help='create srf files tagged with the provided '\
'site name')
parser.add_option('--raw-format', dest="raw_format", default='qseq',
- choices=['qseq', 'srf'],
+ choices=['qseq', 'srf', 'fastq'],
help='Specify which type of raw format to use. '
'Currently supported options: qseq, srf, fastq')
parser.add_option('-u', '--use-run', dest='use_run', default=None,