Source code for modalysis.cli.handlers.pileup

"""CLI handlers for pileup commands."""

import argparse
import logging

from modalysis.client.pileup import pileup_format, pileup_merge

logger = logging.getLogger(__name__)




def handle_pileup_format(args: argparse.Namespace) -> None:
    """Handle `modalysis pileup format` CLI command."""
    with open(args.allowed_chromosomes) as f:
        allowed_chromosomes = [line.strip() for line in f if line.strip()]
    base_url = f"http://localhost:{args.port}"
    result = pileup_format(
        input_path=args.input_path,
        output_path=args.output_path,
        output_name=args.output_name,
        allowed_chromosomes=allowed_chromosomes,
        base_url=base_url,
    )
    print(result)





def handle_pileup_merge(args: argparse.Namespace) -> None:
    """Handle `modalysis pileup merge` CLI command."""
    base_url = f"http://localhost:{args.port}"
    result = pileup_merge(
        pileup_paths=args.pileup_paths,
        output_path=args.output_path,
        output_name=args.output_name,
        min_files=args.min_files,
        min_file_coverage=args.min_file_coverage,
        min_reads=args.min_reads,
        base_url=base_url,
    )
    print(result)