v0.6.2

0.6.2 (2025-12-15)

Documentation

• refer to release-please docs for help debugging releases (#282) (99f3fa3)

v0.6.0

0.6.0 (2025-12-10)

Features

• --maf option for filtering output of transform command (#274) (cf4219f)
• add --chunk-size parameter to simgenotype and fix RuntimeError when reference coordinates extend past the final map file coordinate (#268) (4c22846)
• use chunking when reading from PGENs in simgenotype (#270) (5ae546d)

Performance Improvements

• use less memory when loading specific regions from PVAR files and exit quickly once a specific set of variants have been found (#275) (aa24abf)

v0.5.0

0.5.0 (2024-12-11)

Features

• a new Haplotypes.merge() method (#256) (cf4ccb2)
• allow for specifying the order of population labels in Breakpoints.encode() (#262) (09a916a)
• allow multiple variants in pearson_corr_ld() (#258) (808c31e)
• support for Apple M1 silicon (#255) (3f055ac)
• support for numpy 2.0 (#250) (69192d0)

Bug Fixes

• 1. improve error in transform when providing an empty hap file and a --region and 2) allow for calling write() on Genotypes objects without variants (#264) (4e84178)
• allow simphenotype to accept TR PGENs without --repeats (#263) (16a84d1)
• issue warnings instead of errors when trying to check the header of hap files and issue error when output of transform is not provided to simphenotype (#254) (0226653)
• load an empty array if there are no variants in GenotypesVCF.read (#257) (9eedc3a)

Documentation

• creating an .hanc file from a .bp file (#260) (b6dcd0c)

v0.4.2

0.4.2 (2024-06-14)

Bug Fixes

• mention that versions must be synced in CI/CD (35e14c0)

v0.4.1

0.4.1 (2024-06-13)

Bug Fixes

• disable numpy 2.0 since our dependencies don't yet work with it (#246) (7f646b2)

Documentation

• move google drive images to github (#240) (e8b60c0)

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)

v0.3.0

0.3.0 (2023-06-02)

Features

• .snplist input to simphenotype (#217) (cb18970)
• Added ability to read tandem repeats with GenotypesTR (#204) (6257264)
• Added ability to set vcftype for reading str files (#214) (0d734cd)
• Clump (#211) (3740ec1)
• do not require sorting .hap lines by line type (#208) (f221397)
• new Phenotypes.subset() method (#203) (c5594d9)
• simphenotype --environment option (#216) (bf69147)
• Simphenotype and Index Repeat Support (#209) (9e2ffe1)

Bug Fixes

• Covariates.__init__ after updates to parent class (#206) (ce2337b)
• Added logic to finding all coord files (#201) (be1d992)
• check missing to check for 254 (#213) (afeab85)
• explicitly ignore repeats in the ld command (#218) (b9d0da1)
• GenotypesTR to properly load repeat count instead of GT (#212) (93a4eb2)

v0.2.1

0.2.1 (2023-03-22)

Bug Fixes

• NoneType error in Haplotypes.__iter__ (#197) (aade751)
• precision of phenotypes written to pheno file (#199) (a397c96)

v0.2.0

0.2.0 (2023-03-06)

Features

• Phenotypes.check missing() method (#191) (621fc62)
• Sampling without replacement option for simgenotype (#194) (85bd494)

Bug Fixes

• Fixed faulty coord file parsing logic (#196) (f9819b1)
• regression in multiallelic support for simgenotype (#195) (b57f91f)

Documentation

• describe how to add to our CLI (#193) (2056c7e)

v0.1.3

0.1.3 (2023-02-10)

Bug Fixes

• build workflow for comment bot (#186) (ebcf6cd)
• comment bot in build pipeline (#184) (b3fb839)

Documentation

• warn about pysam pip issue (#187) (bda0157)

Dependencies

• we now require Pgenlib>=0.81.3 (resolves #138)