Merge branch 'feature-bamstats' into 'develop'

Feature bamstats

Fixes #308 

- [x] Multi sample base with scala futures
- [x] Base stats like total number of reads
- [x] mapping quality histogram
- [x] insertsize histogram
- [x] Clipping stats

- [x] Add unit testing

See merge request !435

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala

@@ -18,12 +18,13 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.tools.flagstat
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class BiopetFlagstat(val root: Configurable) extends ToolCommandFunction with Summarizable {
-  def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
+  def toolObject = flagstat.BiopetFlagstat
 
   @Input(doc = "Input bam", shortName = "input", required = true)
   var input: File = _

biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

@@ -22,10 +22,11 @@ object BiopetToolsExecutable extends BiopetExecutable {
 
   def tools: List[MainCommand] = List(
     nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed,
+    nl.lumc.sasc.biopet.tools.bamstats.BamStats,
     nl.lumc.sasc.biopet.tools.BaseCounter,
     nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
     nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
-    nl.lumc.sasc.biopet.tools.BiopetFlagstat,
+    nl.lumc.sasc.biopet.tools.flagstat.BiopetFlagstat,
     nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
     nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
     nl.lumc.sasc.biopet.tools.FastqSplitter,

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

-/**
- * Biopet is built on top of GATK Queue for building bioinformatic
- * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
- * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
- * should also be able to execute Biopet tools and pipelines.
- *
- * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
- *
- * Contact us at: sasc@lumc.nl
- *
- * A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
- * license; For commercial users or users who do not want to follow the AGPL
- * license, please contact us to obtain a separate license.
- */
-package nl.lumc.sasc.biopet.tools
-
-import java.io.{ File, PrintWriter }
-
-import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
-import nl.lumc.sasc.biopet.utils.{ ToolCommand, ConfigUtils }
-
-import scala.collection.JavaConversions._
-import scala.collection.mutable
-
-object BiopetFlagstat extends ToolCommand {
-
-  case class Args(inputFile: File = null,
-                  outputFile: Option[File] = None,
-                  summaryFile: Option[File] = None,
-                  region: Option[String] = None) extends AbstractArgs
-
-  class OptParser extends AbstractOptParser {
-    opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
-      c.copy(inputFile = x)
-    } text "input bam file"
-    opt[File]('o', "outputFile") valueName "<file>" action { (x, c) =>
-      c.copy(outputFile = Some(x))
-    } text "output file"
-    opt[File]('s', "summaryFile") valueName "<file>" action { (x, c) =>
-      c.copy(summaryFile = Some(x))
-    } text "summary output file"
-    opt[String]('r', "region") valueName "<chr:start-stop>" action { (x, c) =>
-      c.copy(region = Some(x))
-    } text "Region to calculate the statistics on"
-  }
-
-  /**
-   * @param args the command line arguments
-   */
-  def main(args: Array[String]): Unit = {
-    val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
-
-    val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
-    val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {
-      val regionRegex = """(.*):(.*)-(.*)""".r
-      commandArgs.region.get match {
-        case regionRegex(chr, start, stop) => inputSam.query(chr, start.toInt, stop.toInt, false)
-        case _                             => sys.error("Region wrong format")
-      }
-    }
-
-    val flagstatCollector = new FlagstatCollector
-    flagstatCollector.loadDefaultFunctions()
-    val m = 10
-    val max = 60
-    for (t <- 0 to (max / m))
-      flagstatCollector.addFunction("MAPQ>" + (t * m), record => record.getMappingQuality > (t * m))
-    flagstatCollector.addFunction("First normal, second read inverted (paired end orientation)", record => {
-      if (record.getReadPairedFlag &&
-        record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
-        ((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
-      else false
-    })
-    flagstatCollector.addFunction("First normal, second read normal", record => {
-      if (record.getReadPairedFlag &&
-        record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
-        ((record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
-      else false
-    })
-    flagstatCollector.addFunction("First inverted, second read inverted", record => {
-      if (record.getReadPairedFlag &&
-        record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag == record.getMateNegativeStrandFlag &&
-        ((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
-      else false
-    })
-    flagstatCollector.addFunction("First inverted, second read normal", record => {
-      if (record.getReadPairedFlag &&
-        record.getReferenceIndex == record.getMateReferenceIndex && record.getReadNegativeStrandFlag != record.getMateNegativeStrandFlag &&
-        ((record.getFirstOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getFirstOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && record.getReadNegativeStrandFlag && record.getAlignmentStart < record.getMateAlignmentStart) ||
-          (record.getSecondOfPairFlag && !record.getReadNegativeStrandFlag && record.getAlignmentStart > record.getMateAlignmentStart))) true
-      else false
-    })
-    flagstatCollector.addFunction("Mate in same strand", record => record.getReadPairedFlag && record.getReadNegativeStrandFlag && record.getMateNegativeStrandFlag &&
-      record.getReferenceIndex == record.getMateReferenceIndex)
-    flagstatCollector.addFunction("Mate on other chr", record => record.getReadPairedFlag && record.getReferenceIndex != record.getMateReferenceIndex)
-
-    logger.info("Start reading file: " + commandArgs.inputFile)
-    for (record <- iterSam) {
-      if (flagstatCollector.readsCount % 1e6 == 0 && flagstatCollector.readsCount > 0)
-        logger.info("Reads prosessed: " + flagstatCollector.readsCount)
-      flagstatCollector.loadRecord(record)
-    }
-
-    commandArgs.summaryFile.foreach {
-      case file =>
-        val writer = new PrintWriter(file)
-        writer.println(flagstatCollector.summary)
-        writer.close()
-    }
-
-    commandArgs.outputFile match {
-      case Some(file) => {
-        val writer = new PrintWriter(file)
-        writer.println(flagstatCollector.report)
-        writer.close()
-      }
-      case _ => println(flagstatCollector.report)
-    }
-  }
-
-  class FlagstatCollector {
-    private var functionCount = 0
-    var readsCount = 0
-    private val names: mutable.Map[Int, String] = mutable.Map()
-    private var functions: Array[SAMRecord => Boolean] = Array()
-    private var totalCounts: Array[Long] = Array()
-    private var crossCounts = Array.ofDim[Long](1, 1)
-
-    def loadDefaultFunctions() {
-      addFunction("All", record => true)
-      addFunction("Mapped", record => !record.getReadUnmappedFlag)
-      addFunction("Duplicates", record => record.getDuplicateReadFlag)
-      addFunction("FirstOfPair", record => if (record.getReadPairedFlag) record.getFirstOfPairFlag else false)
-      addFunction("SecondOfPair", record => if (record.getReadPairedFlag) record.getSecondOfPairFlag else false)
-
-      addFunction("ReadNegativeStrand", record => record.getReadNegativeStrandFlag)
-
-      addFunction("NotPrimaryAlignment", record => record.getNotPrimaryAlignmentFlag)
-
-      addFunction("ReadPaired", record => record.getReadPairedFlag)
-      addFunction("ProperPair", record => if (record.getReadPairedFlag) record.getProperPairFlag else false)
-
-      addFunction("MateNegativeStrand", record => if (record.getReadPairedFlag) record.getMateNegativeStrandFlag else false)
-      addFunction("MateUnmapped", record => if (record.getReadPairedFlag) record.getMateUnmappedFlag else false)
-
-      addFunction("ReadFailsVendorQualityCheck", record => record.getReadFailsVendorQualityCheckFlag)
-      addFunction("SupplementaryAlignment", record => record.getSupplementaryAlignmentFlag)
-      addFunction("SecondaryOrSupplementary", record => record.isSecondaryOrSupplementary)
-    }
-
-    def loadRecord(record: SAMRecord) {
-      readsCount += 1
-      val values: Array[Boolean] = new Array(names.size)
-      for (t <- 0 until names.size) {
-        values(t) = functions(t)(record)
-        if (values(t)) {
-          totalCounts(t) += 1
-        }
-      }
-      for (t <- 0 until names.size) {
-        for (t2 <- 0 until names.size) {
-          if (values(t) && values(t2)) {
-            crossCounts(t)(t2) += 1
-          }
-        }
-      }
-    }
-
-    def addFunction(name: String, function: SAMRecord => Boolean) {
-      functionCount += 1
-      crossCounts = Array.ofDim[Long](functionCount, functionCount)
-      totalCounts = new Array[Long](functionCount)
-      val temp = new Array[SAMRecord => Boolean](functionCount)
-      for (t <- 0 until (temp.length - 1)) temp(t) = functions(t)
-      functions = temp
-
-      val index = functionCount - 1
-      names += (index -> name)
-      functions(index) = function
-      totalCounts(index) = 0
-    }
-
-    def report: String = {
-      val buffer = new StringBuilder
-      buffer.append("Number\tTotal Flags\tFraction\tName\n")
-      for (t <- 0 until names.size) {
-        val precentage = (totalCounts(t).toFloat / readsCount) * 100
-        buffer.append("#" + (t + 1) + "\t" + totalCounts(t) + "\t" + f"$precentage%.4f" + "%\t" + names(t) + "\n")
-      }
-      buffer.append("\n")
-
-      buffer.append(crossReport() + "\n")
-      buffer.append(crossReport(fraction = true) + "\n")
-
-      buffer.toString()
-    }
-
-    def summary: String = {
-      val map = (for (t <- 0 until names.size) yield {
-        names(t) -> totalCounts(t)
-      }).toMap ++ Map("Singletons" -> crossCounts(names.find(_._2 == "Mapped").map(_._1).getOrElse(-1))(names.find(_._2 == "MateUnmapped").map(_._1).getOrElse(-1))
-      )
-
-      ConfigUtils.mapToJson(map).spaces4
-    }
-
-    def crossReport(fraction: Boolean = false): String = {
-      val buffer = new StringBuilder
-
-      for (t <- 0 until names.size) // Header for table
-        buffer.append("\t#" + (t + 1))
-      buffer.append("\n")
-
-      for (t <- 0 until names.size) {
-        buffer.append("#" + (t + 1) + "\t")
-        for (t2 <- 0 until names.size) {
-          val reads = crossCounts(t)(t2)
-          if (fraction) {
-            val precentage = (reads.toFloat / totalCounts(t).toFloat) * 100
-            buffer.append(f"$precentage%.4f" + "%")
-          } else buffer.append(reads)
-          if (t2 == names.size - 1) buffer.append("\n")
-          else buffer.append("\t")
-        }
-      }
-      buffer.toString()
-    }
-  } // End of class
-
-}

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala

+package nl.lumc.sasc.biopet.tools.bamstats
+
+import java.io.File
+import java.util.concurrent.TimeoutException
+
+import htsjdk.samtools.reference.FastaSequenceFile
+import htsjdk.samtools.{ SAMSequenceDictionary, SamReaderFactory }
+import nl.lumc.sasc.biopet.utils.BamUtils.SamDictCheck
+import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
+
+import scala.collection.JavaConversions._
+import scala.concurrent.ExecutionContext.Implicits.global
+import scala.concurrent.duration._
+import scala.concurrent.{ Await, Future }
+import scala.language.postfixOps
+
+/**
+ * This tool will collect stats from a bamfile
+ *
+ * Created by pjvanthof on 25/05/16.
+ */
+object BamStats extends ToolCommand {
+  case class Args(outputDir: File = null,
+                  bamFile: File = null,
+                  referenceFasta: Option[File] = None,
+                  binSize: Int = 10000,
+                  threadBinSize: Int = 10000000) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('R', "reference") valueName "<file>" action { (x, c) =>
+      c.copy(referenceFasta = Some(x))
+    } text "Fasta file of reference"
+    opt[File]('o', "outputDir") required () valueName "<directory>" action { (x, c) =>
+      c.copy(outputDir = x)
+    } text "Output directory"
+    opt[File]('b', "bam") required () valueName "<file>" action { (x, c) =>
+      c.copy(bamFile = x)
+    } text "Input bam file"
+    opt[Int]("binSize") valueName "<int>" action { (x, c) =>
+      c.copy(binSize = x)
+    } text "Bin size of stats (beta)"
+    opt[Int]("threadBinSize") valueName "<int>" action { (x, c) =>
+      c.copy(threadBinSize = x)
+    } text "Size of region per thread"
+  }
+
+  /** This is the main entry to [[BamStats]], this will do the argument parsing. */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    logger.info("Start")
+
+    val sequenceDict = validateReferenceInBam(cmdArgs.bamFile, cmdArgs.referenceFasta)
+
+    init(cmdArgs.outputDir, cmdArgs.bamFile, sequenceDict, cmdArgs.binSize, cmdArgs.threadBinSize)
+
+    logger.info("Done")
+  }
+
+  /**
+   * This will retrieve the [[SAMSequenceDictionary]] from the bam file.
+   * When `referenceFasta is given he will validate this against the bam file.`
+   */
+  def validateReferenceInBam(bamFile: File, referenceFasta: Option[File]) = {
+    val samReader = SamReaderFactory.makeDefault().open(bamFile)
+    val samHeader = samReader.getFileHeader
+    samReader.close()
+    referenceFasta.map { f =>
+      val referenceReader = new FastaSequenceFile(f, true)
+      val referenceDict = referenceReader.getSequenceDictionary
+      samHeader.getSequenceDictionary.assertSameDictionary(referenceDict, false)
+      referenceReader.close()
+      referenceDict
+    }.getOrElse(samHeader.getSequenceDictionary)
+  }
+
+  /**
+   * This is the main running function of [[BamStats]]. This will start the threads and collect and write the results.
+   *
+   * @param outputDir All output files will be placed here
+   * @param bamFile Input bam file
+   * @param referenceDict Dict for scattering
+   * @param binSize stats binsize
+   * @param threadBinSize Thread binsize
+   */
+  def init(outputDir: File, bamFile: File, referenceDict: SAMSequenceDictionary, binSize: Int, threadBinSize: Int): Unit = {
+    val contigsFutures = BedRecordList.fromDict(referenceDict).allRecords.map { contig =>
+      processContig(contig, bamFile, binSize, threadBinSize, outputDir)
+    }
+
+    val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.toList)
+
+    stats.writeStatsToFiles(outputDir)
+  }
+
+  /**
+   * This will start the subjobs for each contig and collect [[Stats]] on contig level
+   *
+   * @param region Region to check, mostly yhis is the complete contig
+   * @param bamFile Input bam file
+   * @param binSize stats binsize
+   * @param threadBinSize Thread binsize
+   * @return Output stats
+   */
+  def processContig(region: BedRecord, bamFile: File, binSize: Int, threadBinSize: Int, outputDir: File): Future[Stats] = Future {
+    val scattersFutures = region
+      .scatter(binSize)
+      .grouped((region.length.toDouble / binSize).ceil.toInt / (region.length.toDouble / threadBinSize).ceil.toInt)
+      .map(scatters => processThread(scatters, bamFile))
+      .toList
+    val stats = waitOnFutures(scattersFutures, Some(region.chr))
+    val contigDir = new File(outputDir, "contigs" + File.separator + region.chr)
+    contigDir.mkdirs()
+    stats.writeStatsToFiles(contigDir)
+    stats
+  }
+
+  /**
+   * This method will wait when all futures are complete and collect a single [[Stats]] instance
+   *
+   * @param futures List of futures to monitor
+   * @param msg Optional message for logging
+   * @return Output stats
+   */
+  def waitOnFutures(futures: List[Future[Stats]], msg: Option[String] = None): Stats = {
+    msg.foreach(m => logger.info(s"Start monitoring jobs for '$m', ${futures.size} jobs"))
+    futures.foreach(_.onFailure { case t => throw new RuntimeException(t) })
+    val stats = Await.result(Future.sequence(futures).map(_.fold(Stats())(_ += _)), Duration.Inf)
+    msg.foreach(m => logger.info(s"All jobs for '$m' are done"))
+    stats
+  }
+
+  /**
+   * This method will process 1 thread bin
+   *
+   * @param scatters bins to check, there should be no gaps withing the scatters
+   * @param bamFile Input bamfile
+   * @return Output stats
+   */
+  def processThread(scatters: List[BedRecord], bamFile: File): Future[Stats] = Future {
+    val totalStats = Stats()
+    val sortedScatters = scatters.sortBy(_.start)
+    val samReader = SamReaderFactory.makeDefault().open(bamFile)
+    val threadChr = sortedScatters.head.chr
+    val threadStart = sortedScatters.head.start
+    val threadEnd = sortedScatters.last.end
+    val it = samReader.query(threadChr, threadStart, threadEnd, false).buffered
+    for (samRecord <- it) {
+
+      // Read based stats
+      if (samRecord.getAlignmentStart > threadStart && samRecord.getAlignmentStart <= threadEnd) {
+        totalStats.flagstat.loadRecord(samRecord)
+        if (!samRecord.getReadUnmappedFlag) { // Mapped read
+          totalStats.mappingQualityHistogram.add(samRecord.getMappingQuality)
+        }
+        if (samRecord.getProperPairFlag && samRecord.getFirstOfPairFlag && !samRecord.getSecondOfPairFlag)
+          totalStats.insertSizeHistogram.add(samRecord.getInferredInsertSize.abs)
+
+        val leftClipping = samRecord.getAlignmentStart - samRecord.getUnclippedStart
+        val rightClipping = samRecord.getUnclippedEnd - samRecord.getAlignmentEnd
+
+        totalStats.clippingHistogram.add(leftClipping + rightClipping)
+        totalStats.leftClippingHistogram.add(leftClipping)
+        totalStats.rightClippingHistogram.add(rightClipping)
+
+        if (samRecord.getReadNegativeStrandFlag) {
+          totalStats._5_ClippingHistogram.add(leftClipping)
+          totalStats._3_ClippingHistogram.add(rightClipping)
+        } else {
+          totalStats._5_ClippingHistogram.add(rightClipping)
+          totalStats._3_ClippingHistogram.add(leftClipping)
+        }
+
+        //TODO: Bin Support
+      }
+
+      //TODO: bases counting
+    }
+    samReader.close()
+
+    totalStats
+  }
+
+  /**
+   * This method will only count the unmapped fragments
+   *
+   * @param bamFile Input bamfile
+   * @return Output stats
+   */
+  def processUnmappedReads(bamFile: File): Future[Stats] = Future {
+    val stats = Stats()
+    val samReader = SamReaderFactory.makeDefault().open(bamFile)
+    for (samRecord <- samReader.queryUnmapped()) {
+      stats.flagstat.loadRecord(samRecord)
+    }
+    samReader.close()
+    stats
+  }
+}

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala

+package nl.lumc.sasc.biopet.tools.bamstats
+
+import java.io.{ File, PrintWriter }
+
+import scala.collection.mutable
+
+/**
+ * Created by pjvanthof on 05/07/16.
+ */
+class Counts[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Ordering[T]) {
+  protected[Counts] val counts: mutable.Map[T, Long] = mutable.Map() ++ _counts
+
+  /** Returns histogram as map */
+  def countsMap = counts.toMap
+
+  /** Returns value if it does exist */
+  def get(key: T) = counts.get(key)
+
+  /** This will add an other histogram to `this` */
+  def +=(other: Counts[T]): Counts[T] = {
+    other.counts.foreach(x => this.counts += x._1 -> (this.counts.getOrElse(x._1, 0L) + x._2))
+    this
+  }
+
+  /** With this a value can be added to the histogram */
+  def add(value: T): Unit = {
+    counts += value -> (counts.getOrElse(value, 0L) + 1)
+  }
+
+  /** Write histogram to a tsv/count file */
+  def writeToTsv(file: File): Unit = {
+    val writer = new PrintWriter(file)
+    writer.println("value\tcount")
+    counts.keys.toList.sorted.foreach(x => writer.println(s"$x\t${counts(x)}"))
+    writer.close()
+  }
+
+  override def equals(other: Any): Boolean = {
+    other match {
+      case c: Counts[T] => this.counts == c.counts
+      case _            => false
+    }
+  }
+}
+
+class Histogram[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Numeric[T]) extends Counts[T](_counts) {
+
+}

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Stats.scala

+package nl.lumc.sasc.biopet.tools.bamstats
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.tools.flagstat.FlagstatCollector
+
+/**
+ * Created by pjvanthof on 05/07/16.
+ */
+case class Stats(flagstat: FlagstatCollector = new FlagstatCollector(),
+                 mappingQualityHistogram: Histogram[Int] = new Histogram[Int](),
+                 insertSizeHistogram: Histogram[Int] = new Histogram[Int](),
+                 clippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 leftClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 rightClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 _5_ClippingHistogram: Histogram[Int] = new Histogram[Int](),
+                 _3_ClippingHistogram: Histogram[Int] = new Histogram[Int]()) {
+
+  flagstat.loadDefaultFunctions()
+  flagstat.loadQualityFunctions(1, 0)
+  flagstat.loadOrientationFunctions
+
+  /** This will add an other [[Stats]] inside `this` */
+  def +=(other: Stats): Stats = {
+    this.flagstat += other.flagstat
+    this.mappingQualityHistogram += other.mappingQualityHistogram
+    this.insertSizeHistogram += other.insertSizeHistogram
+    this.clippingHistogram += other.clippingHistogram
+    this.leftClippingHistogram += other.leftClippingHistogram
+    this.rightClippingHistogram += other.rightClippingHistogram
+    this</