add --barcoding-snps

tb-profiler

@@ -404,7 +404,7 @@ parser_sub.set_defaults(func=main_profile)
 parser_sub = subparsers.add_parser('lineage', help='Profile only lineage', formatter_class=ArgumentDefaultsRichHelpFormatter)
 parser_sub.add_argument('--bam','-a',required=True, help='BAM file. Make sure it has been generated using the H37Rv genome (GCA_000195955.2)')
 parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix')
-parser_sub.add_argument('--snps',action="store_true",help='Sample prefix')
+parser_sub.add_argument('--barcode_snps','--barcode-snps',help='Dump barcoding mutations to a file')
 parser_sub.add_argument('--caller',default='freebayes',choices=["bcftools","freebayes","gatk"],type=str,help="Variant caller")
 parser_sub.add_argument('--kmer_counter','--kmer-counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
 parser_sub.add_argument('--platform','-m',choices=["illumina","nanopore","pacbio"],default="illumina",help='NGS Platform used to generate data')