OptionalReferenceArgumentCollection (picard 2.18.2 API)

Skip navigation links

All Classes

SEARCH:

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method

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.

- Field Summary
  
  Fields
  Modifier and Type Field Description
  
  File REFERENCE_SEQUENCE
- Constructor Summary
  
  Constructors
  Constructor Description
  
  OptionalReferenceArgumentCollection()
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method Description
  
  File getReferenceFile()
  - Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - REFERENCE_SEQUENCE
```
@Argument(shortName="R",
          doc="Reference sequence file.",
          common=true,
          optional=true)
public File REFERENCE_SEQUENCE
```
- Constructor Detail
  - OptionalReferenceArgumentCollection
```
public OptionalReferenceArgumentCollection()
```
- Method Detail
  - getReferenceFile
```
public File getReferenceFile()
```
    Specified by:
    
    getReferenceFile in interface ReferenceArgumentCollection
    
    Returns:
    
    The reference provided by the user, if any, or the default defined by htsjdk.samtools.Defaults.REFERENCE_FASTA

Skip navigation links

All Classes

Summary:
Nested |
Field |
Constr |
Method

Detail:
Field |
Constr |
Method