org.dishevelled.bio.tools

Class FilterGfa1

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterGfa1

All Implemented Interfaces:

Callable<Integer>

public final class FilterGfa1
extends AbstractFilter

Filter assembly in GFA 1.0 format.

Since:

1.3

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterGfa1.Filter Filter.
static class	FilterGfa1.FragmentCountFilter Fragment count filter.
static class	FilterGfa1.KmerCountFilter K-mer count filter.
static class	FilterGfa1.LengthFilter Length filter.
static class	FilterGfa1.MappingQualityFilter Mapping quality filter.
static class	FilterGfa1.MismatchCountFilter Mismatch count filter.
static class	FilterGfa1.ReadCountFilter Read count filter.
static class	FilterGfa1.ScriptFilter Script filter.
static class	FilterGfa1.SegmentFilter Segment filter.

Constructor Summary

Constructors

Constructor and Description
FilterGfa1(List<FilterGfa1.Filter> filters, File inputGfa1File, File outputGfa1File) Filter assembly in GFA 1.0 format.
FilterGfa1(List<FilterGfa1.Filter> filters, Path inputGfa1Path, File outputGfa1File) Filter assembly in GFA 1.0 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

FilterGfa1

public FilterGfa1(List<FilterGfa1.Filter> filters,
                  File inputGfa1File,
                  File outputGfa1File)

Filter assembly in GFA 1.0 format.

Parameters:

filters - list of filters, must not be null

inputGfa1File - input GFA 1.0 file, if any

outputGfa1File - output GFA 1.0 file, if any

FilterGfa1

public FilterGfa1(List<FilterGfa1.Filter> filters,
                  Path inputGfa1Path,
                  File outputGfa1File)

Filter assembly in GFA 1.0 format.

Parameters:

filters - list of filters, must not be null

inputGfa1Path - input GFA 1.0 path, if any

outputGfa1File - output GFA 1.0 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