Value Members

1.  final def !=(arg0: Any): Boolean

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2.  final def ##(): Int

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3.  final def ==(arg0: Any): Boolean

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4.  val AlleleFractionField: String

   The format field for the allele fraction to be written to.

5.  val HeaderLines: Seq[VCFHeaderLine]
6.  val UnknownGtFilter: String

   The filter that is placed on records where the full genotype cannot be computed.

7.  final def asInstanceOf[T0]: T0

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8.  def clone(): AnyRef

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9.  final def eq(arg0: AnyRef): Boolean

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10.  def equals(arg0: Any): Boolean

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11.  def finalize(): Unit

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12.  def genotypeOf(sample: String, ctx: VariantContext, noCallIsHomRef: Boolean): Genotype

    Gets the genotype of the sample, substituting in a HomRef genotype for no-calls if required.

13.  final def getClass(): Class[_]

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14.  def hashCode(): Int

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15.  final def isInstanceOf[T0]: Boolean

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16.  def makeWriter(output: FgBioDef.PathToVcf, in: VCFHeader, lines: Seq[VCFHeaderLine], samples: String*): VariantContextWriter

    Builds a header that can be used to write a mixture VCF.

17.  final def ne(arg0: AnyRef): Boolean

    Definition Classes

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18.  def noCall(sampleName: String): Genotype

    Makes a no-call genotype object with the provided sample name.

19.  final def notify(): Unit

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20.  final def notifyAll(): Unit

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

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22.  def toString(): String

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23.  final def wait(): Unit

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

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25.  final def wait(arg0: Long): Unit

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