org.dishevelled.bio.tools

Class FilterPaf

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterPaf

All Implemented Interfaces:

Callable<Integer>

public final class FilterPaf
extends AbstractFilter

Filter alignments in PAF format.

Since:

1.4

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterPaf.Filter Filter.
static class	FilterPaf.MappingQualityFilter Mapping quality filter.
static class	FilterPaf.QueryRangeFilter Query range filter.
static class	FilterPaf.ScriptFilter Script filter.
static class	FilterPaf.TargetRangeFilter Target range filter.

Constructor Summary

Constructors

Constructor and Description
FilterPaf(List<FilterPaf.Filter> filters, File inputPafFile, File outputPafFile) Filter alignments in PAF format.
FilterPaf(List<FilterPaf.Filter> filters, Path inputPafPath, File outputPafFile) Filter alignments in PAF 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

FilterPaf

public FilterPaf(List<FilterPaf.Filter> filters,
                 File inputPafFile,
                 File outputPafFile)

Filter alignments in PAF format.

Parameters:

filters - list of filters, must not be null

inputPafFile - input PAF file, if any

outputPafFile - output PAF file, if any

FilterPaf

public FilterPaf(List<FilterPaf.Filter> filters,
                 Path inputPafPath,
                 File outputPafFile)

Filter alignments in PAF format.

Parameters:

filters - list of filters, must not be null

inputPafPath - input PAF path, if any

outputPafFile - output PAF 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