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object VcfBuilder

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  1. case class Gt(sample: String, gt: String, dp: Int = -1, ad: Seq[Int] = Seq.empty, pl: Seq[Int] = Seq.empty, attrs: Map[String, Any] = Map.empty) extends Product with Serializable

    Convenience case class used to build up genotypes.

    Convenience case class used to build up genotypes.

    sample

    the name of the sample being genotyped

    gt

    a genotype either in VCF format (e.g. 0/1) or using actual alleles (e.g. A/T)

    dp

    optional depth (DP)

    ad

    optional set of allele depths (AD)

    pl

    optional set of phred-scale genotype likelihoods (PL)

    attrs

    extended attributes (must be in FORMAT headers)

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  4. val DefaultHeader: VcfHeader

    The default header that is used when making a new VcfBuilder.

  5. def apply(samples: Seq[String]): VcfBuilder

    Constructs a VcfBuilder using the DefaultHeader and the set of samples provided.

  6. def apply(header: VcfHeader): VcfBuilder

    Constructs a VcfBuilder using the supplied header.

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