diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java index 5f51c6b80..f972d49fb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/AnalyzePowerWalker.java @@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.By; import org.broadinstitute.sting.gatk.walkers.DataSource; import org.broadinstitute.sting.playground.utils.PoolUtils; +import org.broadinstitute.sting.playground.utils.ReadOffsetQuad; import java.io.FileNotFoundException; import java.io.FileReader; @@ -73,8 +74,8 @@ public class AnalyzePowerWalker extends CoverageAndPowerWalker{ Pair,List> readsFilteredByQuality = filterByQuality(rawContext.getReads(),rawContext.getOffsets(), super.getMinQualityScore()); context = new AlignmentContext(rawContext.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond()); } - - Pair, List>,Pair,List>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets()); + ReadOffsetQuad readsByDirection = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets()); + Pair, List>,Pair,List>> splitReads = new Pair(new Pair(readsByDirection.getFirstReads(),readsByDirection.getSecondReads()),new Pair(readsByDirection.getFirstOffsets(),readsByDirection.getSecondOffsets())); if ( !super.suppress_printing ) { Pair powPair = super.calculatePower(splitReads,false,context);