@Test(expectedExceptions = IllegalStateException.class)
public void testStrandlessReadsFailSetStrand() {
final byte[] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] quals = {20, 20, 20, 20, 20, 20, 20, 20};
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
read.setIsStrandless(true);
read.setReadNegativeStrandFlag(true);
}
@Test
public void testStrandlessReads() {
final byte[] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
final byte[] quals = {20, 20, 20, 20, 20, 20, 20, 20};
GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
Assert.assertEquals(read.isStrandless(), false);
read.setReadNegativeStrandFlag(false);
Assert.assertEquals(read.isStrandless(), false);
Assert.assertEquals(read.getReadNegativeStrandFlag(), false);
read.setReadNegativeStrandFlag(true);
Assert.assertEquals(read.isStrandless(), false);
Assert.assertEquals(read.getReadNegativeStrandFlag(), true);
read.setReadNegativeStrandFlag(true);
read.setIsStrandless(true);
Assert.assertEquals(read.isStrandless(), true);
Assert.assertEquals(
read.getReadNegativeStrandFlag(),
false,
"negative strand flag should return false even through its set for a strandless read");
}