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)