Class JavascriptSamRecordFilter

java.lang.Object
htsjdk.samtools.filter.AbstractJavascriptFilter<SAMFileHeader, SAMRecord>
htsjdk.samtools.filter.JavascriptSamRecordFilter
All Implemented Interfaces:
SamRecordFilter
public class JavascriptSamRecordFilter extends AbstractJavascriptFilter<SAMFileHeader, SAMRecord> implements SamRecordFilter
JavaScript-based SamRecordFilter.

The user-supplied script is evaluated against each SAMRecord with the following variables in scope:

Example: keep only records with mapping quality >= 30: 

    new JavascriptSamRecordFilter("record.getMappingQuality() >= 30;", header)

Runtime requirement: as of htsjdk 5.0.0, htsjdk does not ship a JavaScript engine as a runtime dependency. To use this class, add a JSR-223-compatible JavaScript engine (e.g. org.openjdk.nashorn:nashorn-core) to your runtime classpath. If no engine is available, the constructor throws a RuntimeScriptException whose message lists the dependency coordinates.

  • Constructor Details

    • JavascriptSamRecordFilter

      public JavascriptSamRecordFilter(File scriptFile, SAMFileHeader header) throws IOException
      constructor using a javascript File
      Parameters:
      scriptFile - the javascript file to be compiled
      header - the SAMHeader
      Throws:
      IOException

    • JavascriptSamRecordFilter

      public JavascriptSamRecordFilter(String scriptExpression, SAMFileHeader header)
      constructor using a javascript expression
      Parameters:
      scriptExpression - the javascript expression to be compiled
      header - the SAMHeader

    • JavascriptSamRecordFilter

      public JavascriptSamRecordFilter(Reader scriptReader, SAMFileHeader header)
      constructor using a java.io.Reader
      Parameters:
      scriptReader - the javascript reader to be compiled. will be closed
      header - the SAMHeader

  • Method Details

    • filterOut

      public boolean filterOut(SAMRecord first, SAMRecord second)
      return true of both records are filteredOut (AND)
      Specified by:
      filterOut in interface SamRecordFilter
      Parameters:
      first - the first SAMRecord to evaluate
      second - the second SAMRecord to evaluate
      Returns:
      true if the pair of records matches filter, otherwise false

    • filterOut

      public boolean filterOut(SAMRecord record)
      read is filtered out if the javascript program returns false
      Specified by:
      filterOut in interface SamRecordFilter
      Parameters:
      record - the SAMRecord to evaluate
      Returns:
      true if the SAMRecord matches the filter, otherwise false

    • getRecordKey

      public String getRecordKey()
      Description copied from class: AbstractJavascriptFilter
      returns key used for record binding
      Specified by:
      getRecordKey in class AbstractJavascriptFilter<SAMFileHeader, SAMRecord>