com.milaboratory.core.io.sequence.fastq

Class FastqRecordsReader

java.lang.Object

com.milaboratory.core.io.sequence.fastq.FastqRecordsReader

All Implemented Interfaces:

AutoCloseable

public final class FastqRecordsReader
extends Object
implements AutoCloseable

High performance reader of FASTQ records. Used internally in all FastqReaders.

Constructor Summary

Constructors

Constructor and Description
FastqRecordsReader(boolean lazyReads, InputStream inputStream, int bufferSize, boolean replaceWildcards, boolean autoClose) See main constructor for parameters.
FastqRecordsReader(boolean lazyReads, RandomAccessFile inputStream, int bufferSize, boolean replaceWildcards, boolean autoClose) See main constructor for parameters.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes the output port
SingleRead	createRead(long id, QualityFormat format)
boolean	nextRecord(boolean refillBuffer)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqRecordsReader

public FastqRecordsReader(boolean lazyReads,
                  RandomAccessFile inputStream,
                  int bufferSize,
                  boolean replaceWildcards,
                  boolean autoClose)

See main constructor for parameters.

FastqRecordsReader

public FastqRecordsReader(boolean lazyReads,
                  InputStream inputStream,
                  int bufferSize,
                  boolean replaceWildcards,
                  boolean autoClose)

See main constructor for parameters.

Method Detail

createRead

public SingleRead createRead(long id,
                    QualityFormat format)

nextRecord

public boolean nextRecord(boolean refillBuffer)
                   throws IOException

Throws:

IOException

close

public void close()

Closes the output port

Specified by:

close in interface AutoCloseable