com.milaboratory.core.io.sequence.fastq

Class RandomAccessFastqReader

java.lang.Object

com.milaboratory.core.io.util.AbstractRandomAccessReader<SingleRead>

com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader

All Implemented Interfaces:

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

public final class RandomAccessFastqReader
extends AbstractRandomAccessReader<SingleRead>
implements SingleReader, AutoCloseable

FASTQ file reader with random access.

Field Summary

Fields inherited from class com.milaboratory.core.io.util.AbstractRandomAccessReader

currentRecordNumber, file, fileIndex

Constructor Summary

Constructors

Constructor and Description
RandomAccessFastqReader(File file, FileIndex fileIndex, boolean replaceWildcards, boolean lazyReads) Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(RandomAccessFile file, FileIndex fileIndex, boolean replaceWildcards, boolean lazyReads) Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(String file, String fileIndex) Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(String file, String fileIndex, boolean replaceWildcards) Creates reader of specified FASTQ file with specified index.
RandomAccessFastqReader(String file, String fileIndex, boolean replaceWildcards, boolean lazyReads) Creates reader of specified FASTQ file with specified index.

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
long	getNumberOfReads() For sequential readers returns the number of reads read till this moment, after reader is exhausted returns total number of reads.
protected void	resetBufferOnSeek()
protected void	skip()
SingleRead	take() Returns the next record or null if no more records exist.
SingleRead	take(long recordNumber) Returns the specified record or null if recordNumber is greater than actual number of records in file.
protected SingleRead	take0()

Methods inherited from class com.milaboratory.core.io.util.AbstractRandomAccessReader

getCurrentRecordNumber, seekToRecord

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomAccessFastqReader

public RandomAccessFastqReader(String file,
                       String fileIndex)
                        throws IOException

Creates reader of specified FASTQ file with specified index.

Parameters:

file - FASTQ file

fileIndex - file index

Throws:

IOException

RandomAccessFastqReader

public RandomAccessFastqReader(String file,
                       String fileIndex,
                       boolean replaceWildcards)
                        throws IOException

Creates reader of specified FASTQ file with specified index.

Parameters:

file - FASTQ file

fileIndex - file index

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

Throws:

IOException

RandomAccessFastqReader

public RandomAccessFastqReader(String file,
                       String fileIndex,
                       boolean replaceWildcards,
                       boolean lazyReads)
                        throws IOException

Creates reader of specified FASTQ file with specified index.

Parameters:

file - FASTQ file

fileIndex - file index

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

lazyReads - create reads data on demand

Throws:

IOException

RandomAccessFastqReader

public RandomAccessFastqReader(File file,
                       FileIndex fileIndex,
                       boolean replaceWildcards,
                       boolean lazyReads)
                        throws FileNotFoundException

Creates reader of specified FASTQ file with specified index.

Parameters:

file - FASTQ file

fileIndex - file index

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

lazyReads - create reads data on demand

Throws:

FileNotFoundException

RandomAccessFastqReader

public RandomAccessFastqReader(RandomAccessFile file,
                       FileIndex fileIndex,
                       boolean replaceWildcards,
                       boolean lazyReads)

Creates reader of specified FASTQ file with specified index.

Parameters:

file - FASTQ file

fileIndex - file index

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

lazyReads - create reads data on demand

Method Detail

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

take

public SingleRead take()

Description copied from class: AbstractRandomAccessReader

Returns the next record or null if no more records exist.

Specified by:

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

Overrides:

take in class AbstractRandomAccessReader<SingleRead>

Returns:

next record or null if no more records exist

take

public SingleRead take(long recordNumber)

Description copied from class: AbstractRandomAccessReader

Returns the specified record or null if recordNumber is greater than actual number of records in file.

Overrides:

take in class AbstractRandomAccessReader<SingleRead>

Parameters:

recordNumber - record number

Returns:

record with specified number or null if recordNumber is greater than actual number of records in file

take0

protected SingleRead take0()

Specified by:

take0 in class AbstractRandomAccessReader<SingleRead>

skip

protected void skip()

Overrides:

skip in class AbstractRandomAccessReader<SingleRead>

resetBufferOnSeek

protected void resetBufferOnSeek()

Overrides:

resetBufferOnSeek in class AbstractRandomAccessReader<SingleRead>

close

public void close()

Specified by:

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

Specified by:

close in interface AutoCloseable