Packages

class NormalizeVariantsTransformer extends DataFrameTransformer with HlsEventRecorder

Implements DataFrameTransformer to transform the input DataFrame of variants to an output DataFrame of normalized variants (normalization is as defined in vt normalize or bcftools norm).

A path to the reference genome .fasta file must be provided through the reference_genome_path option. The .fasta file must be accompanied with a .fai index file in the same folder.

The transformer output columns can be controlled by the replace_columns option:

If the replace_columns option is false, the transformer does not touch the original start, end, referenceAllele and alternateAlleles columns. Instead, a StructType column called normalizationResult is added to the DataFrame which contains the normalized start, end, referenceAllele, and alternateAlleles columns as well as the normalizationStatus StructType as the fifth field, which contains the following subfields:

  • changed: A boolean field indicating whether the variant data was changed as a result of normalization.
  • errorMessage: An error message in case the attempt at normalizing the row hit an error. In this case, the changed field will be set to false. If no errors occur this field will be null. In case of error, the first four fields in normalizationResult will be null.

If replace_columns option is true (default), the transformer replaces the original start, end, referenceAllele, and alternateAlleles columns with the normalized value in case they have changed. Otherwise (in case of no change or an error), the original start, end, referenceAllele, and alternateAlleles are not touched. A StructType normalizationStatus column is added to the DataFrame with the same subfields as above.

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HlsEventRecorder, HlsUsageLogging, GlowLogging, LazyLogging, DataFrameTransformer, Named, AnyRef, Any
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  1. NormalizeVariantsTransformer
  2. HlsEventRecorder
  3. HlsUsageLogging
  4. GlowLogging
  5. LazyLogging
  6. DataFrameTransformer
  7. Named
  8. AnyRef
  9. Any
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Instance Constructors

  1. new NormalizeVariantsTransformer()

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def backwardCompatibleTransform(df: DataFrame, refGenomePathString: Option[String], replaceColumns: Boolean, modeOption: Option[String]): DataFrame

    The following function is for backward compatibility with the previous API where the normalizer could act in different modes: The default mode was normalizing the variants without splitting multiallelic ones.

    The following function is for backward compatibility with the previous API where the normalizer could act in different modes: The default mode was normalizing the variants without splitting multiallelic ones. The "mode" option could be used to change this behavior. Setting "mode" to "split" only splits multiallelic variants and skips normalization. Setting "mode" to split_and_normalize splits multiallelic variants and then normalizes the split variants, which is equivalent to using split_multiallelics transformer followed by normalize_variants transformer.

  6. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @native() @throws( ... )
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
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  9. def finalize(): Unit
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    protected[java.lang]
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    AnyRef
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    @throws( classOf[java.lang.Throwable] )
  10. final def getClass(): Class[_]
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    @native()
  11. def hashCode(): Int
    Definition Classes
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    @native()
  12. def hlsJsonBuilder(options: Map[String, Any]): String
    Attributes
    protected
    Definition Classes
    HlsUsageLogging
  13. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  14. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  15. def name: String
    Definition Classes
    NormalizeVariantsTransformer → Named
  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  19. def recordHlsEvent(tag: String, options: Map[String, Any] = Map.empty): Unit
    Definition Classes
    HlsEventRecorder
  20. def recordHlsUsage(metric: MetricDefinition, tags: Map[TagDefinition, String] = Map.empty, blob: String = null): Unit
    Attributes
    protected
    Definition Classes
    HlsUsageLogging
  21. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  22. def toString(): String
    Definition Classes
    AnyRef → Any
  23. def transform(df: DataFrame, options: Map[String, String]): DataFrame
    Definition Classes
    NormalizeVariantsTransformer → DataFrameTransformer
  24. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  25. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
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    @throws( ... )
  26. final def wait(arg0: Long): Unit
    Definition Classes
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    @native() @throws( ... )

Inherited from HlsEventRecorder

Inherited from HlsUsageLogging

Inherited from GlowLogging

Inherited from LazyLogging

Inherited from DataFrameTransformer

Inherited from Named

Inherited from AnyRef

Inherited from Any

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