picard.illumina.parser.readers

Class BarcodeFileReader

java.lang.Object

picard.illumina.parser.readers.BarcodeFileReader

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<java.lang.String>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<java.lang.String>

public class BarcodeFileReader
extends java.lang.Object
implements htsjdk.samtools.util.CloseableIterator<java.lang.String>

Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise. Barcode.txt file Format (consists of tab delimited columns, 1 record per row) sequence_read Matched(Y/N) BarcodeSequenceMatched sequence read - the actual bases at barcode position Matched(y/n) - Y or N indicating if there was a barcode match BarcodeSequenceMatched - matched barcode sequence (empty if read did not match one of the barcodes).

Constructor Summary

Constructors

Constructor and Description
BarcodeFileReader(java.io.File barcodeFile)

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	hasNext()
java.lang.String	next()
void	remove()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

BarcodeFileReader

public BarcodeFileReader(java.io.File barcodeFile)

Method Detail

next

public java.lang.String next()

Specified by:

next in interface java.util.Iterator<java.lang.String>

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<java.lang.String>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<java.lang.String>

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<java.lang.String>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable