args

Type Members

1. trait Arguments extends Base

   Common command-line arguments for loading in one or more sets of reads, and associating a sample-name with each.

2. trait Base extends ReadFilterArgs with NoSequenceDictionaryArgs

3. trait HasReference extends AnyRef

4. trait NoSequenceDictionaryArgs extends AnyRef

   Argument for using / not using sequence dictionaries to get contigs and lengths.

5. trait ReferenceArgs extends HasReference

6. trait SingleSampleArgs extends Base with ReadFilterArgs

   Argument for accepting a single set of reads (for non-somatic variant calling).

7. trait TumorNormalReadsArgs extends Base with ReadFilterArgs

   Arguments for accepting two sets of reads (tumor + normal).