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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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increase our testing coverage
#205
aryarm
opened
1 year ago
0
feat: Added ability to read tandem repeats with GenotypesTR
#204
mlamkin7
closed
1 year ago
0
feat: new `Phenotypes.subset()` method
#203
aryarm
closed
1 year ago
0
chore(main): release 0.3.0
#202
github-actions[bot]
closed
1 year ago
1
fix: Added logic to finding all coord files
#201
mlamkin7
closed
1 year ago
0
test: phenotype writing
#200
aryarm
closed
1 year ago
0
fix: precision of phenotypes written to pheno file
#199
aryarm
closed
1 year ago
0
chore(main): release 0.2.1
#198
github-actions[bot]
closed
1 year ago
1
fix: NoneType error in `Haplotypes.__iter__`
#197
aryarm
closed
1 year ago
0
fix: Fixed faulty coord file parsing logic
#196
mlamkin7
closed
1 year ago
0
fix: regression in multiallelic support for `simgenotype`
#195
aryarm
closed
1 year ago
4
feat: Sampling without replacement option for simgenotype
#194
mlamkin7
closed
1 year ago
0
docs: describe how to add to our CLI
#193
aryarm
closed
1 year ago
1
chore(main): release 0.2.0
#192
github-actions[bot]
closed
1 year ago
1
feat: `Phenotypes.check missing()` method
#191
aryarm
closed
1 year ago
0
feat: code to sample genetic data from input VCF without replacement
#190
amythewilliams
closed
1 year ago
2
build: update to pgenlib v0.81.3
#189
aryarm
closed
1 year ago
0
test: loosen requirements for tbi files output by the `index` command
#188
aryarm
closed
1 year ago
0
docs: warn about pysam pip issue
#187
aryarm
closed
1 year ago
0
fix: build workflow for comment bot
#186
aryarm
closed
1 year ago
1
chore(main): release 0.1.3
#185
github-actions[bot]
closed
1 year ago
3
fix: comment bot in build pipeline
#184
aryarm
closed
1 year ago
0
fix: indentation in checkout build
#183
aryarm
closed
1 year ago
0
fix: checkout ref in comment bot from CD pipeline
#182
aryarm
closed
1 year ago
0
fix: checkout in comment bot workflow for CD pipeline
#181
aryarm
closed
1 year ago
0
fix: comment bot in CD pipeline
#180
aryarm
closed
1 year ago
0
build: create bot to check PR comments
#179
aryarm
closed
1 year ago
2
chore(main): release 0.1.2
#178
github-actions[bot]
closed
1 year ago
6
fix: add poetry readme to fix long_description when publishing to pypi
#177
aryarm
closed
1 year ago
0
chore(main): release 0.1.1
#176
github-actions[bot]
closed
1 year ago
1
docs: add dependency to conda env build
#175
aryarm
closed
1 year ago
0
build: bump the version of poetry used in our CD pipeline
#174
aryarm
closed
1 year ago
0
build!: upgrade to poetry v1.3.2, remove py3.7 support
#173
aryarm
closed
1 year ago
0
fix: Fixed logic error in simgenotype and docs errors
#172
mlamkin7
closed
1 year ago
0
docs: updates for v0.1.0
#171
aryarm
closed
1 year ago
0
fix: Update maps.rst
#170
mlamkin7
closed
1 year ago
0
docs: updates ahead of v0.1.0
#169
aryarm
closed
1 year ago
0
fix: Added an additional test file containing only autosome centromeres
#168
mlamkin7
closed
1 year ago
0
feat: Updated simgenotype to allow only breakpoint generation
#167
mlamkin7
closed
1 year ago
0
docs: better showcase example files and their locations in `simgenotype`
#166
mlamkin7
closed
1 year ago
0
refactor: reduce memory use in GenotypesPLINK
#165
aryarm
closed
1 year ago
0
support for a TR-based Haplotype class
#164
aryarm
closed
1 year ago
2
feat: Significantly decreased runtime of simgenotype
#163
mlamkin7
closed
1 year ago
0
feat: add `--seed` to `simphenotype`
#162
aryarm
closed
1 year ago
0
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
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