forked from bigdatagenomics/adam
/
ADAMPlugin.scala
46 lines (42 loc) · 1.57 KB
/
ADAMPlugin.scala
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/**
* Copyright 2014 Genome Bridge LLC
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.plugins
import org.apache.avro.Schema
import org.apache.spark.rdd.RDD
import org.apache.spark.SparkContext
/**
* Defines the interface for a Plugin for the ADAMSystem.
*
* A simple interface is available in [[org.bdgenomics.adam.plugins.Take10Plugin]]
*/
trait ADAMPlugin[Input, Output] {
/**
* The projection to push down into Parquet
* @return 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
*/
def projection: Option[Schema]
/**
* The records that are applicable to this Plugin
* @return 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
*/
def predicate: Option[Input => Boolean]
/**
* Method to create the transformations on the RDD.
*/
def run(sc: SparkContext, recs: RDD[Input], args: String): RDD[Output]
}