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2.12 Improvements/manual inlining #203

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2.12 Improvements/manual inlining #203

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0915851
inline Read methods
agaszmurlo Aug 13, 2020
be579a9
inlining methods from ContigAggregate
agaszmurlo Aug 13, 2020
320958b
inlining add to cache method
agaszmurlo Aug 13, 2020
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2 changes: 1 addition & 1 deletion src/main/scala/org/biodatageeks/sequila/pileup/model/ContigAggregate.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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12 changes: 7 additions & 5 deletions src/main/scala/org/biodatageeks/sequila/pileup/model/Read.scala
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Expand Up @@ -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

Expand Down Expand Up @@ -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)
}
}
}
Expand Down Expand Up @@ -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)
Expand All @@ -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)
}
}
}
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