parser.add_argument('-np','--no-pickle',dest='dopickle',default=True,action='store_false',help='do not generate pickle database [default: no]')
parser.add_argument('-t','--sub_threads',dest='sub_threads',default=5,nargs='?',type=int,help='threads of submake to tree building [default: 5]')
parser.add_argument('-St','--smart_threads',dest='smart_threads',default=None,nargs='?',type=int,help='threads of submake to tree building [default: 5]')
...
...
@@ -175,12 +175,13 @@ def main(args):
parser.add_argument('-SS','--simplify-include-singleton',dest='simplify_do_singleton_filter',default=True,action='store_false',help='Do not simplify single SNPS')
parser.add_argument('-Coc','--concat-chrom','--concat-chromosome',dest='concat_chromosome',default=None,nargs='?',action='store',type=str,help='Concat - Chromosome to filter [all]')
parser.add_argument('-Coc','--concat-chrom','--concat-chromosome',dest='concat_chromosome',default=None,nargs='?',action='store',type=str,help='Concat - Chromosome to filter [all]')
parser.add_argument('-CoI','--concat-ignore','--concat-skip',dest='concat_ignore',default=[],nargs='*',action='append',type=str,help='Concat - Chromosomes to skip')
parser.add_argument('-Cos','--concat-start',dest='concat_start',default=None,nargs='?',action='store',type=int,help='Concat - Chromosome start position to filter [0]')
parser.add_argument('-Coe','--concat-end',dest='concat_end',default=None,nargs='?',action='store',type=int,help='Concat - Chromosome end position to filter [-1]')
parser.add_argument('-Cot','--concat-threads',dest='concat_threads',default=None,nargs='?',action='store',type=int,help='Concat - Number of threads [num chromosomes]')
parser.add_argument('-Cor','--concat-noref',dest='concat_noref',action='store_false',help='Concat - Do not print reference [default: true]')
parser.add_argument('-Con','--concat-ref-name',dest='concat_refname',default=None,nargs='?',action='store',type=str,help='Concat - Reference name [default: ref]')
parser.add_argument('-CoRm','--concat-RIL-mads',dest='concat_RILmads',default=None,nargs='?',action='store',type=float,help='Concat - RIL percentage of Median Absolute Deviation to use (smaller = more restrictive): 0.25]')
parser.add_argument('-CoRs','--concat-RIL-minsim',dest='concat_RILminsim',default=None,nargs='?',action='store',type=float,help='Concat - RIL percentage of nucleotides identical to reference to classify as reference: 0.75]')
parser.add_argument('-Rm','--RIL-mads',dest='RILmads',default=0.25,action='store',nargs='?',type=float,help='RIL percentage of Median Absolute Deviation to use (smaller = more restrictive): 0.25]')
parser.add_argument('-Rs','--RIL-minsim',dest='RILminsim',default=0.75,action='store',nargs='?',type=float,help='RIL percentage of nucleotides identical to reference to classify as reference: 0.75]')
parser.add_argument('-Rg','--RIL-greedy',dest='RILgreedy',action='store_true',help='RIL greedy convert nucleotides to either the reference sequence or the alternative sequence: false]')
parser.add_argument('-M','--RIL-method',dest='groupMethod',default=dflmethod,action='store',nargs='?',choices=methods.keys(),type=str,help='Clustering method for RIL selection of good and bad sequences ['+','.join(methods.keys())+']')
parser.add_argument('-Rm','--RIL-mads',dest='RILmads',default=0.25,action='store',nargs='?',type=float,help='RIL percentage of Median Absolute Deviation to use (smaller = more restrictive): 0.25]')
parser.add_argument('-Rs','--RIL-minsim',dest='RILminsim',default=0.75,action='store',nargs='?',type=float,help='RIL percentage of nucleotides identical to reference to classify as reference: 0.75]')
parser.add_argument('-Rg','--RIL-greedy',dest='RILgreedy',action='store_true',help='RIL greedy convert nucleotides to either the reference sequence or the alternative sequence: false]')
parser.add_argument('-M','--RIL-method',dest='groupMethod',default=dflmethod,action='store',nargs='?',choices=methods.keys(),type=str,help='Clustering method for RIL selection of good and bad sequences ['+','.join(methods.keys())+']')
assertset(config['idx'].keys())<=set(config['ingffreader'].index.keys()),"VCF chromosomes (%s) are not a subset from GFF (%s)"%(", ".join(config['idx'].keys()),", ".join(config['ingffreader'].index.keys()))
assertset(config['ingffreader'].index.keys()).issubset(set(config['idx'].keys())),"VCF chromosomes (%s) are not a subset from GFF (%s)"%(", ".join(config['idx'].keys()),", ".join(config['ingffreader'].index.keys()))