def setUp(self):
utils.build_ref_index()
self.aligner = BwaAligner510()
self.aligner.reference = utils.reference
self.aligner.hit_visitor = type(self).SimpleVisitor()
self.pairs = []
with open(utils.get_fixture_path("pairs.txt")) as f:
for line in f:
if not line.startswith("#"): # leave #-lines for comments
self.pairs.append(line.rstrip("\r\n").split("\t"))
def test_make_mmap_sa(self):
try:
tu.build_ref_index()
bwa.make_suffix_arrays_for_mmap(tu.reference)
sax_name = "%s.sax" % tu.reference
rsax_name = "%s.rsax" % tu.reference
self.assertTrue(os.path.exists(sax_name))
self.assertTrue(os.path.exists(rsax_name))
# check magic
with open(sax_name) as f:
s = f.read(4)
self.assertEqual(4, len(s))
self.assertEqual(bwa.mmap_magic().value, struct.unpack("=I", s)[0])
with open(rsax_name) as f:
s = f.read(4)
self.assertEqual(4, len(s))
self.assertEqual(bwa.mmap_magic().value, struct.unpack("=I", s)[0])
finally:
tu.remove_ref_index()
def test_make_mmap_sa(self):
try:
tu.build_ref_index()
bwa.make_suffix_arrays_for_mmap(tu.reference)
sax_name = "%s.sax" % tu.reference
rsax_name = "%s.rsax" % tu.reference
self.assertTrue(os.path.exists(sax_name))
self.assertTrue(os.path.exists(rsax_name))
# check magic
with open(sax_name) as f:
s = f.read(4)
self.assertEqual(4, len(s))
self.assertEqual(bwa.mmap_magic().value,
struct.unpack("=I", s)[0])
with open(rsax_name) as f:
s = f.read(4)
self.assertEqual(4, len(s))
self.assertEqual(bwa.mmap_magic().value,
struct.unpack("=I", s)[0])
finally:
tu.remove_ref_index()