org.dishevelled.bio.tools

Class FastaToFastq

java.lang.Object

org.dishevelled.bio.tools.FastaToFastq

All Implemented Interfaces:

Callable<Integer>

public final class FastaToFastq
extends Object
implements Callable<Integer>

Convert DNA sequences in FASTA format to FASTQ format.

Author:

Michael Heuer

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_QUALITY

Constructor Summary

Constructors

Constructor and Description
FastaToFastq(File fastaFile, File fastqFile, int quality) Convert DNA sequences in FASTA format to FASTQ format.
FastaToFastq(Path fastaPath, File fastqFile, int quality) Convert DNA sequences in FASTA format to FASTQ format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_QUALITY

public static final int DEFAULT_QUALITY

See Also:

Constant Field Values

Constructor Detail

FastaToFastq

public FastaToFastq(File fastaFile,
                    File fastqFile,
                    int quality)

Convert DNA sequences in FASTA format to FASTQ format.

Parameters:

fastaFile - input FASTA file, if any

fastqFile - output FASTQ file, if any

quality - quality, must be in the range [0..93]

FastaToFastq

public FastaToFastq(Path fastaPath,
                    File fastqFile,
                    int quality)

Convert DNA sequences in FASTA format to FASTQ format.

Parameters:

fastaPath - input FASTA path, if any

fastqFile - output FASTQ file, if any

quality - quality, must be in the range [0..93]

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args