sgkit-dev bio2zarr issues

sgkit-dev / bio2zarr

Convert bioinformatics file formats to Zarr

Apache License 2.0

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issues

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Run on zarr-python v3 with zarr-format v2

#288 tomwhite opened 3 days ago
1
Drop Python 3.9

#287 tomwhite closed 1 week ago
1
Local alleles updates

#286 Will-Tyler closed 4 weeks ago
2
Remove check on PL values when computing local alleles

#285 jeromekelleher opened 1 month ago
3
Test on Zarr v2 and v3

#284 jeromekelleher opened 1 month ago
3
Unpin numpy

#283 jeromekelleher closed 3 weeks ago
3
Test on Python 3.12

#282 tomwhite closed 1 month ago
1
Draft bed2zarr code

#281 percyfal opened 2 months ago
15
Change local alleles default to false

#280 Will-Tyler closed 3 months ago
1
Add variant_length field

#279 tomwhite closed 3 months ago
2
Add variant length/end coordinate field

#278 jeromekelleher closed 3 months ago
2
LPL no smaller than PL

#277 jeromekelleher opened 4 months ago
14
Inspect fails for datasets with out consolidated metadata

#276 benjeffery opened 4 months ago
0
Fix tests for new numcodecs

#275 benjeffery closed 4 months ago
1
Numcodecs v0.13.0 causing test failures

#274 Will-Tyler closed 4 months ago
1
Local alleles - Add LPL field

#273 Will-Tyler closed 4 months ago
4
Fixup local alleles interface

#272 jeromekelleher closed 4 months ago
1
Fix Char type bug

#271 jeromekelleher closed 4 months ago
1
Handle case where GT is defined in header, but not used in FORMAT

#270 tomwhite closed 4 months ago
4
Make chunks have the same number of dimensions as shape

#269 tomwhite closed 4 months ago
1
Char fields added as Unicode not string

#268 jeromekelleher closed 4 months ago
1
Parsing fails for VCF with GT in header but not in FORMAT field

#267 tomwhite closed 4 months ago
1
Local alleles

#266 Will-Tyler closed 4 months ago
13
Fix missing f string

#265 tomwhite closed 4 months ago
2
Hypothesis tests for VCF

#264 tomwhite closed 4 months ago
5
Optional first phasing symbol introduced in VCF 4.4

#263 timothymillar opened 4 months ago
4
Add descriptions for the fixed fields

#262 Will-Tyler closed 4 months ago
2
Use enums for VCF file and index types

#261 Will-Tyler closed 4 months ago
0
Fix character field bounds update error

#260 jeromekelleher closed 5 months ago
2
Numpy 2 fixups

#259 jeromekelleher closed 5 months ago
2
ICF stores created with numpy 1.x won't work with numpy 2.x

#258 jeromekelleher closed 3 weeks ago
2
Set copy=True in np.array creation for numpy 2.0 compatibility

#257 jeromekelleher closed 5 months ago
1
Run tests against numpy 2

#256 jeromekelleher closed 3 weeks ago
7
Distribution maintenance

#255 jeromekelleher closed 5 months ago
8
Run tests against Zarr 3

#254 tomwhite opened 5 months ago
13
Refactor variable names for consistency

#253 Will-Tyler closed 5 months ago
4
Add multiple-file support to vcfpartition

#252 Will-Tyler closed 5 months ago
8
ValueError: could not broadcast input array

#251 tomwhite closed 5 months ago
0
Pin to zarr < 3

#250 jeromekelleher closed 5 months ago
0
Hypothesis testing for vcf2zarr

#249 tomwhite closed 4 months ago
13
Last docs updates and release

#248 jeromekelleher closed 5 months ago
4
Change num_partitions to option

#247 jeromekelleher closed 5 months ago
4
Add progress/no-progress flag to CLI

#246 jeromekelleher closed 5 months ago
5
Fix syncronous commands bug

#245 jeromekelleher closed 5 months ago
2
Change dencode-init to use --num-partitions

#244 jeromekelleher closed 5 months ago
0
Change dexplode-init to use ``--num-parts``/``-n`` instead of positional

#243 jeromekelleher closed 5 months ago
1
Some more docs3

#242 jeromekelleher closed 5 months ago
2
Bug in dexplode-partition

#241 jeromekelleher closed 5 months ago
0
Add --no-progress (or similar) to suppress progress

#240 jeromekelleher closed 5 months ago
0
Restructure vcf2zarr docs

#239 jeromekelleher opened 5 months ago
0