Related Issues (20)
- Recompute INFO/AC INFO/AN when samples specified. HOT 1
- Output command line provenance in the header
- Remove vcf_header option from write_vcf HOT 1
- Add query command with basic `-f/--format` support HOT 1
- Add support for index `-n/--nrecords`
- Add support for index `-s/--stats`
- Add view `-o/--output` option for uncompressed VCF only
- Performance tests HOT 1
- Code coverage HOT 1
- Move filter expression code to separate module
- Add support for reading samples from a file (-S) HOT 1
- Fail if output type does not match file extension
- Support genotypes in filtering expressions
- Add support for reading regions and targets from a file (-R/-T)
- Add variant and sample filtering to query command
- Add support to exclude samples
- Filtering with samples not outputing info fields correctly HOT 2
- Support bcftools' empty sample subset behaviour HOT 1
- INFO field computation performance HOT 2
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