def test_filter_mapped_paired(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
subprocess.run = MagicMock(side_effect=create_file)
fb.filter_mapped(bam, output, True)
subprocess.run.assert_any_call(
['samtools', 'view', '-b', '-F', '2048', '-f', '2', '-o', ANY, bam],
check=True)
subprocess.run.assert_any_call(['samtools', 'sort', '-o', output, ANY],
check=True)
assert subprocess.run.call_args_list[0].args[0][
8] == subprocess.run.call_args_list[1].args[0][4]
def test_filter_mapped_single_threads(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
threads = 3
subprocess.run = MagicMock(side_effect=create_file)
fb.filter_mapped(bam, output, False, threads)
subprocess.run.assert_any_call([
'samtools', 'view', '-b', '-F', '2048', '-F', '4', '--threads',
str(threads - 1), '-o', ANY, bam
],
check=True)
subprocess.run.assert_any_call(
['samtools', 'sort', '--threads',
str(threads - 1), '-o', output, ANY],
check=True)
assert subprocess.run.call_args_list[0].args[0][
10] == subprocess.run.call_args_list[1].args[0][6]