public class JavascriptSamRecordFilter extends AbstractJavascriptFilter<SAMFileHeader,SAMRecord> implements SamRecordFilter
bindings, DEFAULT_HEADER_KEY
Constructor and Description |
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JavascriptSamRecordFilter(java.io.File scriptFile,
SAMFileHeader header)
constructor using a javascript File
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JavascriptSamRecordFilter(java.io.Reader scriptReader,
SAMFileHeader header)
constructor using a java.io.Reader
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JavascriptSamRecordFilter(java.lang.String scriptExpression,
SAMFileHeader header)
constructor using a javascript expression
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Modifier and Type | Method and Description |
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boolean |
filterOut(SAMRecord record)
read is filtered out if the javascript program returns false
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boolean |
filterOut(SAMRecord first,
SAMRecord second)
return true of both records are filteredOut (AND)
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java.lang.String |
getRecordKey()
returns key used for record binding
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accept, getHeaderKey
public JavascriptSamRecordFilter(java.io.File scriptFile, SAMFileHeader header) throws java.io.IOException
scriptFile
- the javascript file to be compiledheader
- the SAMHeaderjava.io.IOException
public JavascriptSamRecordFilter(java.lang.String scriptExpression, SAMFileHeader header)
scriptExpression
- the javascript expression to be compiledheader
- the SAMHeaderpublic JavascriptSamRecordFilter(java.io.Reader scriptReader, SAMFileHeader header)
scriptReader
- the javascript reader to be compiled. will be closedheader
- the SAMHeaderpublic boolean filterOut(SAMRecord first, SAMRecord second)
filterOut
in interface SamRecordFilter
first
- the first SAMRecord to evaluatesecond
- the second SAMRecord to evaluatepublic boolean filterOut(SAMRecord record)
filterOut
in interface SamRecordFilter
record
- the SAMRecord to evaluatepublic java.lang.String getRecordKey()
AbstractJavascriptFilter
getRecordKey
in class AbstractJavascriptFilter<SAMFileHeader,SAMRecord>