From 56aa98ad30f16e965968a7faf9cc11805933747e Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 10 Apr 2009 04:18:20 +0000
Subject: [PATCH] Ignore null values.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../fourbasecaller/CombineSamAndFourProbs.java      | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
index 723d518b4..849141347 100755
--- a/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
@@ -63,13 +63,14 @@ public class CombineSamAndFourProbs extends CommandLineProgram {
                 String readname = sr.getReadName();
                 byte[] sq = (byte[]) fourprobMap.get(readname);
 
-                if (sr.getReadNegativeStrandFlag()) {
-                    sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
-                }
-                
-                sr.setAttribute("SQ", sq);
+                if (sq != null) {
+                    if (sr.getReadNegativeStrandFlag()) {
+                        sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
+                    }
 
-                sw.addAlignment(sr);
+                    sr.setAttribute("SQ", sq);
+                    sw.addAlignment(sr);
+                }
             }
 
             sf.close();