Class OptionalReferenceArgumentCollection
java.lang.Object
picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- All Implemented Interfaces:
ReferenceArgumentCollection
public class OptionalReferenceArgumentCollection
extends Object
implements ReferenceArgumentCollection
Picard default argument collection for an optional reference.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
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Field Details
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REFERENCE_SEQUENCE
@Argument(shortName="R", doc="Reference sequence file.", common=true, optional=true) public File REFERENCE_SEQUENCE
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Constructor Details
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OptionalReferenceArgumentCollection
public OptionalReferenceArgumentCollection()
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Method Details
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getReferenceFile
- Specified by:
getReferenceFile
in interfaceReferenceArgumentCollection
- Returns:
- The reference provided by the user, if any, or the default defined by
htsjdk.samtools.Defaults.REFERENCE_FASTA
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