@Test
public void basicReadIteratorTest() {
StingSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 100);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
count++;
}
assertEquals(count, 100 * 100);
}
@Test
public void onePerChromosome() {
StingSAMIterator iter = ArtificialSAMUtils.mappedReadIterator(1, 100, 1);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
assertEquals(Integer.valueOf(count), rec.getReferenceIndex());
count++;
}
assertEquals(count, 100 * 1);
}
@Test
public void basicUnmappedIteratorTest() {
StingSAMIterator iter = ArtificialSAMUtils.mappedAndUnmappedReadIterator(1, 100, 100, 1000);
int count = 0;
for (int x = 0; x < (100 * 100); x++) {
if (!iter.hasNext()) {
fail("we didn't get the expected number of reads");
}
SAMRecord rec = iter.next();
assertTrue(rec.getReferenceIndex() >= 0);
count++;
}
assertEquals(100 * 100, count);
// now we should have 1000 unmapped reads
count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
assertTrue(rec.getReferenceIndex() < 0);
count++;
}
assertEquals(count, 1000);
}