Counting quals

qualcounts.scala

.mapPartitions {
        partIterator =>
          //val qualStrings = partIterator.toSeq
          val maxReadQual=150
          val maxReadLength=150
          var pIndex = 0
          val posQualArray = Array.fill[Int](maxReadLength,maxReadQual)(0) //((pos,qualVal),counter)
          for (seq <- partIterator) {
            var qIndex = 0
            for(q<-seq.getQual){
              val qAdj = q-33
              posQualArray(qIndex)(qAdj)+=1
              qIndex+=1
            }
          }
          val posQualMap = scala.collection.mutable.HashMap[(Int,Int),Int]()
          for(i<-posQualArray.indices) {
            for (j <- posQualArray(i).indices)
              if (posQualArray(i)(j) > 0)
                posQualMap.put((i + 1, j), posQualArray(i)(j))
          }
            Iterator(posQualMap)
      }
        .flatMap(r=>r)
        .reduceByKey(_+_)
        .sortBy(r=>r._1)
      qualitiesPerPosition