com.fulcrumgenomics.illumina.RunInfo.scala Maven / Gradle / Ivy

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/*
 * The MIT License
 *
 * Copyright (c) 2017 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.illumina

import java.text.{ParseException, SimpleDateFormat}

import com.fulcrumgenomics.FgBioDef.FilePath
import com.fulcrumgenomics.bam.Template
import com.fulcrumgenomics.util.SegmentType.SampleBarcode
import com.fulcrumgenomics.util.{Metric, ReadSegment, ReadStructure, SegmentType}
import htsjdk.samtools.util.DateParser.InvalidDateException
import htsjdk.samtools.util.Iso8601Date

/** Stores the result of parsing the run info (RunInfo.xml) file from an Illumina run folder.
  *
  * @param run_barcode the unique identifier for the sequencing run and flowcell, stored as
  *                   "_".
  * @param flowcell_barcode the flowcell barcode.
  * @param instrument_name the instrument name.
  * @param run_date the date of the sequencing run.
  * @param read_structure the description of the logical structure of cycles within the sequencing run.  This will only
  *                       contain template and sample barcode segments, as the RunInfo.xml does not contain information
  *                       about other segments (i.e. molecular barcodes and skips).
  * @param num_lanes the number of lanes in the flowcell.
  */
case class RunInfo
( run_barcode: String,
  flowcell_barcode: String,
  instrument_name: String,
  run_date: Iso8601Date,
  read_structure: ReadStructure,
  num_lanes: Int
) extends Metric

object RunInfo {
  /** A set of functions to parse dates in various formats. */
  val DateParsers: Seq[String => Option[Iso8601Date]] = Seq(
    d => {if (d.length == 6) Some(new Iso8601Date("20" + d.substring(0,2) + "-" + d.substring(2,4) + "-" + d.substring(4))) else None },
    d => {if (d.length == 8) Some(new Iso8601Date(d.substring(0,4) + "-" + d.substring(4,6) + "-" + d.substring(6))) else None},
    d => {try {Some(new Iso8601Date(new SimpleDateFormat("M/d/yyyy h:mm:ss a").parse(d)))} catch { case _: ParseException => None }},
    d => {try {Some(new Iso8601Date(d))} catch {case _: InvalidDateException => None}}
  )

  /** Parses the run info file for the flowcell barcode, instrument name, run date, and read structure.
    *
    * @param runInfo the path to the RunInfo.xml file, typically in the run folder.
    */
  def apply(runInfo: FilePath): RunInfo = {
    import scala.xml.XML
    val xml = XML.loadFile(runInfo.toFile)
    val flowcellBarcode = (xml \\ "RunInfo" \\ "Run" \\ "Flowcell").text
    val instrumentName  = (xml \\ "RunInfo" \\ "Run" \\ "Instrument").text
    val runDate         = (xml \\ "RunInfo" \\ "Run" \\ "Date").text
    val segments        = (xml \\ "RunInfo" \\ "Run" \\ "Reads" \\ "Read").map { read =>
      val isIndexedRead = (read \ "@IsIndexedRead").text.equals("Y")
      val numCycles     = (read \ "@NumCycles").text.toInt
      ReadSegment(offset=0, length=Some(numCycles), kind=if (isIndexedRead) SegmentType.SampleBarcode else SegmentType.Template)
    }
    val readStructure = ReadStructure(segments, resetOffsets=true)
    val numLanes = (xml \\ "RunInfo" \\ "Run" \\ "FlowcellLayout" \ "@LaneCount").text.toInt

    RunInfo(
      run_barcode      = s"${instrumentName}_$flowcellBarcode",
      flowcell_barcode = flowcellBarcode,
      instrument_name  = instrumentName,
      run_date         = parseDate(runDate),
      read_structure   = readStructure,
      num_lanes        = numLanes
    )
  }

  /** Parses the date string from the RunInfo file into a date object based on the various formats Illumina
    * has used over the years.
    */
  private def parseDate(date: String): Iso8601Date = {
    DateParsers.iterator.flatMap(p => p(date)).buffered.headOption match {
      case Some(d) => d
      case None    => throw new IllegalArgumentException(s"Could not parse date: $date")
    }
  }
}