dagr.tasks.fgbio.GroupReadsByUmi.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.fgbio

import com.fulcrumgenomics.commons.CommonsDef._
import dagr.core.tasksystem.Pipe
import dagr.tasks.DataTypes.SamOrBam
import dagr.tasks.fgbio.AssignmentStrategy.AssignmentStrategy

import scala.collection.mutable.ListBuffer

/** Enum for assignment strategies. */
object AssignmentStrategy extends Enumeration {
  type AssignmentStrategy = Value
  val Identity, Edit, Adjacency, Paired = Value
}

/** Task to invoke GroupReadsByUmi. */
class GroupReadsByUmi(val in:  PathToBam,
                      val out: PathToBam,
                      val familySizeOut: Option[FilePath] = None,
                      val rawTag: Option[String] = None,
                      val assignTag: Option[String] = None,
                      val minMapQ: Option[Int] = None,
                      val strategy: AssignmentStrategy = AssignmentStrategy.Adjacency,
                      val edits: Option[Int] = None,
                      tmpDir: Option[DirPath] = None) extends FgBioTask(tmpDir=tmpDir) with Pipe[SamOrBam, SamOrBam] {

  /** Implement this to add the tool-specific arguments */
  override protected def addFgBioArgs(buffer: ListBuffer[Any]): Unit = {
    buffer.append("-i", in)
    buffer.append("-o", out)
    familySizeOut.foreach(f => buffer.append("-f", f))
    rawTag.foreach(t => buffer.append("-t", t))
    assignTag.foreach(t => buffer.append("-T", t))
    minMapQ.foreach(m => buffer.append("-m", m))
    buffer.append("-s", strategy.toString.toLowerCase)
    edits.foreach(e => buffer.append("-e", e))
    tmpDir.foreach(d => buffer.append(s"--tmp-dir=${d}"))
  }
}