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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.fastq;
import java.io.InputStream;
import java.io.IOException;
import java.net.URL;
/**
* Unit test for IlluminaFastqReader.
*/
public final class IlluminaFastqReaderTest
extends AbstractFastqReaderTest
{
/** {@inheritDoc} */
protected Fastq createFastq()
{
return new FastqBuilder()
.withDescription("description")
.withSequence("sequence")
.withQuality("quality_")
.withVariant(FastqVariant.FASTQ_ILLUMINA)
.build();
}
/** {@inheritDoc} */
protected FastqReader createFastqReader()
{
return new IlluminaFastqReader();
}
/** {@inheritDoc} */
protected FastqWriter createFastqWriter()
{
return new IlluminaFastqWriter();
}
public void testValidateDescription() throws Exception
{
IlluminaFastqReader reader = new IlluminaFastqReader();
URL invalidDescription = getClass().getResource("illumina-invalid-description.fastq");
try
{
reader.read(invalidDescription);
fail("read(invalidDescription) expected IOException");
}
catch (IOException e)
{
assertTrue(e.getMessage().contains("description must begin with a '@' character"));
}
}
public void testValidateRepeatDescription() throws Exception
{
IlluminaFastqReader reader = new IlluminaFastqReader();
URL invalidRepeatDescription = getClass().getResource("illumina-invalid-repeat-description.fastq");
try
{
reader.read(invalidRepeatDescription);
fail("read(invalidRepeatDescription) expected IOException");
}
catch (IOException e)
{
assertTrue(e.getMessage().contains("repeat description must match description"));
}
}
public void testWrappingAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("wrapping_as_illumina.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(3, count);
inputStream.close();
}
public void testFullRangeAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("illumina_full_range_as_illumina.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(2, count);
inputStream.close();
}
public void testMiscDnaAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_dna_as_illumina.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(4, count);
inputStream.close();
}
public void testMiscRnaAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("misc_rna_as_illumina.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(4, count);
inputStream.close();
}
public void testLongReadsAsIllumina() throws Exception
{
FastqReader reader = createFastqReader();
InputStream inputStream = getClass().getResourceAsStream("longreads_as_illumina.fastq");
Iterable<Fastq> iterable = reader.read(inputStream);
assertNotNull(iterable);
int count = 0;
for (Fastq f : iterable)
{
assertNotNull(f);
count++;
}
assertEquals(10, count);
inputStream.close();
}
}
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