dagr.tasks.picard.CollectQualityYieldMetrics.scala Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of dagr-tasks_2.12 Show documentation
A set of example dagr tasks.
The newest version!
/*
 * The MIT License
 *
 * Copyright (c) 2017 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.picard

import java.nio.file.Path

import dagr.core.tasksystem.PipeIn
import dagr.tasks.DagrDef.PathToBam
import dagr.tasks.DataTypes.SamOrBam

import scala.collection.mutable.ListBuffer

object CollectQualityYieldMetrics {
  def metricsExtension: String = ".quality_yield_metrics"
}

class CollectQualityYieldMetrics(override val in: PathToBam,
                                 override val prefix: Option[Path] = None,
                                 includeSecondary: Option[Boolean] = None,
                                 includeSupplementary: Option[Boolean] = None,
                                 assumeSorted: Boolean = true)
  extends PicardTask with PicardMetricsTask with PipeIn[SamOrBam] {

  override def metricsExtension: String = CollectQualityYieldMetrics.metricsExtension

  override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = {
    buffer.append("I=" + in)
    buffer.append("O=" + metricsFile)
    includeSecondary.foreach(i => buffer.append("INCLUDE_SECONDARY_ALIGNMENTS=" + i))
    includeSupplementary.foreach(i => buffer.append("INCLUDE_SUPPLEMENTAL_ALIGNMENTS=" + i))
    buffer.append("AS=" + assumeSorted)
  }
}