org.bdgenomics.adam.plugins

ADAMPlugin

trait ADAMPlugin[Input, Output] extends AnyRef

Defines the interface for a Plugin for the ADAMSystem.

A simple interface is available in org.bdgenomics.adam.plugins.Take10Plugin.

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Abstract Value Members

  1. abstract def predicate: Option[(Input) ⇒ Boolean]

    The records that are applicable to this Plugin

    The records that are applicable to this Plugin

    returns

    If there is no filter for this plugin, None If a filter is applicable, a true response means record is included; a false means record is excluded

  2. abstract def projection: Option[Schema]

    The projection to push down into Parquet

    The projection to push down into Parquet

    returns

    If all fields are required or the specific projection is not known, None If a subset of fields on Input are required, an Avro schema with those fields

  3. abstract def run(sc: SparkContext, recs: RDD[Input], args: String): RDD[Output]

    Method to create the transformations on the RDD.

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