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io.projectglow.transformers.normalizevariants

NormalizeVariantsTransformer

Related Docs: class NormalizeVariantsTransformer | package normalizevariants

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object NormalizeVariantsTransformer

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  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 NORMALIZER_TRANSFORMER_NAME: String

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  5. val REFERENCE_GENOME_PATH: String

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  6. val REPLACE_COLUMNS: String

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  7. final def asInstanceOf[T0]: T0

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  11. def finalize(): Unit

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

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  16. def normalizeVariants(df: DataFrame, refGenomePathString: String, replaceColumns: Boolean): DataFrame

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    Normalizes the input DataFrame of variants and outputs them as a Dataframe using normalize_variant expression and handles the replace_columns option

    Normalizes the input DataFrame of variants and outputs them as a Dataframe using normalize_variant expression and handles the replace_columns option

    df

    : Input dataframe of variants

    refGenomePathString

    : Path to the underlying reference genome of the variants

    replaceColumns

    : replace original columns or not

    returns

    normalized DataFrame

  17. final def notify(): Unit

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  18. final def notifyAll(): Unit

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

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  20. def toString(): String

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  21. def validateRefGenomeOption(refGenomePathString: Option[String]): Unit

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  22. final def wait(): Unit

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

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Deprecated Value Members

  1. val MODE_KEY: String

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    @deprecated
    Deprecated

    normalize_variants transformer is now for normalization only. split_multiallelics transformer should be used separately for splitting multiallelics

  2. val MODE_NORMALIZE: String

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    @deprecated
    Deprecated

    normalize_variants transformer is now for normalization only. split_multiallelics transformer should be used separately for splitting multiallelics

  3. val MODE_SPLIT: String

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    Annotations
    @deprecated
    Deprecated

    normalize_variants transformer is now for normalization only. split_multiallelics transformer should be used separately for splitting multiallelics

  4. val MODE_SPLIT_NORMALIZE: String

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    Annotations
    @deprecated
    Deprecated

    normalize_variants transformer is now for normalization only. split_multiallelics transformer should be used separately for splitting multiallelics

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