InputCollection

Value Members

1. final def !=(arg0: AnyRef): Boolean

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3. final def ##(): Int

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6. def apply(paths: PerSample[String], sampleNames: PerSample[SampleName] = Vector.empty, tissueTypes: PerSample[String] = Vector.empty, analytes: PerSample[String] = Vector.empty): InputCollection

   Create an InputCollection of one or more inputs.

   Create an InputCollection of one or more inputs.

   Everything except paths is optional. If not specified, the sample names defaults to the basename of the file path with the suffix ".bam" removed, tissue types default to normal for the first sample and tumor for the rest, and analytes defaults to "dna".

   paths

   file paths

   sampleNames

   names to use in VCF output

   tissueTypes

   "normal" or "tumor" for each input

   analytes

   "dna" or "rna" for each input

   returns

   resulting InputCollection

7. def apply(args: Arguments): InputCollection

   Create an InputCollection from parsed commandline arguments.

8. final def asInstanceOf[T0]: T0

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9. def clone(): AnyRef

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16. final def ne(arg0: AnyRef): Boolean

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17. final def notify(): Unit

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