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()