def test_quality_decrease_with_mismatch(self): qual = 20 [base_call, score, cigar] = collapser_functions.call_base_posterior(('A', 'A'), (qual, qual)) [base_call_2, score_2, cigar_2] = collapser_functions.call_base_posterior(('A', 'A', 'T'), (qual, qual, qual)) new_qual = ord(score) - 33 new_qual_2 = ord(score_2) - 33 self.assertGreater(new_qual ,new_qual_2)
def test_quality_increase_with_coverage(self): # Check that increasing coverage increases quality qual = 20 [base_call, score, cigar] = collapser_functions.call_base_posterior(('A','A'), (qual, qual)) new_qual = ord(score) - 33 self.assertEqual(base_call, 'A') self.assertGreater(new_qual, qual)
def test_break_tie(self): [base_call, score, cigar] = collapser_functions.call_base_posterior(('A', 'A', 'T', 'T'), (11, 10, 10, 10)) self.assertEqual(base_call, 'A')
def test_best_base_wins(self): [base_call, score, cigar] = collapser_functions.call_base_posterior(('A', 'G', 'C','T'), (10, 10, 10, 30)) self.assertEqual(base_call, 'T')