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 java.lang.Object
implements ReferenceArgumentCollection

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	REFERENCE_SEQUENCE

Constructor Summary

Constructors

Constructor and Description
CollectAlignmentRefArgCollection()

Method Summary

Modifier and Type	Method and Description
java.io.File	getReferenceFile()

Methods inherited from class java.lang.Object

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

Field Detail

REFERENCE_SEQUENCE

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

Constructor Detail

CollectAlignmentRefArgCollection

public CollectAlignmentRefArgCollection()

Method Detail

getReferenceFile

public java.io.File getReferenceFile()

Specified by:

getReferenceFile in interface ReferenceArgumentCollection

Returns:

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