JavascriptVariantFilter (htsjdk 2.8.1 API)

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(File scriptFile, VCFHeader header)` constructor using a javascript File
`JavascriptVariantFilter(Reader scriptReader, VCFHeader header)` constructor using a Reader
`JavascriptVariantFilter(String scriptExpression, VCFHeader header)` constructor using a javascript expression

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`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(File scriptFile,
                               VCFHeader header)
                        throws IOException
```
    constructor using a javascript File
    
    Parameters:
    
    scriptFile - the javascript file to be compiled
    
    header - the SAMHeader
    
    Throws:
    
    IOException
  - JavascriptVariantFilter
```
public JavascriptVariantFilter(Reader scriptReader,
                               VCFHeader header)
                        throws IOException
```
    constructor using a Reader
    
    Parameters:
    
    scriptReader - the reader for the script to be compiled. Will be closed
    
    header - the SAMHeader
    
    Throws:
    
    IOException
  - JavascriptVariantFilter
```
public JavascriptVariantFilter(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 String getRecordKey()
```
    Description copied from class: AbstractJavascriptFilter
    
    returns key used for record binding
    
    Specified by:
    
    getRecordKey in class AbstractJavascriptFilter<VCFHeader,VariantContext>

Class JavascriptVariantFilter

Field Summary

Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter

Methods inherited from class java.lang.Object

Constructor Detail

JavascriptVariantFilter

JavascriptVariantFilter

JavascriptVariantFilter

Method Detail

test

getRecordKey