org.utgenome.format.illumina
Class QSeqToFASTQ

java.lang.Object
  org.utgenome.format.illumina.QSeqToFASTQ

public class QSeqToFASTQ
extends Object

Converting Illumina's qseq format into FASTQ

Author:

leo

Constructor Summary

QSeqToFASTQ(boolean disableQualityFilter)

QSeqToFASTQ(String readGroup, boolean disableQualityFilter)

Method Summary

void	convert(BufferedReader illuminaSequenceFile, Writer output)
FastqRead	convertToFastq(String line)
static String	sanitizeQualityValue(String qual)
static String	sanitizeReadName(String name)
void	setReadNameSuffix(String suffix)

Methods inherited from class java.lang.Object

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

Constructor Detail

QSeqToFASTQ

public QSeqToFASTQ(boolean disableQualityFilter)

QSeqToFASTQ

public QSeqToFASTQ(String readGroup,
                   boolean disableQualityFilter)

Method Detail

setReadNameSuffix

public void setReadNameSuffix(String suffix)

convertToFastq

public FastqRead convertToFastq(String line)
                         throws UTGBException

Throws:

UTGBException

sanitizeReadName

public static String sanitizeReadName(String name)

sanitizeQualityValue

public static String sanitizeQualityValue(String qual)

convert

public void convert(BufferedReader illuminaSequenceFile,
                    Writer output)
             throws IOException

Throws:

IOException