Package picard.analysis

Class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection

java.lang.Object

picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection

All Implemented Interfaces:

ReferenceArgumentCollection

Enclosing class:

CollectAlignmentSummaryMetrics

public static class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
extends Object
implements ReferenceArgumentCollection

Field Summary

Fields

Modifier and Type	Field	Description
File	REFERENCE_SEQUENCE

Constructor Summary

Constructors

Constructor	Description
CollectAlignmentRefArgCollection()

Method Summary

Modifier and Type	Method	Description
File	getReferenceFile()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

REFERENCE_SEQUENCE

@Argument(shortName="R",
          doc="Reference sequence file. Note that while this argument isn\'t required, without it a small subset (MISMATCH-related) of the metrics cannot be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.",
          optional=true)
public File REFERENCE_SEQUENCE

Constructor Details

CollectAlignmentRefArgCollection

public CollectAlignmentRefArgCollection()

Method Details

getReferenceFile

public File getReferenceFile()

Specified by:

getReferenceFile in interface ReferenceArgumentCollection

Returns:

The reference provided by the user, if any, or the default, if any.