Merge pull request #298 from jodyphelan/dev

remove redundant arguments

tb-profiler

@@ -349,9 +349,6 @@ algorithm.add_argument('--mapper',default="bwa", choices=["bwa","minimap2","bowt
 algorithm.add_argument('--caller',default="freebayes", choices=["bcftools","gatk","freebayes","pilon","lofreq"],help="Variant calling tool to use.",type=str)
 algorithm.add_argument('--calling_params',type=str,help='Override default parameters for variant calling')
 algorithm.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
-algorithm.add_argument('--min_depth',default=10,type=int,help='Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing')
-algorithm.add_argument('--strand_support',default=5,type=float,help='Minimum number of reads on each strand supporting the alternate allele')
-algorithm.add_argument('--reporting_af',default=0.1,type=float,help='Minimum allele frequency to use variants for prediction')
 algorithm.add_argument('--suspect',action="store_true",help="Use the suspect suite of tools to add ML predictions")
 algorithm.add_argument('--spoligotype',action="store_true",help="Perform in-silico spoligotyping")
 algorithm.add_argument('--update_phylo',action="store_true",help="Update phylogeny using usher (experimental feature)")