Package picard.sam
Class CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
java.lang.Object
picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- All Implemented Interfaces:
ReferenceArgumentCollection
- Enclosing class:
CreateSequenceDictionary
public static class CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
extends Object
implements ReferenceArgumentCollection
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionReturns a PicardHtsPath for the reference input.This 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
getReferencePath
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Field Details
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REFERENCE
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Constructor Details
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CreateSeqDictReferenceArgumentCollection
public CreateSeqDictReferenceArgumentCollection()
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Method Details
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getHtsPath
Description copied from interface:ReferenceArgumentCollection
Returns a PicardHtsPath for the reference input. Maybe be null. Implementers of this interface should override with an appropriate implementation. This currently does not support remote paths set via HtsJdk.Defaults.REFERENCE_FASTA, since that uses a `File` object.- Specified by:
getHtsPath
in interfaceReferenceArgumentCollection
- Returns:
- The reference provided by the user, if any, or the default, if any, as a PicardHtsPath. May be null.
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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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