# open the srf, fastq, or compressed fastq
if is_srf(args[0]):
- source = srf_open(args[0])
+ source = srf_open(args[0], opts.cnf1)
else:
source = autoopen(args[0])
help="show information about what we're doing.")
parser.add_option('--version', default=False, action="store_true",
help="Report software version")
+ parser.add_option('--cnf1', default=False, action="store_true",
+ help="Force cnf1 mode in srf2fastq")
return parser
Make a stream from srf file using srf2fastq
"""
cmd = ['srf2fastq']
- if is_cnf1(filename):
+ if cnf1 or is_cnf1(filename):
cmd.append('-c')
cmd.append(filename)