org.utgenome.format.fastq
Class FastqReader

java.lang.Object
  org.utgenome.format.fastq.FastqReader

public class FastqReader
extends Object

FASTQ format file reader.

FASTQ Format Specification: http://maq.sourceforge.net/fastq.shtml

Introduction

FASTQ format stores sequences and Phred qualities in a single file. It is concise and compact. FASTQ is first widely used in the Sanger Institute and therefore we usually take the Sanger specification and the standard FASTQ format, or simply FASTQ format. Although Solexa/Illumina read file looks pretty much like FASTQ, they are different in that the qualities are scaled differently. In the quality string, if you can see a character with its ASCII code higher than 90, probably your file is in the Solexa/Illumina format.

 Example




Author:
  
leo








Constructor Summary
FastqReader(Reader input)



           
 



Method Summary




 void
close()



           



 FastqRead
next()



          Read the next FASTQ read entry.


 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 





Constructor Detail



FastqReader
public FastqReader(Reader input)






Method Detail



next
public FastqRead next()
               throws UTGBException

Read the next FASTQ read entry.



Returns:
FastqRead entry or null if the end of stream has reached
Throws:
UTGBException





close
public void close()
           throws IOException



Throws:
IOException