/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
 * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
package nl.lumc.sasc.biopet.extensions.sambamba

import java.io.File

import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }

/** Extension for sambemba merge  */
class SambambaMerge(val parent: Configurable) extends Sambamba {

  @Input(doc = "Bam File[s]")
  var input: List[File] = Nil

  @Output(doc = "Output merged bam PATH")
  var output: File = _

  // @doc: compression_level 6 is average, 0 = no compression, 9 = best
  val compressionLevel: Option[Int] = config("compression_level")
  val header: Boolean = config("header", default = false)
  val showProgress: Boolean = config("show-progress", default = true)
  val filter: Option[String] = config("filter")

  override def defaultThreads = 4
  override def defaultCoreMemory = 4.0

  @Output
  private var indexOutput: File = _

  override def beforeGraph(): Unit = {
    indexOutput = new File(output + ".bai")
  }

  /** Returns command to execute */
  def cmdLine: String = required(executable) +
    required("merge") +
    optional("-t", nCoresRequest) +
    optional("-l", compressionLevel) +
    optional("-F", filter) +
    conditional(header, "--header") +
    conditional(showProgress, "--show-progress") +
    required(output) +
    repeat(input)
}