org.utgenome.format.fastq
Class FastqToBAM

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

public class FastqToBAM
extends Object

Converting Illumina's FASTQ read data (single or paired-end) into BAM format, which can be used BLOAD's GATK pipeline. This code is migrated from

Author:

leo

Constructor Summary

FastqToBAM()

Method Summary

int	convert()
int	convert(Reader input1, Reader input2)
static int	execute(String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqToBAM

public FastqToBAM()

Method Detail

execute

public static int execute(String[] args)
                   throws Exception

Throws:

Exception

convert

public int convert()
            throws UTGBException,
                   IOException

Throws:

UTGBException

IOException

convert

public int convert(Reader input1,
                   Reader input2)
            throws UTGBException,
                   IOException

Throws:

UTGBException

IOException