parser.add_argument('-g','--germlines',type=file,default='germlines.data',help='path to the germlines.data file')
parser.add_argument('-g','--germlines',type=file,default='homo-sapiens.g',help='path to the germlines.data file')
parser.add_argument('--deletions','-d',type=list_int,default=[(lambda:5)],help='List -- separated by colons -- of the number of deletions at junctions (or single value, if the number is the same everywhere).')
parser.add_argument('--insertions','-i',type=list_int,default=[(lambda:3)],help='List -- separated by colons -- of the number of insertions at junctions (or single value, if the number is the same everywhere')
parser.add_argument('--random-deletions','-D',type=list_random_tuple,help='List of random deletions at junctions under the format mean,standard_deviation (or single value, if the number is the same everywhere')