org.biojava.bio.program.fastq

Class IlluminaFastqReader

java.lang.Object

org.biojava.bio.program.fastq.IlluminaFastqReader

All Implemented Interfaces:

FastqReader

public final class IlluminaFastqReader
extends Object

Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.

Since:

1.7.1

Constructor Summary

Constructors

Constructor and Description
IlluminaFastqReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected FastqVariant	getVariant() Return the FASTQ sequence format variant for this reader.
<R extends Readable & Closeable> void	parse(com.google.common.io.InputSupplier<R> supplier, ParseListener listener) Deprecated. will be removed in version 1.10, see FastqReader.parse(Readable,ParseListener)
void	parse(Readable readable, ParseListener listener) Parse the specified readable.
Iterable<Fastq>	read(File file) Read zero or more FASTQ formatted sequences from the specified file.
Iterable<Fastq>	read(InputStream inputStream) Read zero or more FASTQ formatted sequences from the specified input stream.
Iterable<Fastq>	read(URL url) Read zero or more FASTQ formatted sequences from the specified url.
<R extends Readable & Closeable> void	stream(com.google.common.io.InputSupplier<R> supplier, StreamListener listener) Deprecated. will be removed in version 1.10, see FastqReader.stream(Readable,StreamListener)
void	stream(Readable readable, StreamListener listener) Stream the specified readable.

Methods inherited from class java.lang.Object

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

Constructor Detail

IlluminaFastqReader

public IlluminaFastqReader()

Method Detail

getVariant

protected FastqVariant getVariant()

Return the FASTQ sequence format variant for this reader.

Returns:

the FASTQ sequence format variant for this reader

parse

public final void parse(Readable readable,
         ParseListener listener)
                 throws IOException

Description copied from interface: FastqReader

Parse the specified readable.

Specified by:

parse in interface FastqReader

Parameters:

readable - readable, must not be null

listener - low-level event based parser callback, must not be null

Throws:

IOException - if an I/O error occurs

parse

public final <R extends Readable & Closeable> void parse(com.google.common.io.InputSupplier<R> supplier,
                                         ParseListener listener)
                 throws IOException

Deprecated. will be removed in version 1.10, see FastqReader.parse(Readable,ParseListener)

Parse the specified input supplier.

Parameters:

supplier - input supplier, must not be null

listener - low-level event based parser callback, must not be null

Throws:

IOException - if an I/O error occurs

Since:

1.8.2

stream

public final void stream(Readable readable,
          StreamListener listener)
                  throws IOException

Description copied from interface: FastqReader

Stream the specified readable.

Specified by:

stream in interface FastqReader

Parameters:

readable - readable, must not be null

listener - event based reader callback, must not be null

Throws:

IOException - if an I/O error occurs

stream

public final <R extends Readable & Closeable> void stream(com.google.common.io.InputSupplier<R> supplier,
                                          StreamListener listener)
                  throws IOException

Deprecated. will be removed in version 1.10, see FastqReader.stream(Readable,StreamListener)

Stream the specified input supplier.

Parameters:

supplier - input supplier, must not be null

listener - event based reader callback, must not be null

Throws:

IOException - if an I/O error occurs

Since:

1.8.2

read

public final Iterable<Fastq> read(File file)
                           throws IOException

Read zero or more FASTQ formatted sequences from the specified file.

Specified by:

read in interface FastqReader

Parameters:

file - file to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified file

Throws:

IOException - if an I/O error occurs

read

public final Iterable<Fastq> read(URL url)
                           throws IOException

Read zero or more FASTQ formatted sequences from the specified url.

Specified by:

read in interface FastqReader

Parameters:

url - URL to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified url

Throws:

IOException - if an I/O error occurs

read

public final Iterable<Fastq> read(InputStream inputStream)
                           throws IOException

Read zero or more FASTQ formatted sequences from the specified input stream.

Specified by:

read in interface FastqReader

Parameters:

inputStream - input stream to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified input stream

Throws:

IOException - if an I/O error occurs