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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
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add a `check_sorted()` method for the `data.Genotypes` class
#161
aryarm
closed
1 year ago
0
a flag for `simgenotype` that disables the extra FORMAT fields
#160
aryarm
closed
1 year ago
0
fix: Added utilization of logging class to karyogram and simgenotype
#159
mlamkin7
closed
1 year ago
0
fix: Implemented logging class and removed print statements simgenotype/karyogram
#158
mlamkin7
closed
1 year ago
0
feat: change default verbosity to INFO
#157
aryarm
closed
1 year ago
0
feat: a new `--no-normalize` parameter for `simphenotype`
#156
aryarm
closed
1 year ago
0
test: all examples in the docs
#155
aryarm
closed
1 year ago
1
fix: logging so that it doesn't affect the root logger
#154
aryarm
closed
1 year ago
0
test: hidden phasing property in `GenotypesPLINK` class
#153
aryarm
closed
1 year ago
0
refactor: `data.Phenotypes` samples parameter to be of type set
#152
aryarm
closed
1 year ago
0
fix: pin numpy to ensure a recent version of numpy
#151
aryarm
closed
1 year ago
0
feat: updated `.vcf.gz` output in simgenotype
#150
mlamkin7
closed
1 year ago
0
numpy error when testing `simgenotype`
#149
armartin
closed
1 year ago
3
VCF writing in simgenotype is very slow
#148
s041629
closed
1 year ago
3
feat: a `--no-normalize` flag for simphenotype
#147
aryarm
closed
1 year ago
1
chore: add pull request template
#146
aryarm
closed
2 years ago
0
fix: case where genotypes are all the same but heritability is specified in `simphenotype`
#145
aryarm
closed
1 year ago
0
fix: issue where breakpoints weren't outputting
#144
mlamkin7
closed
2 years ago
0
chore(main): release 0.1.0
#143
github-actions[bot]
closed
1 year ago
1
chore: test publishing github actions
#142
aryarm
closed
2 years ago
0
feat: github actions for publishing
#141
aryarm
closed
2 years ago
0
feat: github actions for testing
#140
aryarm
closed
2 years ago
0
fix: file reads and writes in py3.10+
#139
aryarm
closed
2 years ago
0
pgenlib/numpy binary incompatibility issue
#138
aryarm
closed
2 years ago
2
Feat/vcf output
#137
mlamkin7
closed
2 years ago
0
Removed brewer2mpl
#136
mlamkin7
closed
2 years ago
2
feat: new github actions
#135
aryarm
closed
2 years ago
0
dep: remove myst-parser
#134
aryarm
closed
2 years ago
0
dep: require <3.11 to resolve pysam install error
#133
aryarm
closed
2 years ago
0
Update sample_info.rst
#132
mlamkin7
closed
2 years ago
0
Update maps.rst
#131
mlamkin7
closed
2 years ago
0
Update maps.rst
#130
mlamkin7
closed
2 years ago
0
Update maps.rst
#129
mlamkin7
closed
2 years ago
0
Update models.rst
#128
mlamkin7
closed
2 years ago
0
Update simgenotype.rst
#127
mlamkin7
closed
2 years ago
0
docs: cleanup and improve descriptions
#126
aryarm
closed
2 years ago
0
improve docs
#125
aryarm
closed
2 years ago
1
feat: `Genotypes.check_maf()` method
#124
aryarm
closed
2 years ago
0
ref: use binary search in `Breakpoints.population_array()`
#123
aryarm
closed
2 years ago
0
test: ld and transform subcommands
#122
aryarm
closed
2 years ago
0
docs: update snp2hap example
#121
aryarm
closed
2 years ago
0
support for bgzipped and tabix-indexed map files
#120
aryarm
opened
2 years ago
1
fix: wideness of phenotype distribution
#119
aryarm
closed
2 years ago
0
describe logging and `--verbosity` better in the docs
#118
aryarm
closed
2 years ago
1
github actions and publishing releases
#117
aryarm
opened
2 years ago
1
Update sim_genotype.py
#116
mlamkin7
closed
2 years ago
0
dep: loosen pysam requirement
#115
aryarm
closed
2 years ago
1
fix: NaNs output by simphenotype
#114
aryarm
closed
2 years ago
0
loosen requirements for pysam
#113
aryarm
closed
2 years ago
0
Fixed END in header issue
#112
mlamkin7
closed
2 years ago
0
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