebcf6cd](https://github.com/CAST-genomics/haptools/commit/ebcf6cd508701951ce2f1785eb3bcfee6aa69041))
* comment bot in build pipeline ([184](https://github.com/CAST-genomics/haptools/issues/184)) ([b3fb839](https://github.com/CAST-genomics/haptools/commit/b3fb83939c6ec9141dc9c0d9b89836cfe0fee394))


Documentation

* warn about pysam pip issue ([187](https://github.com/CAST-genomics/haptools/issues/187)) ([bda0157](https://github.com/CAST-genomics/haptools/commit/bda015751dc5e5aa5d3672e77737d837cd116782))

Dependencies
* we now require Pgenlib>=0.81.3 (resolves 138)

[0.1.2](https://github.com/CAST-genomics/haptools/compare/v0.1.1...v0.1.2) (2023-02-02)


Bug Fixes

* add poetry readme to fix long_description when publishing to pypi ([177](https://github.com/CAST-genomics/haptools/issues/177)) ([4050251](https://github.com/CAST-genomics/haptools/commit/405025161ef99b7c18c6adddb58d74bbcff93570))
* checkout in comment bot workflow for CD pipeline ([181](https://github.com/CAST-genomics/haptools/issues/181)) ([9782d3d](https://github.com/CAST-genomics/haptools/commit/9782d3d5826a7029a74fb845dbfff29a7a0e8f2d))
* checkout ref in comment bot from CD pipeline ([182](https://github.com/CAST-genomics/haptools/issues/182)) ([e3b92f6](https://github.com/CAST-genomics/haptools/commit/e3b92f6ba2764819d9936c7e37418bcd68469dfb))
* comment bot in CD pipeline ([180](https://github.com/CAST-genomics/haptools/issues/180)) ([a2f66bd](https://github.com/CAST-genomics/haptools/commit/a2f66bd74dfb1fae8a81614912cba35366fe003b))
* indentation in checkout build ([183](https://github.com/CAST-genomics/haptools/issues/183)) ([de431ab](https://github.com/CAST-genomics/haptools/commit/de431ab65a15f4dda2e7b6319608331b73ee5771))