Changelog

0.4.2 (2024-06-14)

Bug Fixes

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

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)

0.4.0 (2024-01-14)

Features

a new GenotypesPLINKTR class for reading TRs from PGEN files (#222) (3c7abe6)
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)

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)

0.2.1 (2023-03-22)

Bug Fixes

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

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)

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)

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)

0.1.1 (2023-02-02)

Documentation

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

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)