/
VcfAnnotation2ADAM.scala
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VcfAnnotation2ADAM.scala
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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you 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.cli
import org.apache.hadoop.mapreduce.Job
import org.apache.spark.SparkContext._
import org.apache.spark.{ Logging, SparkContext }
import org.apache.spark.rdd.RDD
import org.bdgenomics.adam.converters.VariantAnnotationConverter
import org.bdgenomics.adam.rdd.ADAMContext._
import org.bdgenomics.adam.rich.RichVariant
import org.bdgenomics.formats.avro._
import org.bdgenomics.utils.cli._
import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
object VcfAnnotation2ADAM extends BDGCommandCompanion {
val commandName = "anno2adam"
val commandDescription = "Convert a annotation file (in VCF format) to the corresponding ADAM format"
def apply(cmdLine: Array[String]) = {
new VcfAnnotation2ADAM(Args4j[VcfAnnotation2ADAMArgs](cmdLine))
}
}
class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs {
@Argument(required = true, metaVar = "VCF", usage = "The VCF file with annotations to convert", index = 0)
var vcfFile: String = _
@Argument(required = true, metaVar = "ADAM", usage = "Location to write ADAM Variant annotations data", index = 1)
var outputPath: String = null
@Args4jOption(required = false, name = "-current_db", usage = "Location of existing ADAM Variant annotations data")
var currentAnnotations: String = null
}
class VcfAnnotation2ADAM(val args: VcfAnnotation2ADAMArgs) extends BDGSparkCommand[VcfAnnotation2ADAMArgs] with Logging {
val companion = VcfAnnotation2ADAM
def run(sc: SparkContext) {
log.info("Reading VCF file from %s".format(args.vcfFile))
val annotations: RDD[DatabaseVariantAnnotation] = sc.loadVcfAnnotations(args.vcfFile)
if (args.currentAnnotations != null) {
val existingAnnotations: RDD[DatabaseVariantAnnotation] = sc.loadVariantAnnotations(args.currentAnnotations)
val keyedAnnotations = existingAnnotations.keyBy(anno => new RichVariant(anno.getVariant))
val joinedAnnotations = keyedAnnotations.join(annotations.keyBy(anno => new RichVariant(anno.getVariant)))
val mergedAnnotations = joinedAnnotations.map(kv => VariantAnnotationConverter.mergeAnnotations(kv._2._1, kv._2._2))
mergedAnnotations.adamParquetSave(args)
} else {
annotations.adamParquetSave(args)
}
}
}