Source code for modalysis.cli.parsers.pileup

"""CLI parser registration for pileup command group."""

import argparse

from modalysis.cli.handlers.pileup import handle_pileup_format, handle_pileup_merge
from modalysis.constants import DEFAULT_PORT




def register_pileup_parser(
    subparsers: argparse._SubParsersAction,
) -> None:
    """Register `pileup` subcommands and arguments."""
    pileup_parser = subparsers.add_parser("pileup", help="Pileup commands")
    pileup_subparsers = pileup_parser.add_subparsers(dest="pileup_command")

    pileup_format_parser = pileup_subparsers.add_parser(
        "format", help="Format a pileup file"
    )
    pileup_format_parser.add_argument(
        "--input-path", required=True, help="Path to the input pileup file"
    )
    pileup_format_parser.add_argument(
        "--output-path", required=True, help="Path to the output directory"
    )
    pileup_format_parser.add_argument(
        "--output-name", required=True, help="Name for the output file"
    )
    pileup_format_parser.add_argument(
        "--allowed-chromosomes",
        required=True,
        help="Path to a file with one valid chromosome name per line",
    )
    pileup_format_parser.add_argument(
        "--port",
        type=int,
        default=DEFAULT_PORT,
        help=f"Port the server is running on (default: {DEFAULT_PORT})",
    )
    pileup_format_parser.set_defaults(func=handle_pileup_format)

    pileup_merge_parser = pileup_subparsers.add_parser(
        "merge", help="Merge formatted pileup files"
    )
    pileup_merge_parser.add_argument(
        "--pileup-paths",
        nargs="+",
        required=True,
        help="Paths to the formatted pileup files to merge",
    )
    pileup_merge_parser.add_argument(
        "--output-path", required=True, help="Path to the output directory"
    )
    pileup_merge_parser.add_argument(
        "--output-name", required=True, help="Name for the output file"
    )
    pileup_merge_parser.add_argument(
        "--min-files",
        type=int,
        default=2,
        help="Minimum number of files a key must appear in (default: 2)",
    )
    pileup_merge_parser.add_argument(
        "--min-file-coverage",
        type=float,
        default=50.0,
        help="Minimum percentage of files a key must appear in (default: 50.0)",
    )
    pileup_merge_parser.add_argument(
        "--min-reads",
        type=int,
        default=5,
        help="Minimum accumulated N_VALID_COV to include a row (default: 5)",
    )
    pileup_merge_parser.add_argument(
        "--port",
        type=int,
        default=DEFAULT_PORT,
        help=f"Port the server is running on (default: {DEFAULT_PORT})",
    )
    pileup_merge_parser.set_defaults(func=handle_pileup_merge)