Validators Module

Input validation and sanity checking

Validation module for variantcentrifuge.

This module provides functions to validate: - VCF files (existence, non-empty) - Phenotype files (existence, non-empty, required columns) - Mandatory parameters (reference, filters, fields) - IGV local FASTA and related files (existence, readability) - CLI cross-argument dependencies

These validations ensure that all critical inputs and parameters are provided correctly before proceeding with the analysis.

variantcentrifuge.validators.validate_vcf_file(vcf_path, logger=None, exit_on_error=False)

Validate that the input VCF file exists, is BGZF/BCF compressed, and has a valid index.

Parameters:

• vcf_path (str | None)

• logger (Logger | None)

• exit_on_error (bool)

Return type:

None

variantcentrifuge.validators.validate_required_tools(args, cfg=None, logger=None, exit_on_error=False)

Validate that required external tools are available in PATH before processing.

Parameters:

• args (Namespace)

• cfg (dict[str, Any] | None)

• logger (Logger | None)

• exit_on_error (bool)

Return type:

None

variantcentrifuge.validators.validate_phenotype_file(phenotype_file, sample_col, value_col, logger=None, exit_on_error=False)

Validate phenotype file presence, non-empty status, and required columns.

Parameters:

• phenotype_file (str | None)

• sample_col (str)

• value_col (str)

• logger (Logger | None)

• exit_on_error (bool)

Return type:

None

variantcentrifuge.validators.validate_mandatory_parameters(reference, filters, fields, exit_on_error=False)

Validate that mandatory parameters (reference, filters, fields) are provided.

Parameters:

• reference (str | None)

• filters (str | None)

• fields (str | None)

• exit_on_error (bool)

Return type:

None

variantcentrifuge.validators.validate_igv_files(local_fasta, ideogram, exit_on_error=False)

Validate the existence and readability of files for IGV integration.

Parameters:

• local_fasta (str | None)

• ideogram (str | None)

• exit_on_error (bool)

Return type:

None

variantcentrifuge.validators.validate_cli_args(args, cfg, parser=None)

Validate cross-argument dependencies and file existence.

Parameters:

• args (Namespace)

• cfg (dict[str, Any])

• parser (ArgumentParser | None)

Return type:

None