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sgkit-dev
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bio2zarr
Convert bioinformatics file formats to Zarr
Apache License 2.0
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7
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Fix missing f string
#190
benjeffery
closed
6 months ago
0
Schema mod tests
#189
jeromekelleher
closed
6 months ago
0
Could `dencode_init` return an upper memory use bound?
#188
benjeffery
closed
6 months ago
3
Add more logging for variant chunk memory
#187
jeromekelleher
closed
6 months ago
0
Improve encoding memory bound estimate
#186
jeromekelleher
opened
6 months ago
0
SVCR Local alleles
#185
jeromekelleher
opened
6 months ago
9
Improved info interface on encode/explode init
#184
jeromekelleher
closed
6 months ago
0
Detect VCF fields that would clobber VCF Zarr
#183
jeromekelleher
closed
6 months ago
0
Bump upload artefact to v4
#182
jeromekelleher
closed
6 months ago
0
CD warnings
#181
jeromekelleher
closed
6 months ago
2
Add explicit tests with indels
#180
jeromekelleher
closed
6 months ago
0
Implement mixed_ploidy support
#179
jeromekelleher
closed
6 months ago
7
Support one-based coordinates in explode/encode partition
#178
jeromekelleher
closed
6 months ago
0
Add CD workflow
#177
ravwojdyla
closed
6 months ago
7
Add tests against sgkit's VCF parsing code
#176
jeromekelleher
closed
6 months ago
1
Progress tests failing on Mac
#175
jeromekelleher
closed
6 months ago
1
Windows support
#174
jeromekelleher
opened
6 months ago
0
Platform and distribution CI
#173
jeromekelleher
closed
6 months ago
0
Rename vcf_partition CLI and document
#172
jeromekelleher
closed
6 months ago
0
Drop plink2zarr from installation for now
#171
jeromekelleher
closed
6 months ago
0
Initial documentation for CLI
#170
jeromekelleher
closed
5 months ago
0
Document platform support
#169
jeromekelleher
closed
6 months ago
0
Add --one-based option to dexplode-partition and dencode-partition
#168
jeromekelleher
closed
6 months ago
2
CHANGELOG for 0.0.9 release
#167
jeromekelleher
closed
6 months ago
0
Numpy deprecation warnings
#166
jeromekelleher
closed
6 months ago
0
Refactoring: standardise on "field" in the code
#165
jeromekelleher
closed
5 months ago
2
Various fixes to ICF
#164
jeromekelleher
closed
6 months ago
1
Add pin for sgkit 0.8.0 to dev requirements
#163
jeromekelleher
closed
6 months ago
0
Add packaging tests to CI
#162
jeromekelleher
closed
6 months ago
0
Fix license classifier
#161
benjeffery
closed
7 months ago
0
Packaging problem
#160
jeromekelleher
closed
7 months ago
0
`dexplode_init` fails if `num_partitions` is < 2*`num_vcfs`.
#159
benjeffery
closed
6 months ago
4
Tests failing in CI due to sgkit
#158
jeromekelleher
closed
6 months ago
0
Fix project email
#157
ravwojdyla
closed
7 months ago
0
Test coverage in CI
#156
jeromekelleher
closed
6 months ago
4
Fix project email
#155
jeromekelleher
closed
7 months ago
2
Setup `release`/CD workflow
#154
ravwojdyla
closed
6 months ago
3
Move dev requirements into pyproject
#153
ravwojdyla
closed
7 months ago
1
CI workflow setup: lint + test
#152
ravwojdyla
closed
7 months ago
2
Consolidate project config under pyproject
#151
ravwojdyla
closed
7 months ago
1
VCF indexes without record counts lead to assertion
#150
shz9
closed
6 months ago
4
Make dexplode-partition synchronous (no progress)
#149
jeromekelleher
closed
6 months ago
0
Intermittent backtraces when running many dexplode-partitions
#148
jeromekelleher
closed
6 months ago
2
Document dexplode/dencode usage on different schedulers
#147
jeromekelleher
opened
7 months ago
2
Bug in check_overlap when region spans whole file
#146
jeromekelleher
closed
6 months ago
0
Better dencode
#145
jeromekelleher
closed
7 months ago
3
`dencode-partition` fails with `AssertionError`
#144
benjeffery
closed
6 months ago
32
Report correct file sizes in inspect
#143
jeromekelleher
closed
7 months ago
0
`inspect` reports incorrect size reported for 2D arrays
#142
benjeffery
closed
7 months ago
2
Memory bound in dencode substantially underestimated
#141
jeromekelleher
closed
6 months ago
4
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