org.bdgenomics.adam.util

Flattener

object Flattener extends Serializable

Utility singleton for flattening down nested Avro records.

When we refer to a schema as flat, we mean that there are no nested records. We do not mean that the schema does not contain maps or arrays.

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  1. final def !=(arg0: AnyRef): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

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  6. val SEPARATOR: String

    This separator is used to generate the flattened name of a nested field.

    This separator is used to generate the flattened name of a nested field. E.g., if a record is nested like so:

    - record Genotype -- variant: Variant --- start: Long --- end: Long -- genotypeState: Int

    With the SEPARATOR "", the flat record will be:

    - record Genotype -- variantstart: Long -- variantend: Long -- genotypeState: Int

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  8. def clone(): AnyRef

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  11. def finalize(): Unit

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  12. def flattenRecord(flatSchema: Schema, record: IndexedRecord): IndexedRecord

    Takes a given nested record and flattens it to correspond to a flattened schema.

    Takes a given nested record and flattens it to correspond to a flattened schema.

    flatSchema

    The flat schema for the new record.

    record

    The nested record to flatten.

    returns

    Returns a new Avro IndexedRecord where every field from the initial record has been copied, but where the schema corresponds to the new flat schema.

  13. def flattenSchema(schema: Schema): Schema

    Given a possibly nested schema, creates a flat schema.

    Given a possibly nested schema, creates a flat schema.

    schema

    The schema to flatten.

    returns

    Returns a flattened representation of the schema.

  14. final def getClass(): Class[_]

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  15. def hashCode(): Int

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