def callHaplogroups(useDefaultCmdLineArgs=False,
suppressOutputAndLog=False,
outDir=None,
residList=None):
'configures run, builds tree, and calls haplogroups'
config = Config(useDefaultCmdLineArgs=useDefaultCmdLineArgs,
suppressOutputAndLog=suppressOutputAndLog,
outDir=outDir,
residList=residList)
tree = Tree(config)
Sample.callHaplogroups(config, tree)
