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

#151 - fix: pin numpy to ensure a recent version of numpy

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

#150 - feat: updated `.vcf.gz` output in simgenotype

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

#149 - numpy error when testing `simgenotype`

Issue - State: closed - Opened by armartin almost 2 years ago - 3 comments

#148 - VCF writing in simgenotype is very slow

Issue - State: closed - Opened by s041629 almost 2 years ago - 3 comments
Labels: enhancement, idea, large-files

#147 - feat: a `--no-normalize` flag for simphenotype

Issue - State: closed - Opened by aryarm about 2 years ago - 1 comment
Labels: enhancement

#146 - chore: add pull request template

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

#144 - fix: issue where breakpoints weren't outputting

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

#143 - chore(main): release 0.1.0

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

#142 - chore: test publishing github actions

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

#141 - feat: github actions for publishing

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

#140 - feat: github actions for testing

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

#139 - fix: file reads and writes in py3.10+

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

#138 - pgenlib/numpy binary incompatibility issue

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

#137 - Feat/vcf output

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

#136 - Removed brewer2mpl

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

#135 - feat: new github actions

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

#134 - dep: remove myst-parser

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

#133 - dep: require <3.11 to resolve pysam install error

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

#132 - Update sample_info.rst

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

#131 - Update maps.rst

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

#130 - Update maps.rst

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

#129 - Update maps.rst

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

#126 - docs: cleanup and improve descriptions

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

#125 - improve docs

Issue - State: closed - Opened by aryarm about 2 years ago - 1 comment

#117 - github actions and publishing releases

Issue - State: open - Opened by aryarm about 2 years ago - 1 comment
Labels: enhancement

#105 - feat: use bp file in `transform`

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

#99 - PGEN support for `simgenotype`

Issue - State: closed - Opened by aryarm about 2 years ago - 5 comments
Labels: enhancement

#95 - genotypes that are all the same can lead to 0s in `simphenotype`

Issue - State: closed - Opened by aryarm about 2 years ago - 2 comments
Labels: bug

#92 - speeding up the `transform` command

Issue - State: open - Opened by aryarm about 2 years ago - 6 comments
Labels: enhancement, help wanted, idea

#82 - feat: add a command or parameter to allow merging of haplotype and genotype VCFs

Issue - State: closed - Opened by aryarm over 2 years ago - 4 comments
Labels: documentation, enhancement

#81 - tests: exception verification in sim_genotype

Pull Request - State: closed - Opened by ciarareeve over 2 years ago

#73 - support for a TR-based GenotypesPLINK class

Issue - State: closed - Opened by aryarm over 2 years ago - 2 comments
Labels: enhancement, idea

#59 - minor cleanups to simgenotype output messages

Pull Request - State: closed - Opened by gymreklab over 2 years ago

#49 - a new strategy for classes in the data module

Issue - State: closed - Opened by aryarm over 2 years ago - 1 comment
Labels: refactor, idea

#47 - feat: a `validate` subcommand to check whether a `.hap` file is valid

Issue - State: open - Opened by aryarm over 2 years ago - 3 comments
Labels: enhancement

#38 - We need a documentation page about our file formats

Issue - State: closed - Opened by gymreklab over 2 years ago - 1 comment
Labels: documentation

#36 - catching user errors in karyogram

Pull Request - State: closed - Opened by gymreklab over 2 years ago

#19 - improvements to the Data module

Issue - State: open - Opened by aryarm over 2 years ago - 2 comments
Labels: enhancement

#4 - add interaction terms

Issue - State: open - Opened by aryarm over 3 years ago - 1 comment
Labels: enhancement