def test_filter_sam(self):
"""Test filter_sam."""
in_sam = op.join(self.data_dir, "test_filter_sam.sam")
out_sam = op.join(self.out_dir, "test_filter_sam.sam")
stdout_sam = op.join(self.stdout_dir, "test_filter_sam.sam")
filter_sam(in_sam=in_sam, out_sam=out_sam)
self.assertTrue(filecmp.cmp(out_sam, stdout_sam))
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=self.getVersion()))
try:
filter_sam(self.args.in_sam, self.args.out_sam)
except ValueError as e:
logging.error(str(e))
import traceback
traceback.print_exc()
return 1
return 0
def run(self):
"""Run"""
logging.info("Running {f} v{v}.".format(f=op.basename(__file__),
v=self.getVersion()))
try:
filter_sam(self.args.in_sam, self.args.out_sam)
except ValueError as e:
logging.error(str(e))
import traceback
traceback.print_exc()
return 1
return 0
