def setUp(self, get_raw_reads_function):
#self.raw_reads = self.mock_get_raw_reads("", "")
self.reads = short_mock_get_alignments('', '')
self.raw_reads = mock_get_raw_reads('', '')
self.matrix = DepthMatrix(3, allow_orphans=True)
self.matrix.make_seq_matrix("", "")
