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CAST-genomics
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haptools
Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
https://haptools.readthedocs.io
MIT License
18
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4
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feat: support for Apple M1 silicon
#255
aryarm
closed
3 weeks ago
0
fix: 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
aryarm
closed
1 month ago
1
parallelize reading from a PGEN file
#253
aryarm
opened
3 months ago
0
chore(main): release 0.5.0
#252
github-actions[bot]
opened
3 months ago
0
chore(main): release 0.5.0
#251
github-actions[bot]
closed
3 months ago
1
feat: support for numpy 2.0
#250
aryarm
closed
3 months ago
0
ci: use trusted publishing with pypi
#249
aryarm
closed
3 months ago
0
chore(main): release 0.4.2
#248
github-actions[bot]
closed
3 months ago
1
ci: make sure release.yml is synced with dev-env.yml
#247
aryarm
closed
3 months ago
1
fix: disable numpy 2.0 since our dependencies don't yet work with it
#246
aryarm
closed
3 months ago
1
snplist support in the `ld` command
#245
aryarm
opened
3 months ago
0
ci: fix broken github actions
#244
aryarm
closed
3 months ago
0
ci: support for python 3.12
#243
aryarm
closed
7 months ago
1
Expanding population before simgenotype?
#242
KangchengHou
closed
7 months ago
3
chore(main): release 0.4.1
#241
github-actions[bot]
closed
3 months ago
1
docs: move google drive images to github
#240
aryarm
closed
8 months ago
1
docs: fix images
#239
aryarm
closed
8 months ago
1
build: try to fix broken releases action
#238
aryarm
closed
8 months ago
1
docs: handle whitespace in blocks2hap example
#237
aryarm
closed
8 months ago
0
docs: fix example of `.blocks.det` to `.hap` conversion in API docs
#236
aryarm
closed
8 months ago
2
Provided blocks.det to .hap code produces error
#235
RJDan
closed
8 months ago
7
fix: Not having 23 chromosomes in genotype blocks when 23 chromosomes listed in centromere file resulted in Value Error
#234
mlamkin7
closed
8 months ago
0
Error when using centromeres file for karyogram
#233
gymreklab
closed
8 months ago
0
feat: allow multiallelic variants in `transform`
#232
aryarm
closed
8 months ago
1
build: add codespace config
#231
aryarm
closed
9 months ago
2
feat: convert `samples` arg in `Genotypes` classes into a set
#230
aryarm
closed
9 months ago
2
fix: `UnboundLocalError` arising from headerless `.hap` files
#229
aryarm
closed
9 months ago
0
feat: add a parameter for reordering genotype samples directly after reading them
#228
aryarm
closed
9 months ago
2
build: add `filprofiler` as a dev dependency and upgrade pysam in lockfile
#227
aryarm
closed
11 months ago
0
fix: bug where `Phenotypes.subset(inplace=True)` would raise an AttributeError
#226
aryarm
closed
11 months ago
0
fix: convert `samples` argument in `Genotypes.read` into a set and fix `tr_harmonizer` bug arising when TRTools is also installed
#225
mlamkin7
closed
8 months ago
3
build: convert pgenlib from an optional to mandatory dependency
#224
aryarm
closed
11 months ago
0
chore(main): release 0.4.0
#223
github-actions[bot]
closed
8 months ago
1
feat: a new `GenotypesPLINKTR` class for reading TRs from PGEN files
#222
aryarm
closed
1 year ago
0
feat: a `dosage` command for storing TR motif counts in PGEN files
#221
aryarm
opened
1 year ago
2
feat: implement a new `validate` command
#220
Ayimany
opened
1 year ago
1
test: increase coverage of logging module
#219
gonzalogc1
closed
1 year ago
0
fix: explicitly ignore repeats in the `ld` command
#218
aryarm
closed
1 year ago
0
feat: `.snplist` input to `simphenotype`
#217
aryarm
closed
1 year ago
2
feat: simphenotype `--environment` option
#216
aryarm
closed
1 year ago
1
refactor: for new haptools release
#215
aryarm
closed
1 year ago
0
feat: Added ability to set vcftype for reading str files
#214
mlamkin7
closed
1 year ago
1
fix: check missing to check for 254
#213
mlamkin7
closed
1 year ago
0
fix: GenotypesTR to properly load repeat count instead of GT
#212
mlamkin7
closed
1 year ago
0
feat: Clump
#211
mlamkin7
closed
1 year ago
0
feat: a `Genotypes.merge_variants` method
#210
aryarm
closed
1 year ago
1
feat: Simphenotype and Index Repeat Support
#209
mlamkin7
closed
1 year ago
0
feat: do not require sorting `.hap` lines by line type
#208
aryarm
closed
1 year ago
2
feat: support for python 3.11
#207
aryarm
closed
8 months ago
2
fix: `Covariates.__init__` after updates to parent class
#206
aryarm
closed
1 year ago
0
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