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object GenomicImplicits

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  1. implicit class GenomicOperations extends AnyRef

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  11. val log: Logger
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  15. final def synchronized[T0](arg0: ⇒ T0): T0
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  16. def toString(): String
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  17. def vcf(files: List[String], referenceGenomePath: Option[String])(implicit spark: SparkSession): DataFrame
  18. def vcf(files: List[String], referenceGenomePath: Option[String], optional: Boolean, split: Boolean)(implicit spark: SparkSession): DataFrame
  19. def vcf(input: String, referenceGenomePath: Option[String])(implicit spark: SparkSession): DataFrame
  20. def vcf(input: String, referenceGenomePath: Option[String], optional: Boolean, split: Boolean)(implicit spark: SparkSession): DataFrame

    Reads vcf files into dataframe and apply transformations:

    Reads vcf files into dataframe and apply transformations:

    • optionally split multiallelics variants
    • 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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  24. object ParentalOrigin
  25. object columns

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