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sgkit-dev
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vcztools
Partial reimplementation of bcftools for VCF Zarr
Apache License 2.0
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Make robust to non-essential missing fields with clear interpretation
#107
jeromekelleher
opened
4 days ago
0
Backward and forward-compatible changes to support zarr-python v3
#106
tomwhite
opened
6 days ago
0
Py39
#105
jeromekelleher
opened
6 days ago
4
Check exit status codes match bcftools
#104
jeromekelleher
opened
6 days ago
0
Pin pyparsing to >= 3
#103
jeromekelleher
closed
6 days ago
0
Undocumented pyparsing version dependency
#102
jeromekelleher
closed
6 days ago
0
Robustness checks
#101
jeromekelleher
opened
6 days ago
0
Documentation
#100
jeromekelleher
opened
6 days ago
0
Handel or ignore non-standard dimensions
#99
timothymillar
opened
1 week ago
3
Run tests against Zarr 3
#98
tomwhite
opened
2 weeks ago
0
Parallelize I/O operations
#97
Will-Tyler
closed
6 days ago
8
Unpin numpy and run tests on numpy 1 and 2
#96
tomwhite
closed
3 weeks ago
0
Drop python 3.9
#95
tomwhite
closed
3 weeks ago
0
vcztools view: write performance
#94
Will-Tyler
opened
1 month ago
7
vcztools view performance
#93
Will-Tyler
closed
1 month ago
2
vcztools view: allow writing to /dev/null
#92
Will-Tyler
closed
1 month ago
2
Add real performance testing data
#91
Will-Tyler
closed
1 month ago
1
vcztools query: implement `%SAMPLE` tag
#90
Will-Tyler
opened
1 month ago
0
Performance tests
#89
Will-Tyler
closed
1 month ago
2
Query samples looping
#88
Will-Tyler
closed
1 month ago
1
Get INFO/FORMAT description from attrs if present
#87
tomwhite
closed
1 month ago
0
Remove vcf_header option from write_vcf
#86
tomwhite
closed
1 month ago
0
Add workflow to publish to PyPi
#85
tomwhite
closed
1 month ago
0
vcztools query: optimize query evaluation
#84
Will-Tyler
opened
2 months ago
2
vcztools query: support looping over samples
#83
Will-Tyler
closed
1 month ago
1
Query variant filtering
#82
Will-Tyler
closed
1 month ago
1
Test on Python 3.12
#81
tomwhite
closed
2 months ago
0
Exclude samples
#80
Will-Tyler
closed
2 months ago
0
vcztools view: INFO field computation performance
#79
Will-Tyler
opened
2 months ago
3
Support bcftools' empty sample subset behaviour
#78
Will-Tyler
closed
2 months ago
1
Recompute INFO fields on sample selection
#77
Will-Tyler
closed
2 months ago
4
Add samples file option to view CLI
#76
Will-Tyler
closed
2 months ago
1
Filtering with samples not outputing info fields correctly
#75
Will-Tyler
closed
2 months ago
2
Add support to exclude samples
#74
tomwhite
closed
2 months ago
0
Add variant and sample filtering to query command
#73
tomwhite
opened
2 months ago
1
Add support for reading regions and targets from a file (-R/-T)
#72
tomwhite
opened
2 months ago
0
Support genotypes in filtering expressions
#71
Will-Tyler
opened
2 months ago
0
Fail on bad output file extension
#70
Will-Tyler
closed
2 months ago
0
Add provenance header
#69
Will-Tyler
closed
2 months ago
2
Fail if output type does not match file extension
#68
Will-Tyler
closed
2 months ago
0
Add support for reading samples from a file (-S)
#67
jeromekelleher
closed
2 months ago
1
Add output option to vcztools view
#66
Will-Tyler
closed
2 months ago
1
Move filter expression code to filter.py
#65
Will-Tyler
closed
3 months ago
0
Query format
#64
Will-Tyler
closed
3 months ago
2
Move filter expression code to separate module
#63
tomwhite
closed
3 months ago
0
Factor out `open_file_like` utility context manager
#62
tomwhite
closed
3 months ago
0
Drop Genotypes
#61
JakeHagen
closed
2 months ago
10
Add support for index -s/--stats
#60
tomwhite
closed
2 months ago
1
Add support for index -n/--nrecords
#59
tomwhite
closed
3 months ago
0
Add query list samples command
#58
Will-Tyler
closed
3 months ago
1
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