Two alignments from the same subread to the CCS read about deepconsensus HOT 3 CLOSED

import sys
import pysam
import natsort
import argparse

class BAM:
    def __init__(self, line):
        # target
        self.tname = line.reference_name
        self.tzmw = self.tname.split("/")[1]
        # query
        self.qname = line.query_name
        self.qzmw = self.qname.split("/")[1]


def parse_args(args):
    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
    )
    parser.add_argument(
        "-i",
        "--input",
        type=str,
        required=True,
        help="path to input BAM file"
    )
    parser.add_argument(
        "-o",
        "--output",
        type=str,
        required=True,
        help="path to output BAM file"
    )
    args = args[1:]
    return parser.parse_args(args)


def bamfilter(infile, outfile):
    insam = pysam.AlignmentFile(infile, "rb", check_sq=False)
    outsam = pysam.AlignmentFile(outfile, "wb", template=insam)
    for line in insam:
        read = BAM(line)
        flag = line.to_string().strip().split()[1]
        if (flag == "0" or flag == "16") and read.tzmw == read.qzmw:
            outsam.write(line)
    outsam.close()
    insam.close()
    pysam.index(outfile)


def main():
    options = parse_args(sys.argv)
    bamfilter(options.input, options.output)
    sys.exit(0)


if __name__ == "__main__":
    main()