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)

v0.1.2

0.1.2 (2023-02-02)

Bug Fixes

• add poetry readme to fix long_description when publishing to pypi (#177) (4050251)
• checkout in comment bot workflow for CD pipeline (#181) (9782d3d)
• checkout ref in comment bot from CD pipeline (#182) (e3b92f6)
• comment bot in CD pipeline (#180) (a2f66bd)
• indentation in checkout build (#183) (de431ab)

v0.1.1

0.1.1 (2023-02-02)

Documentation

• add dependency to conda env build (#175) (6626049)

v0.1.0

0.1.0 (2023-01-31)

Features

• a new --no-normalize parameter for simphenotype (#156) (24a0867)
• add --seed to simphenotype (#162) (9f7890a)
• change default verbosity to INFO (#157) (18ff090)
• github actions for publishing (#141) (5cf6f29)
• Significantly decreased runtime of simgenotype (#163) (de011d0)
• updated .vcf.gz output in simgenotype (#150) (f61f613)
• Updated simgenotype to allow only breakpoint generation (#167) (c0c3c97)

Bug Fixes

• Added an additional test file containing only autosome centromeres (#168) (ca220e7)
• Added utilization of logging class to karyogram and simgenotype (#159) (bcf778a)
• case where genotypes are all the same but heritability is specified in simphenotype (#145) (063b411)
• Fixed logic error in simgenotype and docs errors (#172) (18dd27f)
• issue where breakpoints weren't outputting (#144) (ff90bff)
• logging so that it doesn't affect the root logger (#154) (c1dc1ef)
• pin numpy to ensure a recent version of numpy (#151) (7c84a45)
• Update maps.rst (#170) (8ace893)

Documentation

• better showcase example files and their locations in simgenotype (#166) (6995407)
• updates for v0.1.0 (#171) (714142f)