vcf.utils

client.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.

client.vcf.utils.create_index_file(vcf_uri)

Create a VCF index file in the current working directory.

:param vcf_uri: URI of the VCF file :return: index file name

client.vcf.utils.find_index(vcf_uri)

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

:param vcf_uri: URI of the VCF file :return: URI of the index file

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

Return the record count in a VCF file.

:param vcf_uri: URI of the VCF file :param index_uri: URI of the VCF index file :return: record count or None if there is an error

client.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.

:param vcf_uri: URI of the VCF file :return: sample name

client.vcf.utils.is_bgzipped(vcf_uri)

Returns True if the VCF file is bgzipped.

:param vcf_uri: URI of the VCF file :return: True if the VCF file is bgzipped

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

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

:param vcf_uri: URI of the VCF file :param tmp_space: tmp space URI, defaults to the current directory :return: URI of bgzipped VCF