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