org.dishevelled.bio.tools

Class FilterFastq

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterFastq

All Implemented Interfaces:

Callable<Integer>

public final class FilterFastq
extends AbstractFilter

Filter sequences in FASTQ format.

Since:

1.3.3

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterFastq.Filter Filter.
static class	FilterFastq.LengthFilter Length filter.
static class	FilterFastq.ScriptFilter Script filter.

Constructor Summary

Constructors

Constructor and Description
FilterFastq(List<FilterFastq.Filter> filters, File inputFastqFile, File outputFastqFile) Filter sequences in FASTQ format.
FilterFastq(List<FilterFastq.Filter> filters, Path inputFastqPath, File outputFastqFile) Filter sequences in FASTQ format.

Method Summary

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

Methods inherited from class org.dishevelled.bio.tools.AbstractFilter

createScriptEngine

Methods inherited from class java.lang.Object

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

Constructor Detail

FilterFastq

public FilterFastq(List<FilterFastq.Filter> filters,
                   File inputFastqFile,
                   File outputFastqFile)

Filter sequences in FASTQ format.

Parameters:

filters - list of filters, must not be null

inputFastqFile - input FASTQ file, if any

outputFastqFile - output FASTQ file, if any

FilterFastq

public FilterFastq(List<FilterFastq.Filter> filters,
                   Path inputFastqPath,
                   File outputFastqFile)

Filter sequences in FASTQ format.

Parameters:

filters - list of filters, must not be null

inputFastqPath - input FASTQ path, if any

outputFastqFile - output FASTQ file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args