vcf.utils

cloud.vcf.utils

Functions

Name	Description
create_index_file	Create a VCF index file in the current working directory.
find_index	Find the index file for a VCF file or None if not found.
get_record_count	Return the record count in a VCF file.
get_sample_name	Returns the sample name in a VCF file.
is_bgzipped	Returns True if the VCF file is bgzipped.
sort_and_bgzip	Sort and bgzip a VCF file storing the result in the tmp space.

cloud.vcf.utils.create_index_file(vcf_uri)

Create a VCF index file in the current working directory.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required

Name	Type	Description
	str	index file name

cloud.vcf.utils.find_index(vcf_uri)

Find the index file for a VCF file or None if not found.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required

Name	Type	Description
	Optional[str]	URI of the index file

cloud.vcf.utils.get_record_count(vcf_uri, index_uri)

Return the record count in a VCF file.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required
index_uri	str	URI of the VCF index file	required

Name	Type	Description
	Optional[int]	record count or None if there is an error

cloud.vcf.utils.get_sample_name(vcf_uri)

Returns the sample name in a VCF file.

If there are multiple samples, return a comma-separated list of sample names.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required

Name	Type	Description
	str	sample name

cloud.vcf.utils.is_bgzipped(vcf_uri)

Returns True if the VCF file is bgzipped.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required

Name	Type	Description
	bool	True if the VCF file is bgzipped

cloud.vcf.utils.sort_and_bgzip(vcf_uri, *, tmp_space='.')

Sort and bgzip a VCF file storing the result in the tmp space.

Name	Type	Description	Default
vcf_uri	str	URI of the VCF file	required
tmp_space	str	tmp space URI, defaults to the current directory	`'.'`

Name	Type	Description
	str	URI of bgzipped VCF