import argparse
import gzip
from pathlib import Path
from typing import List


def main():
    parser = get_parser()
    args = parser.parse_args()
    conf = make_conf(args)
    write_conf(args.outfile, conf)


def make_conf(args: argparse.Namespace) -> List[str]:
    """
    The reference and extra reference files are localized in the reference directory at
    the WDL level. Therefore, we only need the basename. However, for the include file,
    the actual path must be provided in order for gemBS to recognize it.

    If a name for an underconversion sequence is not provided, it is assumed that the
    name of the first contig in the extra reference is the name to use.
    """
    conf = [f"reference = reference/{Path(args.reference).name}"]
    if args.extra_reference is not None:
        conf.append(f"extra_references = reference/{Path(args.extra_reference).name}")
    conf.extend(
        [
            "index_dir = indexes",
            "base = .",
            "sequence_dir = ${base}/fastq/@SAMPLE",
            "bam_dir = ${base}/mapping/@BARCODE",
            "bcf_dir = ${base}/calls/@BARCODE",
            "extract_dir = ${base}/extract/@BARCODE",
            "report_dir = ${base}/report",
            f"threads = {args.num_threads}",
            f"jobs = {args.num_jobs}",
        ]
    )

    if args.benchmark_mode:
        conf.append("benchmark_mode = true")

    if args.extra_reference is not None:
        conf.append("[mapping]")
        if args.underconversion_sequence:
            underconversion_sequence = args.underconversion_sequence
        else:
            underconversion_sequence = extract_underconversion_sequence(
                args.extra_reference
            )
        conf.append(f"underconversion_sequence = {underconversion_sequence}")

    if args.include_file:
        conf.append(f"include {args.include_file}")

    return conf


def extract_underconversion_sequence(extra_reference: str) -> str:
    with gzip.open(extra_reference, "rt") as f:
        return f.readline().strip().lstrip(">")


def write_conf(outfile: str, conf: List[str]):
    with open(outfile, "w") as f:
        for line in conf:
            f.write(line + "\n")


def get_parser() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "-t", "--num-threads", help="Number of threads for gemBS", type=int, default=8
    )
    parser.add_argument(
        "-j", "--num-jobs", help="Number of jobs for gemBS", type=int, default=3
    )
    parser.add_argument(
        "-e",
        "--extra-reference",
        help="File name of extra reference for control sequence",
    )
    parser.add_argument(
        "-r", "--reference", help="File name of reference fasta", required=True
    )
    parser.add_argument(
        "-u",
        "--underconversion-sequence",
        help=(
            "Name of contig in extra reference to use as underconversion control. If "
            "not specified, then the name of the first contig in the extra reference "
            "will be used as the underconversion control."
        ),
    )
    parser.add_argument(
        "-i", "--include-file", help="Name of additional conf file to include in "
    )
    parser.add_argument(
        "--benchmark-mode",
        help="Switch gemBS to use benchmark mode",
        action="store_true",
    )
    parser.add_argument(
        "-o",
        "--outfile",
        help="Name of file to write generated conf to",
        default="gembs.conf",
    )
    return parser


if __name__ == "__main__":
    main()