issues
search
sgkit-dev
/
vcztools
Partial reimplementation of bcftools for VCF Zarr
Apache License 2.0
1
stars
3
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Exclude samples
#80
Will-Tyler
opened
1 day ago
0
INFO field computation performance
#79
Will-Tyler
opened
3 days ago
2
Support bcftools' empty sample subset behaviour
#78
Will-Tyler
closed
2 days ago
1
Recompute INFO fields on sample selection
#77
Will-Tyler
closed
2 days ago
4
Add samples file option to view CLI
#76
Will-Tyler
closed
1 week ago
1
Filtering with samples not outputing info fields correctly
#75
Will-Tyler
closed
1 week ago
2
Add support to exclude samples
#74
tomwhite
opened
1 week ago
0
Add variant and sample filtering to query command
#73
tomwhite
opened
1 week ago
0
Add support for reading regions and targets from a file (-R/-T)
#72
tomwhite
opened
1 week ago
0
Support genotypes in filtering expressions
#71
Will-Tyler
opened
1 week ago
0
Fail on bad output file extension
#70
Will-Tyler
closed
1 week ago
0
Add provenance header
#69
Will-Tyler
closed
1 week ago
2
Fail if output type does not match file extension
#68
Will-Tyler
closed
1 week ago
0
Add support for reading samples from a file (-S)
#67
jeromekelleher
closed
1 week ago
1
Add output option to vcztools view
#66
Will-Tyler
closed
1 week ago
1
Move filter expression code to filter.py
#65
Will-Tyler
closed
2 weeks ago
0
Query format
#64
Will-Tyler
closed
2 weeks ago
2
Move filter expression code to separate module
#63
tomwhite
closed
2 weeks ago
0
Factor out `open_file_like` utility context manager
#62
tomwhite
closed
3 weeks ago
0
Drop Genotypes
#61
JakeHagen
closed
2 weeks ago
10
Add support for index -s/--stats
#60
tomwhite
closed
2 weeks ago
1
Add support for index -n/--nrecords
#59
tomwhite
closed
3 weeks ago
0
Add query list samples command
#58
Will-Tyler
closed
3 weeks ago
1
Add pytest coverage
#57
Will-Tyler
closed
3 weeks ago
0
Code coverage
#56
tomwhite
opened
4 weeks ago
1
Performance tests
#55
tomwhite
opened
4 weeks ago
1
Add view `-o/--output` option for uncompressed VCF only
#54
tomwhite
closed
1 week ago
0
Add support for index `-s/--stats`
#53
tomwhite
closed
2 weeks ago
0
Add support for index `-n/--nrecords`
#52
tomwhite
closed
3 weeks ago
0
Add query command to list samples (`-l/--list-samples`)
#51
tomwhite
closed
3 weeks ago
0
Add query command with basic `-f/--format` support
#50
tomwhite
closed
2 weeks ago
1
Filter expressions
#49
Will-Tyler
closed
4 weeks ago
2
Header flags
#48
tomwhite
closed
1 month ago
0
Remove vcf_header option from write_vcf
#47
jeromekelleher
opened
1 month ago
1
Output command line provenance in the header
#46
jeromekelleher
opened
1 month ago
0
Recompute INFO/AC INFO/AN when samples specified.
#45
jeromekelleher
closed
2 days ago
1
Add basic exclude/include expression support
#44
jeromekelleher
closed
4 weeks ago
3
Add cd workflow and post initial package
#43
jeromekelleher
opened
1 month ago
1
Move to sgkit-dev?
#42
jeromekelleher
closed
1 month ago
2
bcftools validation tests
#41
tomwhite
closed
1 month ago
3
Change test_vcf_writer.py to use VCF test cache
#40
tomwhite
closed
1 month ago
0
Add support for -s/--samples
#39
tomwhite
closed
1 month ago
1
Add view -H/--no-header option
#38
tomwhite
closed
1 month ago
0
Regions index
#37
tomwhite
closed
1 month ago
3
Add pre-commit with ruff
#36
tomwhite
closed
1 month ago
4
Remove numba
#35
tomwhite
closed
1 month ago
3
Unit tests for regions
#34
tomwhite
closed
1 month ago
0
Drop numba implementation
#33
jeromekelleher
closed
1 month ago
1
Support '-r/--regions'
#32
tomwhite
closed
1 month ago
2
Roundtrip testing with hypothesis-vcf
#31
tomwhite
opened
1 month ago
1
Next