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object GenomicImplicits

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Type Members

  1. implicit class GenomicOperations extends AnyRef

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  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  10. val id: Column
  11. final def isInstanceOf[T0]: Boolean
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  12. val locus: Seq[Column]
  13. val locusColumnNames: Seq[String]
  14. final def ne(arg0: AnyRef): Boolean
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  15. final def notify(): Unit
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  16. final def notifyAll(): Unit
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  17. final def synchronized[T0](arg0: ⇒ T0): T0
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  18. def toString(): String
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  19. def vcf(files: List[String], referenceGenomePath: Option[String])(implicit spark: SparkSession): DataFrame
  20. def vcf(input: String, referenceGenomePath: Option[String])(implicit spark: SparkSession): DataFrame

    Reads vcf files into dataframe and apply transformations:

    Reads vcf files into dataframe and apply transformations:

    • split_multiallelics
    • optionally normalize_variants if a path to a reference genome is given
    input

    where the vcf files are located

    referenceGenomePath

    reference genome path. This path has to be local for each executors

    spark

    a Spark session

    returns

    data into a dataframe

  21. final def wait(arg0: Long, arg1: Int): Unit
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  23. final def wait(): Unit
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  24. object columns

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  1. def finalize(): Unit
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