Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / pystatgen/sgkit issues and pull requests
#1211 - Update project email address
Pull Request -
State: closed - Opened by hammer 6 months ago
#1210 - `vcf_to_zarr` raises error instead of truncating INFO fields of length `R`
Issue -
State: open - Opened by timothymillar 7 months ago
- 3 comments
Labels: bug, IO
#1209 - read_plink returns bytes for variant_alleles not unicode
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1208 - Partial changes for VCF Character S->U
Pull Request -
State: open - Opened by jeromekelleher 7 months ago
#1207 - Mixed-ploidy VanRaden GRM
Issue -
State: open - Opened by timothymillar 7 months ago
Labels: enhancement
#1205 - Fix xarray repr in doctests
Pull Request -
State: closed - Opened by tomwhite 7 months ago
- 3 comments
Labels: auto-merge
#1204 - Change in Xarray repr is causing doctest failures
Issue -
State: closed - Opened by tomwhite 7 months ago
Labels: upstream
#1203 - partition_into_regions: tabix index returns illegal region with multiple contigs
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1202 - partition_into_regions: CSI indexed BCFs return empty regions
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1201 - partition_into_regions: CSI indexed VCFs have incorrect sequence names
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1200 - partition_into_regions returns empty region for all contigs in header
Issue -
State: closed - Opened by jeromekelleher 7 months ago
- 5 comments
#1199 - Avoid disabling jit on guvectorised functions
Pull Request -
State: closed - Opened by timothymillar 7 months ago
- 3 comments
Labels: auto-merge
#1197 - Cannot round-trip explicitly set missing INFO values in VCF
Issue -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
#1196 - vcf_writer emitting incorrect missing values for INFO fields
Issue -
State: closed - Opened by jeromekelleher 8 months ago
Labels: bug
#1195 - read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields
Issue -
State: open - Opened by jeromekelleher 8 months ago
Labels: bug
#1194 - Numba cache masking compile warnings and deprecations
Issue -
State: closed - Opened by jeromekelleher 8 months ago
- 7 comments
Labels: process + tools
#1193 - Irrelavant change for build
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 1 comment
#1192 - VCF parser returning FILL instead of MISSING values
Issue -
State: closed - Opened by jeromekelleher 8 months ago
Labels: bug
#1191 - Turn off numba cache by default
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
Labels: auto-merge
#1190 - Errors in missing vs pad values in VCF
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 9 comments
Labels: auto-merge
#1188 - Genealogical relatedness greater than 1
Issue -
State: closed - Opened by fouerghi 8 months ago
- 3 comments
#1186 - Do chunk sizes have to be the same for all variables in a given dimension?
Issue -
State: open - Opened by jeromekelleher 8 months ago
- 1 comment
#1185 - Two-pass non-Dask VCF conversion
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
#1184 - Upgrade sphinx to fix build
Pull Request -
State: closed - Opened by tomwhite 8 months ago
- 2 comments
Labels: auto-merge, upstream
#1183 - Sequential VCF parsing
Issue -
State: open - Opened by hammer 8 months ago
- 1 comment
Labels: IO
#1182 - `sgkit.regenie` review. Work in progress
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1182 - `sgkit.regenie` review. Work in progress
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1181 - `sgkit.genee` improvements
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1181 - `sgkit.genee` improvements
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1180 - genee review: sgkit implementation limitations
Issue -
State: open - Opened by jdstamp 8 months ago
- 1 comment
#1180 - genee review: sgkit implementation limitations
Issue -
State: open - Opened by jdstamp 8 months ago
- 1 comment
#1179 - Howto: join biallelic SNPs into a single record?
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1179 - Howto: join biallelic SNPs into a single record?
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1176 - Variant positions less than one?
Issue -
State: open - Opened by hyanwong 8 months ago
#1176 - Variant positions less than one?
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1175 - Add getting REF to how_do_i
Pull Request -
State: open - Opened by hyanwong 8 months ago
#1175 - Add getting REF to how_do_i
Pull Request -
State: open - Opened by hyanwong 8 months ago
#1174 - FAQ - mask out duplicate positions
Issue -
State: open - Opened by hyanwong 8 months ago
#1174 - FAQ - mask out duplicate positions
Issue -
State: open - Opened by hyanwong 8 months ago
#1173 - Document how to use save_dataset to overwrite existing files
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1173 - Document how to use save_dataset to overwrite existing files
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1172 - "missing_pct" misnamed in simulate_genotype_call_dataset
Issue -
State: open - Opened by hyanwong 8 months ago
#1172 - "missing_pct" misnamed in simulate_genotype_call_dataset
Issue -
State: open - Opened by hyanwong 8 months ago
#1171 - Iterating through variants
Issue -
State: open - Opened by hyanwong 8 months ago
#1171 - Iterating through variants
Issue -
State: open - Opened by hyanwong 8 months ago
#1170 - How do I identify the REF from a VCF
Issue -
State: open - Opened by hyanwong 8 months ago
- 4 comments
#1170 - How do I identify the REF from a VCF
Issue -
State: open - Opened by hyanwong 8 months ago
- 4 comments
#1169 - `partition_into_regions` fails to partition correctly in when absent contigs are listed in the header.
Issue -
State: closed - Opened by benjeffery 9 months ago
- 9 comments
Labels: bug
#1169 - `partition_into_regions` fails to partition correctly in when absent contigs are listed in the header.
Issue -
State: open - Opened by benjeffery 9 months ago
- 6 comments
#1168 - VCF parsing memory usage
Issue -
State: open - Opened by benjeffery 9 months ago
- 7 comments
#1168 - VCF parsing memory usage
Issue -
State: open - Opened by benjeffery 9 months ago
- 7 comments
#1167 - Change organization and project name expansion
Issue -
State: open - Opened by hammer 9 months ago
- 13 comments
Labels: documentation, process + tools
#1165 - How do I... additions
Issue -
State: open - Opened by hammer 9 months ago
- 3 comments
Labels: documentation
#1163 - Change `Dataset.dims` to `Dataset.sizes` to address Xarray FutureWarning
Pull Request -
State: closed - Opened by tomwhite 10 months ago
- 1 comment
Labels: auto-merge
#1162 - Main build is failing
Issue -
State: closed - Opened by tomwhite 10 months ago
Labels: upstream
#1161 - Fix broken links in the getting started guide
Pull Request -
State: open - Opened by isumitjha 10 months ago
- 2 comments
Labels: auto-merge
#1160 - Broken dask tutorial links in getting started guide
Issue -
State: open - Opened by isumitjha 10 months ago
Labels: documentation
#1159 - Make copyright year dynamic
Pull Request -
State: open - Opened by isumitjha 10 months ago
Labels: auto-merge
#1158 - Update copyright in the docs
Issue -
State: open - Opened by aktech 10 months ago
#1157 - Don't display attributes expanded for dataset
Issue -
State: open - Opened by jeromekelleher 10 months ago
- 5 comments
Labels: enhancement
#1156 - Set SGKIT_DISABLE_NUMBA_CACHE=1 by default
Issue -
State: open - Opened by jeromekelleher 10 months ago
- 3 comments
Labels: bug
#1155 - Writing a subset of a dataset to VCF
Issue -
State: open - Opened by jeromekelleher 10 months ago
#1154 - Parts of work redone when a dask worker dies
Issue -
State: open - Opened by benjeffery 10 months ago
- 2 comments
#1152 - read_plink scalability
Issue -
State: closed - Opened by hammer 10 months ago
- 4 comments
Labels: IO
#1151 - How do I add a new sample or variant data variable from a file?
Issue -
State: open - Opened by hammer 10 months ago
- 1 comment
Labels: documentation
#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
#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
#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
#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
#1138 - Prevent parts of VCF being reparsed
Pull Request -
State: open - Opened by benjeffery 12 months ago
- 9 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
#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
#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
#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
#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
#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
#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
#1119 - Improve performance of `variant_stats`
Pull Request -
State: closed - Opened by timothymillar about 1 year ago
- 11 comments
Labels: auto-merge
#1118 - Test with Zarr V3
Issue -
State: open - Opened by tomwhite about 1 year ago
Labels: IO, upstream
#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
#1115 - Link between variable and function to compute it
Issue -
State: open - Opened by jeromekelleher about 1 year ago
- 2 comments
Labels: data representation
#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
#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