Class JavascriptVariantFilter
java.lang.Object
htsjdk.samtools.filter.AbstractJavascriptFilter<VCFHeader,VariantContext>
htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
- All Implemented Interfaces:
VariantContextFilter
,Predicate<VariantContext>
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
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Field Summary
Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
bindings, DEFAULT_HEADER_KEY
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Constructor Summary
ConstructorDescriptionJavascriptVariantFilter
(File scriptFile, VCFHeader header) constructor using a javascript FileJavascriptVariantFilter
(Reader scriptReader, VCFHeader header) constructor using a ReaderJavascriptVariantFilter
(String scriptExpression, VCFHeader header) constructor using a javascript expression -
Method Summary
Modifier and TypeMethodDescriptionreturns key used for record bindingboolean
test
(VariantContext record) Determines whether a VariantContext matches this filterMethods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
accept, getHeaderKey
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Constructor Details
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JavascriptVariantFilter
constructor using a javascript File- Parameters:
scriptFile
- the javascript file to be compiledheader
- the SAMHeader- Throws:
IOException
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JavascriptVariantFilter
constructor using a Reader- Parameters:
scriptReader
- the reader for the script to be compiled. Will be closedheader
- the SAMHeader- Throws:
IOException
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JavascriptVariantFilter
constructor using a javascript expression- Parameters:
scriptExpression
- the javascript expression to be compiledheader
- the SAMHeader
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Method Details
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test
Determines whether a VariantContext matches this filter- Specified by:
test
in interfacePredicate<VariantContext>
- Parameters:
record
- the VariantContext to evaluate- Returns:
- true if accept(record) returned true
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getRecordKey
Description copied from class:AbstractJavascriptFilter
returns key used for record binding- Specified by:
getRecordKey
in classAbstractJavascriptFilter<VCFHeader,
VariantContext>
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