#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import sys
import pysam
import collections
import argparse
import pandas as pd
import singlecellmultiomics
import singlecellmultiomics.molecule
import singlecellmultiomics.modularDemultiplexer
TagDefinitions = singlecellmultiomics.modularDemultiplexer.TagDefinitions

if __name__ == '__main__':
    argparser = argparse.ArgumentParser(
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
        description='Obtain duplication rate on the fly')

    argparser.add_argument('alignmentfile', type=str)
    argparser.add_argument('-u', type=int, default=10_000)
    args = argparser.parse_args()

    molecule_count = 0
    read_count = 0
    f = pysam.AlignmentFile(args.alignmentfile)

    for i, read in enumerate(f):
        read_count += 1
        if read.is_duplicate:
            pass
        else:
            molecule_count += 1

        if i % args.u == 0:
            print(f'\r{read_count/molecule_count}             ', end='')