Package picard.analysis

## Interface CollectMultipleMetrics.ProgramInterface

- All Known Implementing Classes:
    `CollectMultipleMetrics.Program`
  Enclosing class:
    CollectMultipleMetrics

      public static interface CollectMultipleMetrics.ProgramInterface

- - ### Method Summary

    All Methods Instance Methods Abstract Methods Default Methods
    Modifier and Type | Method | Description
    --- | --- | ---
    `SinglePassSamProgram` | `makeInstance​(String outbase, String outext, File input, File reference, Set<MetricAccumulationLevel> metricAccumulationLevel, File dbSnp, File intervals, File refflat, Set<String> ignoreSequence)` |

    `default SinglePassSamProgram`

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

    By default, this method calls the `makeInstance(String, String, File, File, Set, File, File, File, Set)` method without 'includeUnpaired' parameter.

    `default boolean` | `needsReferenceSequence()` |
    `default boolean` | `needsRefflatFile()` |
    `default boolean` | `supportsMetricAccumulationLevel()` |

- - ### Method Detail

    - #### 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 includeUnpaired)

      By default, this method calls the `makeInstance(String, String, File, File, Set, File, File, File, 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)

    - #### needsReferenceSequence

          default boolean needsReferenceSequence()

    - #### needsRefflatFile

          default boolean needsRefflatFile()

    - #### supportsMetricAccumulationLevel

          default boolean supportsMetricAccumulationLevel()