com.milaboratory.core.io.sequence.fastq

Class RandomAccessPairedFastqReader

java.lang.Object

com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader

All Implemented Interfaces:

cc.redberry.pipe.OutputPort<PairedRead>, SequenceReader<PairedRead>, AutoCloseable

public final class RandomAccessPairedFastqReader
extends Object
implements SequenceReader<PairedRead>, AutoCloseable

FASTQ file reader for paired reads with random access.

Constructor Summary

Constructors

Constructor and Description
RandomAccessPairedFastqReader(RandomAccessFastqReader reader1, RandomAccessFastqReader reader2)
RandomAccessPairedFastqReader(RandomAccessFile file1, FileIndex index1, RandomAccessFile file2, FileIndex index2)
RandomAccessPairedFastqReader(RandomAccessFile file1, FileIndex index1, RandomAccessFile file2, FileIndex index2, boolean replaceWildcards, boolean lazyReads)
RandomAccessPairedFastqReader(String file1, String index1, String file2, String index2)
RandomAccessPairedFastqReader(String file1, String index1, String file2, String index2, boolean replaceWildcards, boolean lazyReads)

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.
void	seekToRecord(long recordNumber)
PairedRead	take()
PairedRead	take(long recordNumber)

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomAccessPairedFastqReader

public RandomAccessPairedFastqReader(String file1,
                             String index1,
                             String file2,
                             String index2)
                              throws IOException

Throws:

IOException

RandomAccessPairedFastqReader

public RandomAccessPairedFastqReader(RandomAccessFile file1,
                             FileIndex index1,
                             RandomAccessFile file2,
                             FileIndex index2)
                              throws IOException

Throws:

IOException

RandomAccessPairedFastqReader

public RandomAccessPairedFastqReader(String file1,
                             String index1,
                             String file2,
                             String index2,
                             boolean replaceWildcards,
                             boolean lazyReads)
                              throws IOException

Throws:

IOException

RandomAccessPairedFastqReader

public RandomAccessPairedFastqReader(RandomAccessFile file1,
                             FileIndex index1,
                             RandomAccessFile file2,
                             FileIndex index2,
                             boolean replaceWildcards,
                             boolean lazyReads)
                              throws IOException

Throws:

IOException

RandomAccessPairedFastqReader

public RandomAccessPairedFastqReader(RandomAccessFastqReader reader1,
                             RandomAccessFastqReader reader2)

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<PairedRead>

Returns:

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

seekToRecord

public void seekToRecord(long recordNumber)
                  throws IOException

Throws:

IOException

take

public PairedRead take(long recordNumber)

take

public PairedRead take()

Specified by:

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

close

public void close()

Specified by:

close in interface AutoCloseable