org.dishevelled.bio.tools

Class FilterVcf

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterVcf

All Implemented Interfaces:

Callable<Integer>

public final class FilterVcf
extends AbstractFilter

Filter variants in VCF format.

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterVcf.Filter Filter.
static class	FilterVcf.FilterFilter Filter filter.
static class	FilterVcf.IdFilter Id filter.
static class	FilterVcf.QualFilter Quality score filter.
static class	FilterVcf.RangeFilter Range filter.
static class	FilterVcf.ScriptFilter Script filter.

Constructor Summary

Constructors

Constructor and Description
FilterVcf(List<FilterVcf.Filter> filters, File inputVcfFile, File outputVcfFile) Filter variants in VCF format.
FilterVcf(List<FilterVcf.Filter> filters, Path inputVcfPath, File outputVcfFile) Filter variants in VCF 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

FilterVcf

public FilterVcf(List<FilterVcf.Filter> filters,
                 File inputVcfFile,
                 File outputVcfFile)

Filter variants in VCF format.

Parameters:

filters - list of filters, must not be null

inputVcfFile - input VCF file, if any

outputVcfFile - output VCF file, if any

FilterVcf

public FilterVcf(List<FilterVcf.Filter> filters,
                 Path inputVcfPath,
                 File outputVcfFile)

Filter variants in VCF format.

Parameters:

filters - list of filters, must not be null

inputVcfPath - input VCF path, if any

outputVcfFile - output VCF 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