def mini(args):
    """
    %prog mini bamfile minibamfile

    Prepare mini-BAMs that contain only the STR loci.
    """
    p = OptionParser(mini.__doc__)
    p.add_option("--pad", default=20000, type="int",
                 help="Add padding to the STR reigons")
    p.add_option("--treds", default=None,
                 help="Extract specific treds, use comma to separate")
    p.set_outfile()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    bamfile, minibam = args
    treds = opts.treds.split(",") if opts.treds else None
    pad = opts.pad
    bedfile = make_STR_bed(pad=pad, treds=treds)

    get_minibam_bed(bamfile, bedfile, minibam)
    logging.debug("Mini-BAM written to `{}`".format(minibam))
def mini ( args ) : p = OptionParser ( mini . __doc__ ) p . add_option ( "--pad" , default = 20000 , type = "int" , help = "Add padding to the STR reigons" ) p . add_option ( "--treds" , default = None , help = "Extract specific treds, use comma to separate" ) p . set_outfile ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) bamfile , minibam = args treds = opts . treds . split ( "," ) if opts . treds else None pad = opts . pad bedfile = make_STR_bed ( pad = pad , treds = treds ) get_minibam_bed ( bamfile , bedfile , minibam ) logging . debug ( "Mini-BAM written to `{}`" . format ( minibam ) )
%prog mini bamfile minibamfile

    Prepare mini-BAMs that contain only the STR loci.