biocantor.io.vcf.parser

Generic VCF parser. This is the default implementation.

This implementation uses random UUIDs, so that every Variant is unique and maps 1-1 to the VariantInterval produced.

Module Contents

Functions

convert_vcf_records_to_model(→ Dict[str, ...)	Default parser for VCF files. Converts VCF records into VariantIntervalModel.
parse_vcf_file(→ Dict[str, ...)	Wrapper for convert_vcf_records_to_model() that handles file opening. Primary VCF parsing function.

biocantor.io.vcf.parser.convert_vcf_records_to_model(recs: List[vcf.model._Record]) → Dict[str, List[inscripta.biocantor.io.models.VariantIntervalCollectionModel]]

Default parser for VCF files. Converts VCF records into VariantIntervalModel.

biocantor.io.vcf.parser.parse_vcf_file(variant_handle_or_path: Optional[Union[TextIO, str, pathlib.Path]] = None) → Dict[str, List[inscripta.biocantor.io.models.VariantIntervalCollectionModel]]

Wrapper for convert_vcf_records_to_model() that handles file opening. Primary VCF parsing function.