org.utgenome.format.illumina
Class Seq2Fastq

java.lang.Object
  org.utgenome.format.illumina.Seq2Fastq

public class Seq2Fastq
extends Object

For converting Illumina's input into Fastq format

Author:

leo

Constructor Summary

Seq2Fastq()

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

Seq2Fastq

public Seq2Fastq()

Method Detail

convertToFastq

public static FastqRead convertToFastq(String line)
                                throws UTGBException

Throws:

UTGBException

sanitizeReadName

public static String sanitizeReadName(String name)

sanitizeQualityValue

public static String sanitizeQualityValue(String qual)

convert

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

Throws:

IOException