htsjdk.variant.variantcontext.filter

Class JavascriptVariantFilter

java.lang.Object

htsjdk.samtools.filter.AbstractJavascriptFilter<VCFHeader,VariantContext>

htsjdk.variant.variantcontext.filter.JavascriptVariantFilter

All Implemented Interfaces:

VariantContextFilter

public class JavascriptVariantFilter
extends AbstractJavascriptFilter<VCFHeader,VariantContext>
implements VariantContextFilter

javascript based variant filter The script puts the following variables in the script context: - 'header' a htsjdk.variant.vcf.VCFHeader - 'variant' a htsjdk.variant.variantcontext.VariantContext

Field Summary

Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

bindings, DEFAULT_HEADER_KEY

Constructor Summary

Constructors

Constructor and Description
JavascriptVariantFilter(java.io.File scriptFile, VCFHeader header) constructor using a javascript File
JavascriptVariantFilter(java.io.Reader scriptReader, VCFHeader header) constructor using a Reader
JavascriptVariantFilter(java.lang.String scriptExpression, VCFHeader header) constructor using a javascript expression

Method Summary

Modifier and Type	Method and Description
java.lang.String	getRecordKey() returns key used for record binding
boolean	test(VariantContext record) Determines whether a VariantContext matches this filter

Methods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

accept, getHeaderKey

Methods inherited from class java.lang.Object

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

Constructor Detail

JavascriptVariantFilter

public JavascriptVariantFilter(java.io.File scriptFile,
                               VCFHeader header)
                        throws java.io.IOException

constructor using a javascript File

Parameters:

scriptFile - the javascript file to be compiled

header - the SAMHeader

Throws:

java.io.IOException

JavascriptVariantFilter

public JavascriptVariantFilter(java.io.Reader scriptReader,
                               VCFHeader header)
                        throws java.io.IOException

constructor using a Reader

Parameters:

scriptReader - the reader for the script to be compiled. Will be closed

header - the SAMHeader

Throws:

java.io.IOException

JavascriptVariantFilter

public JavascriptVariantFilter(java.lang.String scriptExpression,
                               VCFHeader header)

constructor using a javascript expression

Parameters:

scriptExpression - the javascript expression to be compiled

header - the SAMHeader

Method Detail

test

public boolean test(VariantContext record)

Determines whether a VariantContext matches this filter

Specified by:

test in interface VariantContextFilter

Parameters:

record - the VariantContext to evaluate

Returns:

true if accept(record) returned true

getRecordKey

public java.lang.String getRecordKey()

Description copied from class: AbstractJavascriptFilter

returns key used for record binding

Specified by:

getRecordKey in class AbstractJavascriptFilter<VCFHeader,VariantContext>