def test_alignment_mmap(self):
self.aligner.mmap_enabled = True
# Generate the .sax and .rsax indices. They will be removed by tearDown.
bwa.make_suffix_arrays_for_mmap(utils.reference)
for row in self.pairs:
self.aligner.load_pair_record(row)
self.aligner.run_alignment()
# TODO: write a more useful test, but for that we'll need a complete test fixture
self.assertTrue( len(self.aligner.hit_visitor.output.getvalue()) > 0 )
def main(args):
if len(args) != 1:
usage_error()
index = args[0]
if os.path.exists(index + ".sax"):
usage_error("%s.sax exists. Refusing to overwrite it." % index)
elif os.path.exists(index + ".rsax"):
usage_error("%s.rsax exists. Refusing to overwrite it." % index)
print >>sys.stderr, "Converting indexed reference at %s. This might take a while...." % index
bwa.make_suffix_arrays_for_mmap(index)
print >>sys.stderr, "done!"
return 0
def main(args):
if len(args) != 2:
usage_error()
index = args[1]
if os.path.exists(index + ".sax"):
usage_error("%s.sax exists. Refusing to overwrite it." % index)
elif os.path.exists(index + ".rsax"):
usage_error("%s.rsax exists. Refusing to overwrite it." % index)
print >>sys.stderr, "Converting indexed reference at %s. This might take a while...." % index
bwa.make_suffix_arrays_for_mmap(index)
print >>sys.stderr, "done!"
return 0
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()
