Package picard.analysis
Class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- java.lang.Object
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- picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
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- All Implemented Interfaces:
ReferenceArgumentCollection
- Enclosing class:
- CollectAlignmentSummaryMetrics
public static class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection extends Object implements ReferenceArgumentCollection
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Field Summary
Fields Modifier and Type Field Description File
REFERENCE_SEQUENCE
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Constructor Summary
Constructors Constructor Description CollectAlignmentRefArgCollection()
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Field Detail
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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
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Method Detail
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getReferenceFile
public File getReferenceFile()
- Specified by:
getReferenceFile
in interfaceReferenceArgumentCollection
- Returns:
- The reference provided by the user, if any, or the default, if any.
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