Ecosyste.ms: Issues

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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

#1202 - partition_into_regions: CSI indexed BCFs return empty regions

Issue - State: open - Opened by jeromekelleher 7 months ago
Labels: bug

#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

#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

#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

#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

#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