dagr.tasks.jeanluc.JeanLucTask.scala Maven / Gradle / Ivy

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A set of example dagr tasks.
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/*
 * The MIT License
 *
 * Copyright (c) 2016 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.jeanluc

import java.nio.file.Path

import dagr.tasks.picard.PicardTask
import htsjdk.samtools.ValidationStringency

import scala.collection.mutable.ListBuffer

object JeanLucTask {
  val JeanLucJarConfigPath = "jeanluc.jar"
}

/**
  * Base Task for any task in the JeanLuc jar.
  */
abstract class JeanLucTask(useAdvancedGcOptions: Boolean = true,
                           validationStringency: Option[ValidationStringency] = Some(ValidationStringency.SILENT),
                           useAsyncIo: Boolean = false,
                           compressionLevel: Option[Int] = None,
                           createIndex: Option[Boolean] = Some(true),
                           createMd5File: Option[Boolean] = None)

  extends PicardTask(useAdvancedGcOptions = useAdvancedGcOptions,
                     validationStringency = validationStringency,
                     useAsyncIo           = useAsyncIo,
                     compressionLevel     = compressionLevel,
                     createIndex          = createIndex,
                     createMd5File        = createMd5File) {


  /** Override to return the path to the JeanLuc jar. */
  override def jarPath: Path = configure[Path](JeanLucTask.JeanLucJarConfigPath)

  /** Override to "hide" the addPicardArgs being addJeanLucArgs. */
  final override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = addJeanLucArgs(buffer)

  def addJeanLucArgs(buffer: ListBuffer[Any]): Unit
}