/*
 * Copyright (c) 2011, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

package org.broadinstitute.sting.queue.extensions.gatk

import collection.JavaConversions._
import org.broadinstitute.sting.utils.interval.IntervalUtils
import org.broadinstitute.sting.queue.function.InProcessFunction

/**
 * An interval scatter function.
 */
class IntervalScatterFunction extends GATKScatterFunction with InProcessFunction {
  protected override def maxIntervals =
    GATKScatterFunction.getGATKIntervals(this.originalGATK).locs.size

  override def scatterCount = if (intervalFilesExist) super.scatterCount min this.maxIntervals else super.scatterCount

  def run() {
    val gi = GATKScatterFunction.getGATKIntervals(this.originalGATK)
    val splits = IntervalUtils.splitFixedIntervals(gi.locs, this.scatterOutputFiles.size)
    IntervalUtils.scatterFixedIntervals(gi.samFileHeader, splits, this.scatterOutputFiles)
  }
}
