import sys

from ..api import utils

import fuc
import pysam

description = f"""
Compute copy number from read depth for the target gene.

The command will convert read depth to copy number by performing intra-sample
normalization using summary statistics from the control gene.

During copy number analysis, if the input data is targeted sequencing, the
command will apply inter-sample normalization using summary statistics across
all samples. For best results, it is recommended to specify known samples
without SV using --samples-without-sv.
"""

def create_parser(subparsers):
    parser = fuc.api.common._add_parser(
        subparsers,
        fuc.api.common._script_name(),
        description=description,
        help='Compute copy number from read depth for the target \n'
             'gene.',
    )
    parser.add_argument(
        'read_depth',
        metavar='read-depth',
        help='Archive file with the semantic type \n'
             'CovFrame[ReadDepth].'
    )
    parser.add_argument(
        'control_statistcs',
        metavar='control-statistcs',
        help='Archive file with the semantic type \n'
             'SampleTable[Statistics].'
    )
    parser.add_argument(
        'output',
        help='Archive file with the semantic type \n'
             'CovFrame[CopyNumber].'
    )
    parser.add_argument(
        '--samples-without-sv',
        metavar='TEXT',
        nargs='+',
        help='List of known samples with no SV.'
    )

def main(args):
    result = utils.compute_copy_number(
        args.read_depth, args.control_statistcs,
        samples_without_sv=args.samples_without_sv
    )
    result.to_file(args.output)
