com.milaboratory.core.io.sequence.fastq

Class SingleFastqReader

java.lang.Object

com.milaboratory.core.io.sequence.fastq.SingleFastqReader

All Implemented Interfaces:

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

public final class SingleFastqReader
extends Object
implements SingleReader, CanReportProgress, SequenceReaderCloseable<SingleRead>

Author:

Dmitry Bolotin, Stanislav Poslavsky

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BUFFER_SIZE
static QualityFormat	DEFAULT_QUALITY_FORMAT If FastqReader fails to guess file format, this value will be used by default.

Constructor Summary

Constructors

Constructor and Description
SingleFastqReader(File file) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File file, boolean replaceWildcards) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File file, boolean replaceWildcards, boolean lazyReads) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File file, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(File file, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream stream) Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream stream, boolean replaceWildcards) Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream stream, CompressionType ct) Creates a SingleRead stream from a FASTQ stream with single-end reads data
SingleFastqReader(InputStream stream, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(InputStream stream, QualityFormat format, CompressionType ct, boolean guessQualityFormat, int bufferSize, boolean replaceWildcards, boolean lazyReads) Creates a SingleFastqReader stream from a FASTQ files with single-end read data
SingleFastqReader(String file) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String file, boolean replaceWildcards) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String file, boolean replaceWildcards, boolean lazyReads) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String file, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data
SingleFastqReader(String file, QualityFormat format, CompressionType ct) Creates a SingleRead stream from a FASTQ files with single-end read data

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes the output port
long	getNumberOfReads() For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.
double	getProgress()
QualityFormat	getQualityFormat()
boolean	isFinished()
SingleFastqReader	setTotalSize(long totalSize)
SingleRead	take()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

DEFAULT_QUALITY_FORMAT

public static final QualityFormat DEFAULT_QUALITY_FORMAT

If FastqReader fails to guess file format, this value will be used by default. Old value (version <= 1.1.2) was null, which leads to WrongQualityFormat exception in case of failed format guessing.

Constructor Detail

SingleFastqReader

public SingleFastqReader(String file,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

replaceWildcards - if true, all wildcards (like N) will be converted to a random basic letters matching corresponding wildcards, and their corresponding quality scores will be set to a minimum possible values

lazyReads - allow lazy initialization of single reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(String file,
                 boolean replaceWildcards)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

replaceWildcards - if true, all wildcards (like N) will be converted to a random basic letters matching corresponding wildcards, and their corresponding quality scores will be set to a minimum possible values

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(String file)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(String file,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(String file,
                 QualityFormat format,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

format - read quality encoding format (use null to guess format automatically)

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(File file,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

replaceWildcards - if true, all wildcards (like N) will be converted to a random basic letters matching corresponding wildcards, and their corresponding quality scores will be set to a minimum possible values

lazyReads - allow lazy initialization of single reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(File file,
                 boolean replaceWildcards)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

replaceWildcards - if true, all wildcards (like N) will be converted to a random basic letters matching corresponding wildcards, and their corresponding quality scores will be set to a minimum possible values

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(File file)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(File file,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(File file,
                 QualityFormat format,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

file - file with reads

format - read quality encoding format (use null to guess format automatically)

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(InputStream stream,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ stream with single-end reads data

Parameters:

stream - stream with reads

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(InputStream stream)
                  throws IOException

Creates a SingleRead stream from a FASTQ stream with single-end reads data

Parameters:

stream - stream with reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(InputStream stream,
                 boolean replaceWildcards)
                  throws IOException

Creates a SingleRead stream from a FASTQ stream with single-end reads data

Parameters:

stream - stream with reads

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(InputStream stream,
                 QualityFormat format,
                 CompressionType ct)
                  throws IOException

Creates a SingleRead stream from a FASTQ files with single-end read data

Parameters:

stream - stream with reads

format - read quality encoding format

ct - type of compression (NONE, GZIP, etc)

Throws:

IOException - in case there is problem with reading from files

SingleFastqReader

public SingleFastqReader(InputStream stream,
                 QualityFormat format,
                 CompressionType ct,
                 boolean guessQualityFormat,
                 int bufferSize,
                 boolean replaceWildcards,
                 boolean lazyReads)
                  throws IOException

Creates a SingleFastqReader stream from a FASTQ files with single-end read data

Parameters:

stream - stream with reads

format - read quality encoding format, if guessQualityFormat is true this value is used as a default format

ct - type of compression (NONE, GZIP, etc)

guessQualityFormat - if true reader will try to guess quality string format, if guess fails format will be used as a default quality string format, if format==null exception will be thrown

bufferSize - size of buffer

replaceWildcards - if true, all wildcards (like N) will be converted to a random basic letters matching corresponding wildcards, and their corresponding quality scores will be set to a minimum possible values

lazyReads - specifies whether created reads should be lazy initialized @throws java.io.IOException

Throws:

IOException

Method Detail

setTotalSize

public SingleFastqReader setTotalSize(long totalSize)

getQualityFormat

public QualityFormat getQualityFormat()

getProgress

public double getProgress()

Specified by:

getProgress in interface CanReportProgress

isFinished

public boolean isFinished()

Specified by:

isFinished in interface CanReportProgress

take

public SingleRead take()

Specified by:

take in interface cc.redberry.pipe.OutputPort<SingleRead>

getNumberOfReads

public long getNumberOfReads()

Description copied from interface: SequenceReader

For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads. For random access readers returns total number of reads.

This method is thread-safe.

Specified by:

getNumberOfReads in interface SequenceReader<SingleRead>

Returns:

number of reads read till this moment for sequential readers and total number of reads for random access readers

close

public void close()

Closes the output port

Specified by:

close in interface cc.redberry.pipe.OutputPortCloseable<SingleRead>

Specified by:

close in interface AutoCloseable