@Test(dataProvider = "seekingTests")
public void seekToTileTest(
Integer firstSeekPos, Integer firstTile, Integer secondSeekPos, Integer secondTile) {
final PerTileParser<DummyDt> ddts = new MockPerTileParser(FILE_MAP);
for (int i = 1; i <= firstSeekPos; i++) {
Assert.assertTrue(ddts.hasNext());
Assert.assertEquals(ddts.next().value, new Integer(i));
}
ddts.seekToTile(firstTile);
int start = firstTile * 5 - 4;
if (secondSeekPos != null) {
for (int i = start; i <= secondSeekPos; i++) {
Assert.assertTrue(ddts.hasNext());
Assert.assertEquals(ddts.next().value, new Integer(i));
}
ddts.seekToTile(secondTile);
start = secondTile * 5 - 4;
}
for (int i = start; i <= 25; i++) {
Assert.assertTrue(ddts.hasNext());
Assert.assertEquals(ddts.next().value, new Integer(i));
}
Assert.assertFalse(ddts.hasNext());
}
@Test
public void basicIterationTest() {
final IlluminaFileMap fm = new IlluminaFileMap();
fm.put(1, new File("s_1_1"));
fm.put(2, new File("s_1_2"));
fm.put(3, new File("s_1_3"));
fm.put(4, new File("s_1_4"));
fm.put(5, new File("s_1_5"));
final PerTileParser<DummyDt> ddts = new MockPerTileParser(fm);
for (int i = 0; i < 25; i++) {
Assert.assertTrue(ddts.hasNext());
Assert.assertEquals(ddts.next().value, new Integer(i + 1));
}
Assert.assertFalse(ddts.hasNext());
}
@Test
public void passVerifyTest() {
final PerTileParser<DummyDt> ddts = new MockPerTileParser(FILE_MAP);
ddts.verifyData(makeList(1, 2, 3, 4, 5), null);
}
@Test(expectedExceptions = PicardException.class)
public void failVerifyTestMissingTile() {
final PerTileParser<DummyDt> ddts = new MockPerTileParser(FILE_MAP);
ddts.verifyData(makeList(1, 2, 4, 5), null);
}
@Test(expectedExceptions = PicardException.class, dataProvider = "missingTiles")
public void missingTileTest(final Integer missingTile) {
final PerTileParser<DummyDt> ddts = new MockPerTileParser(FILE_MAP);
ddts.seekToTile(missingTile);
}
