ReferenceArgumentCollectionpublic static class CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection extends Object implements ReferenceArgumentCollection
| Modifier and Type | Field | Description |
|---|---|---|
File |
REFERENCE_SEQUENCE |
| Constructor | Description |
|---|---|
CollectAlignmentRefArgCollection() |
@Argument(shortName="R",
doc="Reference sequence file. Note that while this argument isn\'t required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.",
optional=true)
public File REFERENCE_SEQUENCE
public File getReferenceFile()
getReferenceFile in interface ReferenceArgumentCollection