From 8e0f5bc5a568387ec0d9913eba4812abfedaaad0 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Apr 2011 19:59:59 +0000
Subject: [PATCH] Prevent NullPointerException in cases where SNP is filtered

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5641 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../ReadBasedPhasingValidationWalker.java     | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
index ad2972d9d..698dceee8 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
@@ -73,7 +73,9 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
     private final static int NUM_IN_PAIR = 2; // trivial
 
     // enable deletions in the pileup
-    public boolean includeReadsWithDeletionAtLoci() { return true; }
+    public boolean includeReadsWithDeletionAtLoci() {
+        return true;
+    }
 
     public void initialize() {
         rodNames = new LinkedList<String>();
@@ -85,8 +87,7 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
         InputStream sitePairsStream = null;
         try {
             sitePairsStream = new FileInputStream(sitePairsFile);
-        }
-        catch (FileNotFoundException fnfe) {
+        } catch (FileNotFoundException fnfe) {
             fnfe.printStackTrace();
             throw new UserException("Problem opening file: " + sitePairsFile);
         }
@@ -96,8 +97,7 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
             String line = null;
             try {
                 line = sitePairsReader.readLine();
-            }
-            catch (IOException ioe) {
+            } catch (IOException ioe) {
                 ioe.printStackTrace();
                 throw new UserException("Problem reading file: " + sitePairsFile);
             }
@@ -261,12 +261,14 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
             System.out.println("% MATCHING reads: " + percentMatchingReads + " [of " + totalCount + " TOTAL reads]");
 
             out.print(sp);
-            for (Haplotype hap : allPossibleHaplotypes) {
-                Integer count = haplotypeCounts.get(hap);
-                if (count == null) // haplotype may not have been observed in ANY reads
-                    count = 0;
+            if (allPossibleHaplotypes != null) {
+                for (Haplotype hap : allPossibleHaplotypes) {
+                    Integer count = haplotypeCounts.get(hap);
+                    if (count == null) // haplotype may not have been observed in ANY reads
+                        count = 0;
 
-                out.print("\t" + count);
+                    out.print("\t" + count);
+                }
             }
             out.println();
         }