Interface CollectMultipleMetrics.ProgramInterface

All Known Implementing Classes:
CollectMultipleMetrics.Program
Enclosing class:
CollectMultipleMetrics
public static interface CollectMultipleMetrics.ProgramInterface

  • Method Details

    • makeInstance

      default SinglePassSamProgram makeInstance(String outbase, String outext, File input, File reference, Set<MetricAccumulationLevel> metricAccumulationLevel, File dbSnp, File intervals, File refflat, Set<String> ignoreSequence, boolean skipPlotting, boolean includeUnpaired)
      By default, this method calls the
      invalid reference 
      #makeInstance(String, String, File, File, Set, File, File, File, boolean, Set)
      method without 'includeUnpaired' parameter.

    • makeInstance

      SinglePassSamProgram makeInstance(String outbase, String outext, File input, File reference, Set<MetricAccumulationLevel> metricAccumulationLevel, File dbSnp, File intervals, File refflat, Set<String> ignoreSequence, boolean skipPlotting)

    • needsReferenceSequence

      default boolean needsReferenceSequence()

    • needsRefflatFile

      default boolean needsRefflatFile()

    • supportsMetricAccumulationLevel

      default boolean supportsMetricAccumulationLevel()