public class JavascriptSamRecordFilter extends AbstractJavascriptFilter<SAMFileHeader,SAMRecord> implements SamRecordFilter
bindings, DEFAULT_HEADER_KEY| Constructor and Description |
|---|
JavascriptSamRecordFilter(java.io.File scriptFile,
SAMFileHeader header)
constructor using a javascript File
|
JavascriptSamRecordFilter(java.io.Reader scriptReader,
SAMFileHeader header)
constructor using a java.io.Reader
|
JavascriptSamRecordFilter(java.lang.String scriptExpression,
SAMFileHeader header)
constructor using a javascript expression
|
| Modifier and Type | Method and 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)
|
java.lang.String |
getRecordKey()
returns key used for record binding
|
accept, getHeaderKeypublic JavascriptSamRecordFilter(java.io.File scriptFile,
SAMFileHeader header)
throws java.io.IOException
scriptFile - the javascript file to be compiledheader - the SAMHeaderjava.io.IOExceptionpublic 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 SamRecordFilterfirst - the first SAMRecord to evaluatesecond - the second SAMRecord to evaluatepublic boolean filterOut(SAMRecord record)
filterOut in interface SamRecordFilterrecord - the SAMRecord to evaluatepublic java.lang.String getRecordKey()
AbstractJavascriptFiltergetRecordKey in class AbstractJavascriptFilter<SAMFileHeader,SAMRecord>