CLI Module

The command-line interface module provides the main entry point for VariantCentrifuge.

Command-line interface for VariantCentrifuge.

variantcentrifuge.cli.create_parser()

Create and return the argument parser for variantcentrifuge CLI.

Return type:

ArgumentParser

variantcentrifuge.cli.main(argv=None)

Run main entry point for variantcentrifuge CLI.

Parameters:

argv (list[str] | None)

Return type:

int

variantcentrifuge.cli.parse_args(args_list=None)

Parse command line arguments.

Parameters:

args_list (list[str] | None) – List of arguments to parse. If None, uses sys.argv

Returns:

Parsed arguments

Return type:

Namespace

variantcentrifuge.cli.resolve_tumor_normal_indices(vcf_path=None, *, cli_tumor_idx=None, cli_normal_idx=None, cfg_tumor_idx=None, cfg_normal_idx=None, header_text=None, require_tumor=None, require_normal=None)

Resolve (tumor_idx, normal_idx) from VCF header, CLI, or config.

Parameters:

• vcf_path (str | None)

• cli_tumor_idx (int | str | None)

• cli_normal_idx (int | str | None)

• cfg_tumor_idx (int | str | None)

• cfg_normal_idx (int | str | None)

• header_text (str | None)

• require_tumor (bool | None)

• require_normal (bool | None)

Return type:

tuple[str, str]

variantcentrifuge.cli.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