Type Members

1.  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).

   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.