dagr.tasks.gatk.SplitNCigarReads.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.gatk

import dagr.tasks.DagrDef
import DagrDef.{PathToFasta, PathToBam}

import scala.collection.mutable.ListBuffer

/**
  * Runs the GATK walker that splits reads at N operators in cigars so that RNA-seq
  * BAMs can be fed into the HaplotypeCaller
  */
class SplitNCigarReads(val in: PathToBam, val out: PathToBam, ref:PathToFasta, bamCompression: Option[Int] = None)
  extends GatkTask(walker="SplitNCigarReads", ref=ref, bamCompression=bamCompression) {

  override protected def addWalkerArgs(buffer: ListBuffer[Any]): Unit = {
    buffer.append("-I", in)
    buffer.append("-o", out)
    buffer.append("-U", "ALLOW_N_CIGAR_READS")
  }
}