org.dishevelled.bio.tools

Class ExtractFastq

java.lang.Object

org.dishevelled.bio.tools.ExtractFastq

All Implemented Interfaces:

Callable<Integer>

public final class ExtractFastq
extends Object
implements Callable<Integer>

Extract matching DNA sequences in FASTQ format.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
ExtractFastq(File inputFastqFile, File outputFastqFile, String name, String description) Extract matching DNA sequences in FASTQ format.
ExtractFastq(Path inputFastqPath, File outputFastqFile, String name, String description) Extract matching DNA sequences in 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

Constructor Detail

ExtractFastq

public ExtractFastq(File inputFastqFile,
                    File outputFastqFile,
                    String name,
                    String description)

Extract matching DNA sequences in FASTQ format.

Parameters:

inputFastqFile - input FASTQ file, if any

outputFastqFile - output FASTQ file, if any

name - exact sequence name to match, if any

description - FASTQ description regex pattern to match, if any

ExtractFastq

public ExtractFastq(Path inputFastqPath,
                    File outputFastqFile,
                    String name,
                    String description)

Extract matching DNA sequences in FASTQ format.

Parameters:

inputFastqPath - input FASTQ path, if any

outputFastqFile - output FASTQ file, if any

name - exact sequence name to match, if any

description - FASTQ description regex pattern to match, if any

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