def test_randomer_match_pos(self): """ same start same randomer pos """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file("test_cross_contamination/positive_match.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_randomer_match_neg2(self): """ same start same randomer neg, with the other offset """ bam1 = tests.get_file("test_cross_contamination/negative2.bam") bam2 = tests.get_file("test_cross_contamination/negative_match.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_duplicate_pos(self): """ same start / with target having both a matching and not matching randomer at that location """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file("test_cross_contamination/positive_duplicate.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_randomer_mismatch_neg(self): """ same start different randomer neg """ bam1 = tests.get_file("test_cross_contamination/negative1.bam") bam2 = tests.get_file("test_cross_contamination/negative_mismatch.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)
def test_pos_vs_neg(self): """ tests same read with same barcode but different strand """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file("test_cross_contamination/negative1.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)
def test_randomer_match_neg2(self): """ same start same randomer neg, with the other offset """ bam1 = tests.get_file("test_cross_contamination/negative2.bam") bam2 = tests.get_file("test_cross_contamination/negative_match.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_randomer_match_pos(self): """ same start same randomer pos """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file("test_cross_contamination/positive_match.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_randomer_mismatch_neg(self): """ same start different randomer neg """ bam1 = tests.get_file("test_cross_contamination/negative1.bam") bam2 = tests.get_file("test_cross_contamination/negative_mismatch.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)
def test_randomer_off_by_one_neg(self): """ test off by one bug same randomer by off by one neg """ bam1 = tests.get_file("test_cross_contamination/negative1.bam") bam2 = tests.get_file("test_cross_contamination/negative_off_by_one.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)
def test_pos_vs_neg(self): """ tests same read with same barcode but different strand """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file("test_cross_contamination/negative1.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)
def test_duplicate_pos(self): """ same start / with target having both a matching and not matching randomer at that location """ bam1 = tests.get_file("test_cross_contamination/positive1.bam") bam2 = tests.get_file( "test_cross_contamination/positive_duplicate.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 1)
def test_randomer_off_by_one_neg(self): """ test off by one bug same randomer by off by one neg """ bam1 = tests.get_file("test_cross_contamination/negative1.bam") bam2 = tests.get_file( "test_cross_contamination/negative_off_by_one.bam") matched, total = correlation(bam1, bam2, "out.sam") self.assertEqual(total, 1) self.assertEqual(matched, 0)