VCFOutput

Value Members

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

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2. final def !=(arg0: Any): Boolean

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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6. final def asInstanceOf[T0]: T0

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7. def clone(): AnyRef

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8. final def eq(arg0: AnyRef): Boolean

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10. def finalize(): Unit

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13. final def isInstanceOf[T0]: Boolean

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14. def makeHtsjdVariantContext(samplesEvidence: MultiSampleSingleAlleleEvidence, subInputs: InputCollection, includePooledNormal: Boolean, includePooledTumor: Boolean, reference: ReferenceBroadcast): VariantContext

    Make an htsjdk VariantContext for the given AlleleEvidenceAcrossSamples instance.

    Make an htsjdk VariantContext for the given AlleleEvidenceAcrossSamples instance.

    samplesEvidence

    evidence for the call (or non-call)

    subInputs

    subset of inputs to include in this VariantContext

    includePooledNormal

    whether to include the pooled normal data as a sample in the result

    includePooledTumor

    whether to include the pooled tumor data as a sample in the result

    reference

    reference genome

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

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16. final def notify(): Unit

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17. final def notifyAll(): Unit

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18. final def synchronized[T0](arg0: ⇒ T0): T0

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19. def toString(): String

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20. final def wait(): Unit

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21. final def wait(arg0: Long, arg1: Int): Unit

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22. final def wait(arg0: Long): Unit

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23. def writeVcf(path: String, calls: Seq[MultiSampleMultiAlleleEvidence], inputs: InputCollection, includePooledNormal: Boolean, includePooledTumor: Boolean, parameters: Parameters, sequenceDictionary: SAMSequenceDictionary, reference: ReferenceBroadcast, extraHeaderMetadata: Seq[(String, String)] = Seq.empty): Unit

    Write a VCF to a local file.

    Write a VCF to a local file.

    path

    file to write to

    calls

    MultipleAllelesEvidenceAcrossSamples instances giving calls to write. Currently each allele contained therein results in a variant call.

    inputs

    sample inputs to write genotypes for, can be a subset of the full set of inputs

    includePooledNormal

    whether to include the pooled normal dna reads as its own sample

    includePooledTumor

    whether to include the pooled tumor dna reads as its own sample

    parameters

    variant calling parameters, written to VCF header

    sequenceDictionary

    contig lengths

    reference

    reference genome