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• Registrar.scala

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org.hammerlab.bam.spark.load.Registrar.scala Maven / Gradle / Ivy

package org.hammerlab.bam.spark.load

import htsjdk.samtools.SAMFileHeader
import org.hammerlab.bam.header.{ ContigLengths, Header }
import org.hammerlab.bam.index.Index.Chunk
import org.hammerlab.bam.kryo.registerSAMFileHeader
import org.hammerlab.bgzf.Pos
import org.hammerlab.genomics.loci.set.LociSet
import org.hammerlab.hadoop.Configuration
import org.hammerlab.kryo._

import scala.collection.mutable

case class Registrar()
  extends spark.Registrar(
    /** Several [[CanLoadBam]] methods broadcast [[Header]] and/or [[ContigLengths]] */
    cls[Header],
    cls[ContigLengths],
    cls[Configuration],

    /** [[CanLoadBam.loadSam]] broadcasts a [[htsjdk.samtools.SAMFileHeader]] */
    cls[SAMFileHeader],

    /**
     * An [[org.apache.spark.rdd.RDD]] of [[Pos]] is [[org.apache.spark.rdd.RDD.collect collect]]ed in
     * [[CanLoadBam.loadSplitsAndReads]]
     */
    cls[mutable.WrappedArray.ofRef[_]],
    arr[Pos],

    /** [[CanLoadBam.loadBamIntervals]] broadcasts a [[org.hammerlab.genomics.loci.set.LociSet]] */
    cls[LociSet],

    /** [[CanLoadBam.loadBamIntervals]] [[org.apache.spark.SparkContext.parallelize parallelize]]s some [[Vector]]s */
    arr[Vector[_]],
    cls[Chunk]
  )