From 5cf1d6c104b7acdbe55750a11ad267752b062566 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 13 Sep 2009 19:39:23 +0000
Subject: [PATCH] Bugfix - this walker was never changed to work with the new
 PoolUtils methods after those methods were changed to return ReadOffsetQuad
 objects rather than nested pairs. This broke the build :(.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1608 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/poolseq/AnalyzePowerWalker.java  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

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<SAMRecord>,List<Integer>> readsFilteredByQuality = filterByQuality(rawContext.getReads(),rawContext.getOffsets(), super.getMinQualityScore());
             context = new AlignmentContext(rawContext.getLocation(),readsFilteredByQuality.getFirst(),readsFilteredByQuality.getSecond());
         }
-
-        Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
+        ReadOffsetQuad readsByDirection = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());
+        Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = new Pair(new Pair(readsByDirection.getFirstReads(),readsByDirection.getSecondReads()),new Pair(readsByDirection.getFirstOffsets(),readsByDirection.getSecondOffsets()));
         if ( !super.suppress_printing )
         {
             Pair<double[],byte[]> powPair = super.calculatePower(splitReads,false,context);