org.dishevelled.bio.tools

Class FilterRgfa

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterRgfa

All Implemented Interfaces:

Callable<Integer>

public final class FilterRgfa
extends AbstractFilter

Filter assembly in rGFA format.

Since:

2.1

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterRgfa.Filter Filter.
static class	FilterRgfa.FragmentCountFilter Fragment count filter.
static class	FilterRgfa.KmerCountFilter K-mer count filter.
static class	FilterRgfa.LengthFilter Length filter.
static class	FilterRgfa.MappingQualityFilter Mapping quality filter.
static class	FilterRgfa.MismatchCountFilter Mismatch count filter.
static class	FilterRgfa.ReadCountFilter Read count filter.
static class	FilterRgfa.ScriptFilter Script filter.
static class	FilterRgfa.SegmentFilter Segment filter.

Constructor Summary

Constructors

Constructor and Description
FilterRgfa(List<FilterRgfa.Filter> filters, File inputRgfaFile, File outputRgfaFile) Filter assembly in rGFA format.
FilterRgfa(List<FilterRgfa.Filter> filters, Path inputRgfaPath, File outputRgfaFile) Filter assembly in rGFA 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

FilterRgfa

public FilterRgfa(List<FilterRgfa.Filter> filters,
                  File inputRgfaFile,
                  File outputRgfaFile)

Filter assembly in rGFA format.

Parameters:

filters - list of filters, must not be null

inputRgfaFile - input rGFA file, if any

outputRgfaFile - output rGFA file, if any

FilterRgfa

public FilterRgfa(List<FilterRgfa.Filter> filters,
                  Path inputRgfaPath,
                  File outputRgfaFile)

Filter assembly in rGFA format.

Parameters:

filters - list of filters, must not be null

inputRgfaPath - input rGFA path, if any

outputRgfaFile - output rGFA file, if any

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args