com.milaboratory.core.io.sequence.fastq

Class PairedFastqReader

java.lang.Object

com.milaboratory.core.io.sequence.AbstractSequenceReader<R>

com.milaboratory.core.io.sequence.AbstractMultiReader<PairedRead>

com.milaboratory.core.io.sequence.PairedReader

com.milaboratory.core.io.sequence.fastq.PairedFastqReader

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<PairedRead>, cc.redberry.pipe.OutputPortCloseable<PairedRead>, SequenceReader<PairedRead>, SequenceReaderCloseable<PairedRead>, CanReportProgress, AutoCloseable

public final class PairedFastqReader
extends PairedReader

Created by dbolotin on 23/06/14.

Field Summary

Fields inherited from class com.milaboratory.core.io.sequence.AbstractSequenceReader

readsCounter

Constructor Summary

Constructors

Constructor and Description
PairedFastqReader(File file1, File file2)
PairedFastqReader(File file1, File file2, boolean replaceWildcards)
PairedFastqReader(File file1, File file2, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(File file1, File file2, QualityFormat format, CompressionType ct)
PairedFastqReader(File file1, File file2, QualityFormat format, CompressionType ct, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(InputStream stream1, InputStream stream2)
PairedFastqReader(InputStream stream1, InputStream stream2, boolean replaceWildcards)
PairedFastqReader(InputStream stream1, InputStream stream2, CompressionType compressionType)
PairedFastqReader(InputStream stream1, InputStream stream2, QualityFormat format, CompressionType ct, boolean guessQualityFormat, int bufferSize, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(SingleFastqReader reader1, SingleFastqReader reader2)
PairedFastqReader(String fileName1, String fileName2)
PairedFastqReader(String fileName1, String fileName2, boolean replaceWildcards)
PairedFastqReader(String fileName1, String fileName2, boolean replaceWildcards, boolean lazyReads)
PairedFastqReader(String fileName1, String fileName2, QualityFormat format, CompressionType ct)
PairedFastqReader(String fileName1, String fileName2, QualityFormat format, CompressionType ct, boolean replaceWildcards, boolean lazyReads)

Method Summary

Methods inherited from class com.milaboratory.core.io.sequence.PairedReader

take

Methods inherited from class com.milaboratory.core.io.sequence.AbstractMultiReader

close, getProgress, isFinished, takeReads

Methods inherited from class com.milaboratory.core.io.sequence.AbstractSequenceReader

addOneRead, getNumberOfReads

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.milaboratory.core.io.sequence.SequenceReader

getNumberOfReads

Constructor Detail

PairedFastqReader

public PairedFastqReader(File file1,
                 File file2)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(String fileName1,
                 String fileName2)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(File file1,
                 File file2,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(String fileName1,
                 String fileName2,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(File file1,
                 File file2,
                 boolean replaceWildcards)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(String fileName1,
                 String fileName2,
                 boolean replaceWildcards)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(File file1,
                 File file2,
                 QualityFormat format,
                 CompressionType ct)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(String fileName1,
                 String fileName2,
                 QualityFormat format,
                 CompressionType ct)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(File file1,
                 File file2,
                 QualityFormat format,
                 CompressionType ct,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(String fileName1,
                 String fileName2,
                 QualityFormat format,
                 CompressionType ct,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(InputStream stream1,
                 InputStream stream2,
                 QualityFormat format,
                 CompressionType ct,
                 boolean guessQualityFormat,
                 int bufferSize,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(InputStream stream1,
                 InputStream stream2)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(InputStream stream1,
                 InputStream stream2,
                 boolean replaceWildcards)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(InputStream stream1,
                 InputStream stream2,
                 CompressionType compressionType)
                  throws IOException

Throws:

IOException

PairedFastqReader

public PairedFastqReader(SingleFastqReader reader1,
                 SingleFastqReader reader2)