org.utgenome.format.illumina
Class Seq2Fastq

java.lang.Object
  extended by 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


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