def test_MultipleDuplicates_ReturnOneR1AndOneR2(self):
r1, r2 = bam2fastq.get_unique_reads_pairs(self.reads[:9])
expected_r1 = [self.reads[0]]
expected_r2 = [self.reads[4]]
self.assertListEqual(r1, expected_r1)
self.assertListEqual(r2, expected_r2)
def test_EmptyReads_ReturnEmptyLists(self):
r1, r2 = bam2fastq.get_unique_reads_pairs([])
expected_r1 = []
expected_r2 = []
self.assertListEqual(r1, expected_r1)
self.assertListEqual(r2, expected_r2)
def test_OneR1OneR2_ReturnOneR1AndOneR2(self):
r1, r2 = bam2fastq.get_unique_reads_pairs(
[self.reads[0], self.reads[4]])
expected_r1 = [self.reads[0]]
expected_r2 = [self.reads[4]]
self.assertListEqual(r1, expected_r1)
self.assertListEqual(r2, expected_r2)
def test_MultipleDuplicatesNoPrimary_ReturnOneR1AndOneR2(self):
r1, r2 = bam2fastq.get_unique_reads_pairs(
[self.reads[2], self.reads[3], self.reads[6]])
expected_r1 = [self.reads[2]]
expected_r2 = [self.reads[6]]
self.assertListEqual(r1, expected_r1)
self.assertListEqual(r2, expected_r2)
def test_MultipleDuplicatesTwoReadGroups_ReturnTwoPairsOfReads(self):
self.reads[1].set_tag('RG', 'test')
self.reads[6].set_tag('RG', 'test')
r1, r2 = bam2fastq.get_unique_reads_pairs(self.reads)
expected_r1 = self.reads[:2]
expected_r2 = [self.reads[4], self.reads[6]]
self.assertListEqual(r1, expected_r1)
self.assertListEqual(r2, expected_r2)
def test_OneR2_RaiseAssertError(self):
with self.assertRaises(AssertionError):
bam2fastq.get_unique_reads_pairs(self.reads[4:5])