@Test
public void testEqualsQuality() {
frag.getQuality().append("AAAA".getBytes(), 0, 4);
assertFalse(frag.equals(frag2));
frag2.getQuality().append("AAAA".getBytes(), 0, 4);
assertTrue(frag.equals(frag2));
}
@Test
public void testConvertQualitySangerToIllumina() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("[[[[[[[[[[[[[[[[[[[[[[[[[[[[[["));
SequencedFragment.convertQuality(
frag.getQuality(),
FormatConstants.BaseQualityEncoding.Sanger,
FormatConstants.BaseQualityEncoding.Illumina);
assertEquals("zzzzzzzzzzzzzzzzzzzzzzzzzzzzzz", frag.getQuality().toString());
}
@Test
public void testVerifyQualitySangerOutOfRange() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(
new Text("#############################" + Character.toString((char) 127))); // over range
assertEquals(
29,
SequencedFragment.verifyQuality(
frag.getQuality(), FormatConstants.BaseQualityEncoding.Sanger));
frag.setQuality(new Text("##### ########################")); // under range
assertEquals(
5,
SequencedFragment.verifyQuality(
frag.getQuality(), FormatConstants.BaseQualityEncoding.Sanger));
}
@Test(expected = FormatException.class)
public void testConvertQualitySangerUnderRange() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("### ##########################"));
SequencedFragment.convertQuality(
frag.getQuality(),
FormatConstants.BaseQualityEncoding.Sanger,
FormatConstants.BaseQualityEncoding.Illumina);
}
@Test(expected = IllegalArgumentException.class)
public void testConvertQualityNoop() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("[[[[[[[[[[[[[[[[[[[[[[[[[[[[[["));
SequencedFragment.convertQuality(
frag.getQuality(),
FormatConstants.BaseQualityEncoding.Sanger,
FormatConstants.BaseQualityEncoding.Sanger);
}
@Test
public void testVerifyQualityIlluminaOutOfRange() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("zzz=zzzzzzzzzzzzzzzzzzzzzzzzzz"));
assertEquals(
3,
SequencedFragment.verifyQuality(
frag.getQuality(), FormatConstants.BaseQualityEncoding.Illumina));
}
@Test
public void testVerifyQualitySangerOk() {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("##############################"));
assertEquals(
-1,
SequencedFragment.verifyQuality(
frag.getQuality(), FormatConstants.BaseQualityEncoding.Sanger));
}
@Test
public void testInitialState() {
assertNotNull(frag.getSequence());
assertNotNull(frag.getQuality());
assertNull(frag.getInstrument());
assertNull(frag.getRunNumber());
assertNull(frag.getFlowcellId());
assertNull(frag.getLane());
assertNull(frag.getTile());
assertNull(frag.getXpos());
assertNull(frag.getYpos());
assertNull(frag.getRead());
assertNull(frag.getFilterPassed());
assertNull(frag.getControlNumber());
assertNull(frag.getIndexSequence());
assertNotNull(frag.toString());
}
