def test_write_sam_pairs(self):
reader = ["line1\n", "line2\n"]
read1 = MockSplitRead("key1", "L")
read2 = MockSplitRead("key2", "R")
builder = MockSplitReadBuilder({'line1': read1, 'line2' : read2}, set(["@header1", "@header2"]))
read_group_pairs = {}
_write_sam_pairs(read_group_pairs, reader, builder, MockWriter(), MockLogger())
self.assertEqual(1, read1.write_sam_pairs_called)
self.assertEqual(1, read2.write_sam_pairs_called)
def test_write_sam_pairs_headersPassThrough(self):
reader = ["@header1\n","@header2\n"]
builder = MockSplitReadBuilder({}, set(["@header1", "@header2"]))
writer = MockWriter()
read_group_pairs = {}
_write_sam_pairs(read_group_pairs, reader, builder, writer, MockLogger())
actual_lines = writer.lines()
self.assertEqual(2, len(actual_lines))
self.assertEqual("@header1", actual_lines[0])
self.assertEqual("@header2", actual_lines[1])
