Class JavascriptVariantFilter
- java.lang.Object
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- htsjdk.samtools.filter.AbstractJavascriptFilter<VCFHeader,VariantContext>
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- htsjdk.variant.variantcontext.filter.JavascriptVariantFilter
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- 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
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Fields inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
bindings, DEFAULT_HEADER_KEY
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Constructor Summary
Constructors Constructor Description JavascriptVariantFilter(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
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getRecordKey()
returns key used for record bindingboolean
test(VariantContext record)
Determines whether a VariantContext matches this filter-
Methods inherited from class htsjdk.samtools.filter.AbstractJavascriptFilter
accept, getHeaderKey
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Constructor Detail
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JavascriptVariantFilter
public JavascriptVariantFilter(File scriptFile, VCFHeader header) throws IOException
constructor using a javascript File- Parameters:
scriptFile
- the javascript file to be compiledheader
- the SAMHeader- Throws:
IOException
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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 closedheader
- the SAMHeader- Throws:
IOException
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Method Detail
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test
public boolean test(VariantContext record)
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
public String getRecordKey()
Description copied from class:AbstractJavascriptFilter
returns key used for record binding- Specified by:
getRecordKey
in classAbstractJavascriptFilter<VCFHeader,VariantContext>
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