dagr.tasks.misc.CalculateDownsamplingProportion.scala Maven / Gradle / Ivy

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A set of example dagr tasks.

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/*
 * The MIT License
 *
 * Copyright (c) 2015 Fulcrum Genomics LLC
 *
 * 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 dagr.tasks.misc

import java.nio.file.Path

import dagr.core.tasksystem.SimpleInJvmTask
import htsjdk.samtools.metrics.MetricsFile
import picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics

/** In JVM Task that pulls the total number of reads from the quality yield metrics file, and calculates a downsampling fraction. */
class CalculateDownsamplingProportion(qualityYieldMetrics: Path, targetReads: Long) extends SimpleInJvmTask {
  this.name = "CalculateDownsamplingProportion"
  var proportion: Double = 1

  override def run(): Unit = {
    val metrics = MetricsFile.readBeans(qualityYieldMetrics.toFile).get(0).asInstanceOf[QualityYieldMetrics]
    proportion = targetReads / metrics.PF_READS.toDouble
  }
}