@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 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));
}