Package picard.util
Class ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
java.lang.Object
picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- All Implemented Interfaces:
ReferenceArgumentCollection
- Enclosing class:
ScatterIntervalsByNs
public static class ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
extends Object
implements ReferenceArgumentCollection
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionThis method is retained for backward compatibility with legacy tools that have not been updated to support PicardHtsPath input files.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface picard.cmdline.argumentcollections.ReferenceArgumentCollection
getHtsPath, getReferencePath
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Field Details
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REFERENCE
@Argument(shortName="R", doc="Reference sequence to use. Note: this tool requires that the reference fasta has both an associated index and a dictionary.") public File REFERENCE
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Constructor Details
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ScatterIntervalsByNReferenceArgumentCollection
public ScatterIntervalsByNReferenceArgumentCollection()
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Method Details
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getReferenceFile
Description copied from interface:ReferenceArgumentCollection
This method is retained for backward compatibility with legacy tools that have not been updated to support PicardHtsPath input files. The preferred methods for accessing the reference file provided on the command line is either getHtsPath() or getReferencePath(). TODO: update tools that call this method to use getHtsPath()- Specified by:
getReferenceFile
in interfaceReferenceArgumentCollection
- Returns:
- The reference provided by the user, or the default defined by
htsjdk.samtools.Defaults.REFERENCE_FASTA
. May be null.
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