def setUp(self):
self.parser = argparse.ArgumentParser()
self.parser.set_defaults(level=logging.DEBUG)
self.args = self.parser.parse_args([])
self.logger = main.setup_logging(self.args)
current_dir = os.path.dirname(os.path.realpath(__file__))
sam = os.path.join(current_dir, 'data', SAMFILE)
self.bam = util.subprocess_make_bam(sam, self.logger)
def setUp(self):
self.parser = argparse.ArgumentParser()
self.parser.set_defaults(level=logging.DEBUG)
self.args = self.parser.parse_args([])
self.logger = main.setup_logging(self.args)
current_dir = os.path.dirname(os.path.realpath(__file__))
sam = os.path.join(current_dir, 'data', SAMFILE)
expectedjson = os.path.join(current_dir, 'data', EXPECTEDJSON)
with open(expectedjson, 'r') as f:
self.expecteddata = json.load(f)
self.bam = util.make_bam(sam)