def __init__(self, args):
super().__init__(args)
self.control_bam = args.control_bam
self.control_var = args.control_var
self.g1k_var = args.g1k_var
self.germ_het_var = args.germ_het_var
if self.true_file_ok:
self.true_jid = ''
self.q.__class__.is_1st_print = False
skip_msg('truefile', 'For all samples')
else:
self.true_jid = self._truefile()
run_msg('truefile', 'For all samples')
def _run_msg(self, jname):
run_msg(jname, '{}.all'.format(self.sample_name))