@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(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
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());
}
@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
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(expected = IllegalArgumentException.class)
public void testNoNullSequence() {
frag.setSequence(null);
}
@Test
public void testSerializationWithSeq() throws IOException {
frag.setSequence(new Text("AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"));
frag.setQuality(new Text("##############################"));
assertEquals(frag, cloneBySerialization(frag));
}