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

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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.picard

import java.nio.file.Path

import dagr.tasks.DagrDef
import DagrDef.PathToBam

import scala.collection.mutable.ListBuffer

object EstimateLibraryComplexity {
  def minIdenticalBasesFor(minIdenticalBases: Int, numPfReads: Option[Long]): Int = {
    numPfReads match {
      case None => minIdenticalBases
      case Some(n) if n < 10000000 => minIdenticalBases
      case Some(n) => math.ceil( (math.log(n) / math.log(4)) - 7 ).toInt
    }
  }

  val MetricsExtension = ".els_duplicate_metrics"
}

class EstimateLibraryComplexity(override val in: PathToBam,
                                override val prefix: Option[Path],
                                var minIdenticalBases: Int = 5,
                                var numPfReads: Option[Long] = None,
                                templateUmiTag: Option[String] = None,
                                read1UmiTag: Option[String] = None,
                                read2UmiTag: Option[String] = None)
  extends PicardTask with PicardMetricsTask {

  override def metricsExtension: String = EstimateLibraryComplexity.MetricsExtension

  override protected def addPicardArgs(buffer: ListBuffer[Any]): Unit = {
    buffer.append("I=" + in)
    buffer.append("O=" + metricsFile)
    buffer.append("MIN_IDENTICAL_BASES=" +
      EstimateLibraryComplexity.minIdenticalBasesFor(minIdenticalBases=minIdenticalBases, numPfReads=numPfReads)
    )
    templateUmiTag.foreach(v => buffer.append("BARCODE_TAG=" + v))
    read1UmiTag.foreach(v => buffer.append("READ_ONE_BARCODE_TAG=" + v))
    read2UmiTag.foreach(v => buffer.append("READ_TWO_BARCODE_TAG=" + v))
  }
}