def usage(msg=None):
    if msg:
        sys.stdout.write('%s\n\n' % msg)
    sys.stdout.write(__doc__)
    sys.stdout.write('''\
Usage: bamutils pcrdup {options} infile.bam

Options:
    -frag                The reads are single-end fragments, so mark PCR
                         duplicated based only on the location of the read 
                         (not-recommended)

    -bam filename        Output BAM file with PCR duplicates marked

    -counts filename     Output of the number of reads at each position 

                         Note: this is actually the number of duplicate reads
                         at each position. If a position has multiple reads
                         mapped to it, but they are not pcr duplicates, then
                         there each will be reported separately.

    You must set either -bam or -counts (or both).

''')

    sys.exit(1)
dataset/ETHPy150Open ngsutils/ngsutils/ngsutils/bam/pcrdup.py/usage/original