From aa1d2f3a5b47412a8aa75e34e60e5f5c683a1780 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 13 Aug 2012 17:11:12 -0400
Subject: [PATCH] Not every consensus is well aligned. Need to check more, but
 starting position has been fixed.

---
 .../gatk/walkers/compression/reducereads/SlidingWindow.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
index 0adea416e..2db1e7cf9 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
@@ -416,7 +416,7 @@ public class SlidingWindow {
      */
     private void addToFilteredData(LinkedList<HeaderElement> header, int start, int end) {
         if (filteredDataConsensus == null)
-            filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, windowHeader.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
+            filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
 
         ListIterator<HeaderElement> headerElementIterator = header.listIterator(start);
         for (int index = start; index < end; index++) {
@@ -445,7 +445,7 @@ public class SlidingWindow {
      */
     private void addToRunningConsensus(LinkedList<HeaderElement> header, int start, int end) {
         if (runningConsensus == null)
-            runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, windowHeader.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
+            runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, getStartLocation(header), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
 
         Iterator<HeaderElement> headerElementIterator = header.listIterator(start);
         for (int index = start; index < end; index++) {