Class OptionalReferenceArgumentCollection
- java.lang.Object
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- picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
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- 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 Modifier and Type Field Description File
REFERENCE_SEQUENCE
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Constructor Summary
Constructors Constructor Description OptionalReferenceArgumentCollection()
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Field Detail
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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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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 defined by
htsjdk.samtools.Defaults.REFERENCE_FASTA
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