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')