Merge pull request #13 from martinghunt/limit_total_alleles

Bug fix parsing options with adjudicate

scripts/minos

@@ -30,7 +30,7 @@ subparser_adjudicate = subparsers.add_parser(
 
 subparser_adjudicate.add_argument('--max_read_length', type=int, help='Maximum read length, this is used by gramtools [%(default)s]', default=150, metavar='INT')
 subparser_adjudicate.add_argument('--read_error_rate', type=float, help='Read error rate. If not given, is estimated from quality scores of first 10,000 reads', metavar='FLOAT')
-subparser_cluster_vcfs.add_argument('--max_alleles_per_cluster', type=int, help='Maximum allowed alleles in one cluster. If there are too many alleles then combinations of SNPs are not generated. Default is no maximum', metavar='INT')
+subparser_adjudicate.add_argument('--max_alleles_per_cluster', type=int, help='Maximum allowed alleles in one cluster. If there are too many alleles then combinations of SNPs are not generated. Default is no maximum', metavar='INT')
 subparser_adjudicate.add_argument('--force', action='store_true', help='Replace outdir, if it already exists')
 subparser_adjudicate.add_argument('--reads', action='append', required=True, help='REQUIRED. Reads file. Can be any format compatible with htslib. Use this option more than once for >1 reads files', metavar='FILENAME')
 subparser_adjudicate.add_argument('outdir', help='Name of output directory')