@Test
public void testEqualsFilterPassed() {
frag.setFilterPassed(false);
assertFalse(frag.equals(frag2));
frag2.setFilterPassed(false);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsControlNumber() {
frag.setControlNumber(314);
assertFalse(frag.equals(frag2));
frag2.setControlNumber(314);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsYpos() {
frag.setYpos(1234);
assertFalse(frag.equals(frag2));
frag2.setYpos(1234);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsRead() {
frag.setRead(2);
assertFalse(frag.equals(frag2));
frag2.setRead(2);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsTile() {
frag.setTile(1000);
assertFalse(frag.equals(frag2));
frag2.setTile(1000);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsLane() {
frag.setLane(2);
assertFalse(frag.equals(frag2));
frag2.setLane(2);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsFlowcellId() {
frag.setFlowcellId("id");
assertFalse(frag.equals(frag2));
frag2.setFlowcellId("id");
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsIndexSequence() {
frag.setIndexSequence("ABC");
assertFalse(frag.equals(frag2));
frag2.setIndexSequence("ABC");
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsSequence() {
frag.getSequence().append("AAAA".getBytes(), 0, 4);
assertFalse(frag.equals(frag2));
frag2.getSequence().append("AAAA".getBytes(), 0, 4);
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsInstrument() {
frag.setInstrument("instrument");
assertFalse(frag.equals(frag2));
frag2.setInstrument("instrument");
assertTrue(frag.equals(frag2));
}
@Test
public void testEqualsRunNumber() {
frag.setRunNumber(240);
assertFalse(frag.equals(frag2));
frag2.setRunNumber(240);
assertTrue(frag.equals(frag2));
}
@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 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());
}
///////////////////////////////////////////////////////////////
// serialization
///////////////////////////////////////////////////////////////
private static SequencedFragment cloneBySerialization(SequencedFragment original)
throws IOException {
ByteArrayOutputStream outputBuffer = new ByteArrayOutputStream();
DataOutputStream dataOutput = new DataOutputStream(outputBuffer);
original.write(dataOutput);
dataOutput.close();
SequencedFragment newFrag = new SequencedFragment();
newFrag.readFields(new DataInputStream(new ByteArrayInputStream(outputBuffer.toByteArray())));
return newFrag;
}
@Test
public void testSerializationWithFields() throws IOException {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB"));
frag.setInstrument("machine");
frag.setLane(3);
frag.setRead(1);
frag.setIndexSequence("CAT");
assertEquals(frag, cloneBySerialization(frag));
}
@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 = IllegalArgumentException.class)
public void testNoNullQuality() {
frag.setQuality(null);
}
@Test(expected = IllegalArgumentException.class)
public void testNoNullSequence() {
frag.setSequence(null);
}
@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());
}
@Test
public void testToString() {
String seq = "AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT";
String qual = "##############################";
frag.setSequence(new Text(seq));
frag.setQuality(new Text(qual));
frag.setInstrument("machine");
frag.setRunNumber(123);
frag.setFlowcellId("flowcell");
frag.setLane(3);
frag.setTile(1001);
frag.setXpos(1234);
frag.setYpos(4321);
frag.setIndexSequence("CAT");
frag.setRead(1);
assertEquals(
"machine\t123\tflowcell\t3\t1001\t1234\t4321\tCAT\t1\t" + seq + "\t" + qual + "\t1",
frag.toString());
}
@Test
public void testSerializationWithSeq() throws IOException {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("##############################"));
assertEquals(frag, cloneBySerialization(frag));
}