Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / CAST-genomics/haptools issues and pull requests

#255 - feat: support for Apple M1 silicon

Pull Request - State: closed - Opened by aryarm 3 months ago

#253 - parallelize reading from a PGEN file

Issue - State: open - Opened by aryarm 5 months ago

#252 - chore(main): release 0.5.0

Pull Request - State: open - Opened by github-actions[bot] 5 months ago
Labels: autorelease: pending

#251 - chore(main): release 0.5.0

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: pending

#250 - feat: support for numpy 2.0

Pull Request - State: closed - Opened by aryarm 5 months ago

#249 - ci: use trusted publishing with pypi

Pull Request - State: closed - Opened by aryarm 5 months ago

#248 - chore(main): release 0.4.2

Pull Request - State: closed - Opened by github-actions[bot] 5 months ago - 1 comment
Labels: autorelease: tagged

#247 - ci: make sure release.yml is synced with dev-env.yml

Pull Request - State: closed - Opened by aryarm 5 months ago - 1 comment

#246 - fix: disable numpy 2.0 since our dependencies don't yet work with it

Pull Request - State: closed - Opened by aryarm 6 months ago - 1 comment

#245 - snplist support in the `ld` command

Issue - State: open - Opened by aryarm 6 months ago

#244 - ci: fix broken github actions

Pull Request - State: closed - Opened by aryarm 6 months ago

#243 - ci: support for python 3.12

Pull Request - State: closed - Opened by aryarm 10 months ago - 1 comment

#242 - Expanding population before simgenotype?

Issue - State: closed - Opened by KangchengHou 10 months ago - 3 comments

#241 - chore(main): release 0.4.1

Pull Request - State: closed - Opened by github-actions[bot] 10 months ago - 1 comment
Labels: autorelease: tagged

#240 - docs: move google drive images to github

Pull Request - State: closed - Opened by aryarm 10 months ago - 1 comment

#239 - docs: fix images

Issue - State: closed - Opened by aryarm 10 months ago - 1 comment

#238 - build: try to fix broken releases action

Pull Request - State: closed - Opened by aryarm 10 months ago - 1 comment

#237 - docs: handle whitespace in blocks2hap example

Pull Request - State: closed - Opened by aryarm 10 months ago

#236 - docs: fix example of `.blocks.det` to `.hap` conversion in API docs

Pull Request - State: closed - Opened by aryarm 11 months ago - 2 comments

#235 - Provided blocks.det to .hap code produces error

Issue - State: closed - Opened by RJDan 11 months ago - 7 comments

#233 - Error when using centromeres file for karyogram

Issue - State: closed - Opened by gymreklab 11 months ago

#232 - feat: allow multiallelic variants in `transform`

Pull Request - State: closed - Opened by aryarm 11 months ago - 1 comment

#231 - build: add codespace config

Pull Request - State: closed - Opened by aryarm 11 months ago - 2 comments

#230 - feat: convert `samples` arg in `Genotypes` classes into a set

Pull Request - State: closed - Opened by aryarm 12 months ago - 2 comments

#229 - fix: `UnboundLocalError` arising from headerless `.hap` files

Pull Request - State: closed - Opened by aryarm 12 months ago

#228 - feat: add a parameter for reordering genotype samples directly after reading them

Pull Request - State: closed - Opened by aryarm about 1 year ago - 2 comments

#224 - build: convert pgenlib from an optional to mandatory dependency

Pull Request - State: closed - Opened by aryarm about 1 year ago

#223 - chore(main): release 0.4.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment
Labels: autorelease: tagged

#222 - feat: a new `GenotypesPLINKTR` class for reading TRs from PGEN files

Pull Request - State: closed - Opened by aryarm about 1 year ago

#221 - feat: a `dosage` command for storing TR motif counts in PGEN files

Issue - State: open - Opened by aryarm about 1 year ago - 2 comments
Labels: enhancement

#220 - feat: implement a new `validate` command

Pull Request - State: open - Opened by Ayimany over 1 year ago - 1 comment

#219 - test: increase coverage of logging module

Pull Request - State: closed - Opened by gonzalogc1 over 1 year ago

#214 - feat: Added ability to set vcftype for reading str files

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago - 1 comment

#213 - fix: check missing to check for 254

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#212 - fix: GenotypesTR to properly load repeat count instead of GT

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#211 - feat: Clump

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#210 - feat: a `Genotypes.merge_variants` method

Pull Request - State: closed - Opened by aryarm over 1 year ago - 1 comment

#209 - feat: Simphenotype and Index Repeat Support

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#208 - feat: do not require sorting `.hap` lines by line type

Pull Request - State: closed - Opened by aryarm over 1 year ago - 2 comments
Labels: refactor

#207 - feat: support for python 3.11

Pull Request - State: closed - Opened by aryarm over 1 year ago - 2 comments

#206 - fix: `Covariates.__init__` after updates to parent class

Pull Request - State: closed - Opened by aryarm over 1 year ago

#205 - increase our testing coverage

Issue - State: open - Opened by aryarm over 1 year ago

#204 - feat: Added ability to read tandem repeats with GenotypesTR

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#203 - feat: new `Phenotypes.subset()` method

Pull Request - State: closed - Opened by aryarm over 1 year ago

#202 - chore(main): release 0.3.0

Pull Request - State: open - Opened by github-actions[bot] over 1 year ago
Labels: autorelease: pending

#201 - fix: Added logic to finding all coord files

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#200 - test: phenotype writing

Pull Request - State: closed - Opened by aryarm over 1 year ago

#199 - fix: precision of phenotypes written to pheno file

Pull Request - State: closed - Opened by aryarm over 1 year ago

#198 - chore(main): release 0.2.1

Pull Request - State: closed - Opened by github-actions[bot] over 1 year ago - 1 comment
Labels: autorelease: tagged

#197 - fix: NoneType error in `Haplotypes.__iter__`

Pull Request - State: closed - Opened by aryarm over 1 year ago

#196 - fix: Fixed faulty coord file parsing logic

Pull Request - State: closed - Opened by mlamkin7 over 1 year ago

#195 - fix: regression in multiallelic support for `simgenotype`

Pull Request - State: closed - Opened by aryarm over 1 year ago - 4 comments

#194 - feat: Sampling without replacement option for simgenotype

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#193 - docs: describe how to add to our CLI

Pull Request - State: closed - Opened by aryarm almost 2 years ago - 1 comment

#192 - chore(main): release 0.2.0

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#191 - feat: `Phenotypes.check missing()` method

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#190 - feat: code to sample genetic data from input VCF without replacement

Pull Request - State: closed - Opened by amythewilliams almost 2 years ago - 2 comments

#189 - build: update to pgenlib v0.81.3

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#188 - test: loosen requirements for tbi files output by the `index` command

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#187 - docs: warn about pysam pip issue

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#186 - fix: build workflow for comment bot

Pull Request - State: closed - Opened by aryarm almost 2 years ago - 1 comment

#185 - chore(main): release 0.1.3

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 3 comments
Labels: autorelease: tagged

#184 - fix: comment bot in build pipeline

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#183 - fix: indentation in checkout build

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#182 - fix: checkout ref in comment bot from CD pipeline

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#181 - fix: checkout in comment bot workflow for CD pipeline

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#180 - fix: comment bot in CD pipeline

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#179 - build: create bot to check PR comments

Pull Request - State: closed - Opened by aryarm almost 2 years ago - 2 comments

#178 - chore(main): release 0.1.2

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 6 comments
Labels: autorelease: tagged

#177 - fix: add poetry readme to fix long_description when publishing to pypi

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#176 - chore(main): release 0.1.1

Pull Request - State: closed - Opened by github-actions[bot] almost 2 years ago - 1 comment
Labels: autorelease: tagged

#175 - docs: add dependency to conda env build

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#174 - build: bump the version of poetry used in our CD pipeline

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#173 - build!: upgrade to poetry v1.3.2, remove py3.7 support

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#172 - fix: Fixed logic error in simgenotype and docs errors

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#171 - docs: updates for v0.1.0

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#170 - fix: Update maps.rst

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#169 - docs: updates ahead of v0.1.0

Issue - State: closed - Opened by aryarm almost 2 years ago

#168 - fix: Added an additional test file containing only autosome centromeres

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#167 - feat: Updated simgenotype to allow only breakpoint generation

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#166 - docs: better showcase example files and their locations in `simgenotype`

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#165 - refactor: reduce memory use in GenotypesPLINK

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#164 - support for a TR-based Haplotype class

Issue - State: closed - Opened by aryarm almost 2 years ago - 2 comments

#163 - feat: Significantly decreased runtime of simgenotype

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#162 - feat: add `--seed` to `simphenotype`

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#161 - add a `check_sorted()` method for the `data.Genotypes` class

Issue - State: closed - Opened by aryarm almost 2 years ago

#160 - a flag for `simgenotype` that disables the extra FORMAT fields

Issue - State: closed - Opened by aryarm almost 2 years ago

#159 - fix: Added utilization of logging class to karyogram and simgenotype

Pull Request - State: closed - Opened by mlamkin7 almost 2 years ago

#157 - feat: change default verbosity to INFO

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#156 - feat: a new `--no-normalize` parameter for `simphenotype`

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#155 - test: all examples in the docs

Pull Request - State: closed - Opened by aryarm almost 2 years ago - 1 comment

#154 - fix: logging so that it doesn't affect the root logger

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#153 - test: hidden phasing property in `GenotypesPLINK` class

Pull Request - State: closed - Opened by aryarm almost 2 years ago

#152 - refactor: `data.Phenotypes` samples parameter to be of type set

Pull Request - State: closed - Opened by aryarm almost 2 years ago