sgkit-dev/sgkit issues and pull requests

#1150 - read_plink from cloud storage

Issue - State: open - Opened by hammer 10 months ago - 1 comment
Labels: IO

#1149 - read_plink failing with 0.7.0 release

Issue - State: closed - Opened by hammer 10 months ago - 5 comments
Labels: bug, IO, upstream

#1148 - Format matrix in pairwise docs

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment
Labels: auto-merge

#1148 - Format matrix in pairwise docs

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment
Labels: auto-merge

#1147 - Improve formatting in the `pairwise_distance` docs

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

#1146 - Methods doc categories

Pull Request - State: closed - Opened by benjeffery 10 months ago - 9 comments
Labels: auto-merge

#1146 - Methods doc categories

Pull Request - State: closed - Opened by benjeffery 10 months ago - 9 comments
Labels: auto-merge

#1145 - Add pairwise_distance to docs

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment
Labels: auto-merge

#1145 - Add pairwise_distance to docs

Pull Request - State: closed - Opened by benjeffery 10 months ago - 1 comment
Labels: auto-merge

#1142 - pairwise_distance not in documented API

Issue - State: closed - Opened by jeromekelleher 11 months ago - 3 comments

#1141 - Add pickleshare as docs requirement to satisfy Sphinx

Pull Request - State: closed - Opened by tomwhite 11 months ago
Labels: auto-merge

#1141 - Add pickleshare as docs requirement to satisfy Sphinx

Pull Request - State: closed - Opened by tomwhite 11 months ago
Labels: auto-merge

#1140 - Sphinx build is failing

Issue - State: closed - Opened by tomwhite 11 months ago
Labels: upstream

#1140 - Sphinx build is failing

Issue - State: closed - Opened by tomwhite 11 months ago
Labels: upstream

#1139 - Add gene-drop simulation method

Pull Request - State: closed - Opened by timothymillar 12 months ago - 9 comments
Labels: auto-merge

#1139 - Add gene-drop simulation method

Pull Request - State: closed - Opened by timothymillar 12 months ago - 9 comments
Labels: auto-merge

#1138 - Prevent parts of VCF being reparsed

Pull Request - State: open - Opened by benjeffery 12 months ago - 9 comments

#1138 - Prevent parts of VCF being reparsed

Pull Request - State: closed - Opened by benjeffery 12 months ago - 10 comments

#1136 - Remove Python 3.8 on Windows from mergify config

Pull Request - State: closed - Opened by tomwhite 12 months ago - 1 comment
Labels: auto-merge

#1136 - Remove Python 3.8 on Windows from mergify config

Pull Request - State: closed - Opened by tomwhite 12 months ago - 1 comment
Labels: auto-merge

#1134 - Mergify has stopped working

Issue - State: closed - Opened by tomwhite 12 months ago - 1 comment
Labels: process + tools

#1134 - Mergify has stopped working

Issue - State: closed - Opened by tomwhite 12 months ago - 1 comment
Labels: process + tools

#1133 - Use Xarray's `map_blocks` rather than Dask's

Issue - State: open - Opened by tomwhite about 1 year ago
Labels: dispatching

#1133 - Use Xarray's `apply_ufunc` rather than Dask's `map_blocks`

Issue - State: open - Opened by tomwhite about 1 year ago - 1 comment
Labels: dispatching

#1132 - Skip parts of a VCF that have already been done

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

#1132 - Skip parts of a VCF that have already been done

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

#1131 - Single-step VCF to Zarr conversion

Issue - State: open - Opened by tomwhite about 1 year ago
Labels: IO

#1131 - Single-step VCF to Zarr conversion

Issue - State: open - Opened by tomwhite about 1 year ago
Labels: IO

#1130 - Alternative execution engines for VCF conversion

Issue - State: open - Opened by tomwhite about 1 year ago - 5 comments
Labels: IO

#1129 - Fix memory leak (see cyvcf2 #280)

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 9 comments

#1129 - Fix memory leak (see cyvcf2 #280)

Pull Request - State: closed - Opened by benjeffery about 1 year ago - 9 comments

#1128 - Docs: what is the cost of ``read_chunk_length`` in vcf_to_zare

Issue - State: open - Opened by jeromekelleher about 1 year ago - 4 comments

#1128 - Docs: what is the cost of ``read_chunk_length`` in vcf_to_zare

Issue - State: open - Opened by jeromekelleher about 1 year ago - 4 comments

#1127 - Can we use KvikIO?

Issue - State: open - Opened by hammer about 1 year ago
Labels: IO

#1127 - Can we use KvikIO?

Issue - State: open - Opened by hammer about 1 year ago
Labels: IO

#1126 - Docs: favicon not set?

Issue - State: open - Opened by jeromekelleher about 1 year ago - 1 comment
Labels: documentation, enhancement

#1126 - Docs: favicon not set?

Issue - State: open - Opened by jeromekelleher about 1 year ago - 1 comment
Labels: documentation, enhancement

#1125 - Docs: how do I update a dataset on file?

Issue - State: open - Opened by jeromekelleher about 1 year ago - 3 comments
Labels: documentation

#1123 - Utilities to help with and/or automatically select VCF ingestion parameters

Issue - State: open - Opened by benjeffery about 1 year ago - 1 comment
Labels: IO

#1123 - Utilities to help with and/or automatically select VCF ingestion parameters

Issue - State: open - Opened by benjeffery about 1 year ago - 1 comment
Labels: IO

#1122 - Fix main build and windows build

Pull Request - State: closed - Opened by tomwhite about 1 year ago - 4 comments
Labels: auto-merge

#1122 - Fix main build and windows build

Pull Request - State: closed - Opened by tomwhite about 1 year ago - 4 comments
Labels: auto-merge

#1121 - Main build is failing with Pandas 2.1.0

Issue - State: closed - Opened by tomwhite about 1 year ago
Labels: process + tools, upstream

#1121 - Main build is failing with Pandas 2.1.0

Issue - State: closed - Opened by tomwhite about 1 year ago
Labels: process + tools, upstream

#1119 - Improve performance of `variant_stats`

Pull Request - State: closed - Opened by timothymillar about 1 year ago - 11 comments
Labels: auto-merge

#1119 - Improve performance of `variant_stats`

Pull Request - State: closed - Opened by timothymillar about 1 year ago - 11 comments
Labels: auto-merge

#1117 - "show source" for function in docs shows rst code

Issue - State: open - Opened by jeromekelleher about 1 year ago
Labels: documentation

#1116 - Compute variables in variant_stats concurrently

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 9 comments
Labels: performance

#1116 - Compute variables in variant_stats concurrently

Issue - State: closed - Opened by jeromekelleher about 1 year ago - 9 comments
Labels: performance

#1114 - Basic CLI structure

Issue - State: closed - Opened by jeromekelleher about 1 year ago

#1112 - Validation build is failing

Issue - State: open - Opened by hammer about 1 year ago
Labels: process + tools

#1112 - Validation build is failing

Issue - State: open - Opened by hammer about 1 year ago
Labels: process + tools

#1111 - Update minimum Dask dependency versions

Pull Request - State: closed - Opened by tomwhite about 1 year ago - 5 comments

#1111 - Update minimum Dask dependency versions

Pull Request - State: closed - Opened by tomwhite about 1 year ago - 5 comments

#1110 - Upstream build is failing

Issue - State: closed - Opened by tomwhite about 1 year ago - 1 comment
Labels: upstream

#1109 - Windows build is failing

Issue - State: closed - Opened by tomwhite about 1 year ago - 2 comments
Labels: upstream

#1109 - Windows build is failing

Issue - State: closed - Opened by tomwhite about 1 year ago - 2 comments
Labels: upstream

#1107 - Gene-drop estimation of genotype probabilities

Issue - State: closed - Opened by timothymillar about 1 year ago - 6 comments

#1107 - Gene-drop estimation of genotype probabilities

Issue - State: closed - Opened by timothymillar about 1 year ago - 6 comments

#1104 - Add `display_pedigree` method

Pull Request - State: closed - Opened by timothymillar about 1 year ago - 4 comments
Labels: auto-merge

#1104 - Add `display_pedigree` method

Pull Request - State: closed - Opened by timothymillar about 1 year ago - 4 comments
Labels: auto-merge

#1101 - Use contig_id and filter_id arrays instead of attributes in write_vcf

Issue - State: open - Opened by timothymillar about 1 year ago - 1 comment
Labels: bug

#1097 - Pedigree visualisation

Issue - State: closed - Opened by timothymillar over 1 year ago - 3 comments

#1097 - Pedigree visualisation

Issue - State: closed - Opened by timothymillar over 1 year ago - 3 comments

#1090 - `vcf_to_zarr` creates zero-sized first chunk which results in incorrect dtype.

Issue - State: open - Opened by benjeffery over 1 year ago - 8 comments
Labels: bug, upstream

#1081 - Benchmarks have stopped working

Issue - State: open - Opened by tomwhite over 1 year ago - 1 comment
Labels: process + tools

#1081 - Benchmarks have stopped working

Issue - State: open - Opened by tomwhite over 1 year ago - 1 comment
Labels: process + tools

#1080 - Test on Python 3.11

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 3 comments
Labels: auto-merge, upstream

#1080 - Test on Python 3.11

Pull Request - State: closed - Opened by tomwhite over 1 year ago - 3 comments
Labels: auto-merge, upstream

#1057 - Copy contigs from attribute to array in `load_dataset`

Issue - State: open - Opened by tomwhite over 1 year ago
Labels: IO

#1051 - Tests should use process-based dask

Issue - State: open - Opened by benjeffery over 1 year ago - 3 comments

#915 - Test on Python 3.11

Issue - State: closed - Opened by tomwhite about 2 years ago - 1 comment
Labels: process + tools

#915 - Test on Python 3.11

Issue - State: closed - Opened by tomwhite about 2 years ago - 1 comment
Labels: process + tools

#910 - Logging from vcf_to_zarr

Issue - State: open - Opened by jeromekelleher about 2 years ago - 2 comments
Labels: enhancement

#910 - Logging from vcf_to_zarr

Issue - State: open - Opened by jeromekelleher about 2 years ago - 2 comments
Labels: enhancement

#908 - Run on Cubed

Issue - State: open - Opened by tomwhite about 2 years ago - 5 comments
Labels: dispatching

#892 - Add mean imputation function

Pull Request - State: open - Opened by tszfungc about 2 years ago - 9 comments
Labels: conflict

#687 - Provide progress bar for `vcf_to_zarr`

Issue - State: closed - Opened by hammer about 3 years ago - 10 comments
Labels: IO

#347 - Add documentation on how to persist computations in a workflow

Issue - State: open - Opened by eric-czech almost 4 years ago - 5 comments
Labels: documentation

#347 - Add documentation on how to persist computations in a workflow

Issue - State: open - Opened by eric-czech almost 4 years ago - 5 comments
Labels: documentation

GitHub / sgkit-dev/sgkit issues and pull requests