#!/usr/bin/env python
#usage: python filter_out_reads_with_less_than_80QC.py bwa_mem_ont2d_CB_2D_1D_to_GRCm38_cdna_all.sorted.no_secondary.bam bwa_mem_ont2d_CB_2D_1D_to_GRCm38_cdna_all.sorted.no_secondary.no_read_less_than_80QC.bam
import pysam
import sys

inputFile = pysam.AlignmentFile(sys.argv[1], "rb")
outputFile = pysam.AlignmentFile(sys.argv[2], "wb", template=inputFile)

def analyzeRead(x):
    if (x.is_secondary):
        pass
    elif (x.is_supplementary):
        pass
    elif (x.is_unmapped):
        pass
    else:
        lengthRead = x.infer_query_length()
        lengthAlignment = x.query_alignment_length
        percentAlignment = lengthAlignment / float(lengthRead)
        if percentAlignment>=0.8:
          outputFile.write(x)

def main():
    for read in inputFile:
      analyzeRead(read)
    inputFile.close()
    outputFile.close()


if __name__ == "__main__":
    main()