sgkit-dev sgkit issues - Githubissues

sgkit-dev / sgkit

Scalable genetics toolkit

https://sgkit-dev.github.io/sgkit

Apache License 2.0

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issues

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partition_into_regions: CSI indexed BCFs return empty regions

#1202 jeromekelleher opened 7 months ago
0
partition_into_regions: CSI indexed VCFs have incorrect sequence names

#1201 jeromekelleher opened 7 months ago
0
partition_into_regions returns empty region for all contigs in header

#1200 jeromekelleher closed 7 months ago
5
Avoid disabling jit on guvectorised functions

#1199 timothymillar closed 6 months ago
3
Cannot round-trip explicitly set missing INFO values in VCF

#1197 jeromekelleher closed 7 months ago
3
vcf_writer emitting incorrect missing values for INFO fields

#1196 jeromekelleher closed 7 months ago
0
read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields

#1195 jeromekelleher opened 7 months ago
0
Numba cache masking compile warnings and deprecations

#1194 jeromekelleher closed 6 months ago
7
Irrelavant change for build

#1193 jeromekelleher closed 7 months ago
1
VCF parser returning FILL instead of MISSING values

#1192 jeromekelleher closed 7 months ago
0
Turn off numba cache by default

#1191 jeromekelleher closed 7 months ago
3
Errors in missing vs pad values in VCF

#1190 jeromekelleher closed 7 months ago
9
Genealogical relatedness greater than 1

#1188 fouerghi closed 7 months ago
3
Do chunk sizes have to be the same for all variables in a given dimension?

#1186 jeromekelleher opened 8 months ago
1
Two-pass non-Dask VCF conversion

#1185 jeromekelleher closed 7 months ago
3
Upgrade sphinx to fix build

#1184 tomwhite closed 8 months ago
2
Sequential VCF parsing

#1183 hammer closed 1 month ago
2
`sgkit.regenie` review. Work in progress

#1182 jdstamp opened 8 months ago
0
`sgkit.genee` improvements

#1181 jdstamp opened 8 months ago
0
genee review: sgkit implementation limitations

#1180 jdstamp opened 8 months ago
1
Howto: join biallelic SNPs into a single record?

#1179 hyanwong opened 8 months ago
1
Variant positions less than one?

#1176 hyanwong opened 8 months ago
1
Add getting REF to how_do_i

#1175 hyanwong opened 8 months ago
0
FAQ - mask out duplicate positions

#1174 hyanwong opened 8 months ago
0
Document how to use save_dataset to overwrite existing files

#1173 hyanwong opened 8 months ago
1
"missing_pct" misnamed in simulate_genotype_call_dataset

#1172 hyanwong opened 8 months ago
0
Iterating through variants

#1171 hyanwong opened 8 months ago
0
How do I identify the REF from a VCF

#1170 hyanwong opened 8 months ago
4
`partition_into_regions` fails to partition correctly in when absent contigs are listed in the header.

#1169 benjeffery closed 7 months ago
9
VCF parsing memory usage

#1168 benjeffery opened 8 months ago
7
Change organization and project name expansion

#1167 hammer closed 6 months ago
18
How do I... additions

#1165 hammer opened 9 months ago
3
Change `Dataset.dims` to `Dataset.sizes` to address Xarray FutureWarning

#1163 tomwhite closed 9 months ago
1
Main build is failing

#1162 tomwhite closed 9 months ago
0
Fix broken links in the getting started guide

#1161 isumitjha opened 9 months ago
2
Broken dask tutorial links in getting started guide

#1160 isumitjha opened 9 months ago
0
Make copyright year dynamic

#1159 isumitjha opened 9 months ago
0
Update copyright in the docs

#1158 aktech opened 9 months ago
0
Don't display attributes expanded for dataset

#1157 jeromekelleher opened 9 months ago
5
Set SGKIT_DISABLE_NUMBA_CACHE=1 by default

#1156 jeromekelleher opened 9 months ago
3
Writing a subset of a dataset to VCF

#1155 jeromekelleher opened 10 months ago
0
Parts of work redone when a dask worker dies

#1154 benjeffery opened 10 months ago
2
read_plink scalability

#1152 hammer closed 10 months ago
4
How do I add a new sample or variant data variable from a file?

#1151 hammer opened 10 months ago
1
read_plink from cloud storage

#1150 hammer opened 10 months ago
1
read_plink failing with 0.7.0 release

#1149 hammer closed 10 months ago
5
Format matrix in pairwise docs

#1148 benjeffery closed 10 months ago
1
Improve formatting in the `pairwise_distance` docs

#1147 aktech closed 10 months ago
1
Methods doc categories

#1146 benjeffery closed 10 months ago
9
Add pairwise_distance to docs

#1145 benjeffery closed 10 months ago
1

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