diff --git a/src/main/scala/org/biodatageeks/sequila/pileup/model/ContigAggregate.scala b/src/main/scala/org/biodatageeks/sequila/pileup/model/ContigAggregate.scala
index db9c2ba0..7d8cf202 100644
--- a/src/main/scala/org/biodatageeks/sequila/pileup/model/ContigAggregate.scala
+++ b/src/main/scala/org/biodatageeks/sequila/pileup/model/ContigAggregate.scala
@@ -31,7 +31,7 @@ case class ContigAggregate(
                             qualityCache: QualityCache
                                 ) {
 
-  private val altsKeyCache  = mutable.TreeSet.empty[Int]
+  val altsKeyCache  = mutable.TreeSet.empty[Int]
 
   def hasAltOnPosition(pos:Int):Boolean = alts.contains(pos)
   def getRange: broadcast.Range = broadcast.Range(contig, startPosition, maxPosition)
diff --git a/src/main/scala/org/biodatageeks/sequila/pileup/model/Read.scala b/src/main/scala/org/biodatageeks/sequila/pileup/model/Read.scala
index 535f787e..44fd70b5 100644
--- a/src/main/scala/org/biodatageeks/sequila/pileup/model/Read.scala
+++ b/src/main/scala/org/biodatageeks/sequila/pileup/model/Read.scala
@@ -6,6 +6,7 @@ import org.biodatageeks.sequila.pileup.MDTagParser
 import org.biodatageeks.sequila.pileup.conf.{Conf, QualityConstants}
 import org.biodatageeks.sequila.pileup.timers.PileupTimers.{AnalyzeReadsCalculateAltsParseMDTimer, AnalyzeReadsCalculateAltsTimer, AnalyzeReadsCalculateEventsTimer}
 import org.biodatageeks.sequila.pileup.timers.PileupTimers._
+import org.biodatageeks.sequila.pileup.model.Quals._
 
 import scala.collection.mutable
 
@@ -35,7 +36,7 @@ case class ExtendedReads(r:SAMRecord) {
           val cigarConf = CigarDerivedConf.create(start, cigar)
           val readQualSummary = ReadQualSummary(start, r.getEnd, r.getBaseQualities, cigarConf)
           ReadQualSummaryFillExisitingQualTimer.time { fillBaseQualitiesForExistingAlts(agg, foundAlts, readQualSummary) }
-          agg.addToCache(readQualSummary)
+          agg.qualityCache.addOrReplace(readQualSummary)
         }
       }
   }
@@ -117,8 +118,8 @@ case class ExtendedReads(r:SAMRecord) {
         position += 1
 
         val indexInSeq = calculatePositionInReadSeq(position - read.getStart -delCounter)
-        val altBase = getAltBaseFromSequence(indexInSeq)
-        val altBaseQual = getAltBaseQualFromSequence(indexInSeq)
+        val altBase = this.r.getReadString.charAt(indexInSeq-1)
+        val altBaseQual = this.r.getBaseQualities()(indexInSeq-1)
         val altPosition = position - clipLen - 1
         val newAlt = !aggregate.hasAltOnPosition(altPosition)
         aggregate.updateAlts(altPosition, altBase)
@@ -142,14 +143,15 @@ case class ExtendedReads(r:SAMRecord) {
 
   //~100s
   def fillBaseQualitiesForExistingAlts(agg: ContigAggregate, blackList:scala.collection.Set[Int], readQualSummary: ReadQualSummary): Unit = {
-    val altsPositions =  agg.getAltPositionsForRange(r.getStart, r.getEnd) //~1s
+    //val altsPositions =  agg.getAltPositionsForRange(r.getStart, r.getEnd) //~1s
+    val altsPositions =  agg.altsKeyCache.range(r.getStart,r.getEnd+1)
     val positionsToFill =  altsPositions diff blackList //~1s
     for (pos <- positionsToFill.iterator) { //~10s empty loop
       if(!readQualSummary.cigarDerivedConf.hasDel || !readQualSummary.hasDeletionOnPosition(pos) ) {
         val relativePos = if(!readQualSummary.cigarDerivedConf.hasIndel && !readQualSummary.cigarDerivedConf.hasClip ) pos - readQualSummary.start
         else readQualSummary.relativePosition(pos)
         val qual = readQualSummary.qualsArray(relativePos)
-        agg.updateQuals(pos, QualityConstants.REF_SYMBOL, qual, false)
+        agg.quals.updateQuals(pos, QualityConstants.REF_SYMBOL,qual, false, true)
       }
     }
   }