Package picard.sam
Class ReorderSam.ReorderSamReferenceArgumentCollection
- java.lang.Object
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- picard.sam.ReorderSam.ReorderSamReferenceArgumentCollection
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- All Implemented Interfaces:
ReferenceArgumentCollection
- Enclosing class:
- ReorderSam
public static class ReorderSam.ReorderSamReferenceArgumentCollection extends Object implements ReferenceArgumentCollection
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Constructor Summary
Constructors Constructor Description ReorderSamReferenceArgumentCollection()
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Field Detail
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REFERENCE
@Argument(shortName="R", common=false, doc="Reference sequence to reorder reads to match. A sequence dictionary corresponding to the reference fasta is required. Create one with CreateSequenceDictionary.") public File REFERENCE
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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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