com.fulcrumgenomics.util.IlluminaAdapters.scala Maven / Gradle / Ivy

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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 com.fulcrumgenomics.util

import htsjdk.samtools.util.SequenceUtil

/** An object providing access to various Illumina adapter sequences. */
object IlluminaAdapters {
  sealed abstract class AdapterPair(fivePrime: String, threePrime: String) {
    val      both = Seq(fivePrime, threePrime)
    val      threePrimeReadOrder = threePrime
    lazy val fivePrimeReadOrder  = SequenceUtil.reverseComplement(fivePrime)
  }

  case object PairedEnd extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                                            "AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG")

  case object Indexed extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                                          "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG")

  case object SingleEnd extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                                            "AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG")

  case object NexteraV1 extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG",
                                            "CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCGNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG")

  case object NexteraV2 extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG",
                                            "CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG")

  case object DualIndexed extends AdapterPair("AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT",
                                              "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG")

  val all = Seq(PairedEnd, Indexed, SingleEnd, NexteraV1, NexteraV2, DualIndexed)
}