def run( o_options ):
    """The Main function/pipeline for duplication filter.
    
    """
    # Parse options...
    options = opt_validate( o_options )
    # end of parsing commandline options
    info = options.info
    warn = options.warn
    debug = options.debug
    error = options.error
    #0 output arguments
    assert options.format != 'BAMPE', "Pair-end data with BAMPE option currently doesn't work with pileup command. You can pretend your data to be single-end with -f BAM. Please try again!"

    #0 prepare output file
    outfile = os.path.join( options.outdir, options.outputfile )
    if os.path.isfile( outfile ):
        info("# Existing file %s will be replaced!" % outfile )
        os.unlink( outfile )

    #1 Read tag files
    info("# read alignment files...")
    (tsize, treat) = load_tag_files_options  (options)
    
    info("# tag size = %d", tsize)
    
    t0 = treat.total
    info("# total tags in alignment file: %d", t0)

    if options.bothdirection:
        info("# Pileup alignment file, extend each read towards up/downstream direction with %d bps" % options.extsize)
        pileup_and_write(treat, outfile, options.extsize * 2, 1, directional=False, halfextension=False)
    else:
        info("# Pileup alignment file, extend each read towards downstream direction with %d bps" % options.extsize)
        pileup_and_write(treat, outfile, options.extsize, 1, directional=True, halfextension=False)

    info("# Done! Check %s" % options.outputfile)
dataset/ETHPy150Open taoliu/MACS/MACS2/pileup_cmd.py/run/original