From 6313aae2c4b7f2a8921cf80044cba3b2462396a3 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 9 Nov 2011 22:37:26 -0500
Subject: [PATCH] Adding checks for hasBasePileup() before calling
 getBasePileup() as per GS thread

---
 .../sting/gatk/walkers/annotator/AlleleBalance.java            | 2 +-
 .../sting/gatk/walkers/annotator/AlleleBalanceBySample.java    | 3 +++
 .../gatk/walkers/validation/GenotypeAndValidateWalker.java     | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index e5f75f06d..3a21e97a4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -69,7 +69,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
             if ( context == null )
                 continue;
 
-            if ( vc.isSNP() ) {
+            if ( vc.isSNP() && context.hasBasePileup() ) {
                 final String bases = new String(context.getBasePileup().getBases());
                 if ( bases.length() == 0 )
                     return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 820fd248a..06e91bf26 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -51,6 +51,9 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
         if ( altAlleles.size() == 0 )
             return null;
 
+        if ( !stratifiedContext.hasBasePileup() )
+            return null;
+
         final String bases = new String(stratifiedContext.getBasePileup().getBases());
         if ( bases.length() == 0 )
             return null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
index fd55d78a0..e64d00bf5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
@@ -365,7 +365,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
             return counter;
 
         // Do not operate on variants that are not covered to the optional minimum depth
-        if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
+        if (!context.hasReads() || !context.hasBasePileup() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
             counter.nUncovered = 1L;
             if (vcComp.getAttribute("GV").equals("T"))
                 counter.nAltNotCalled = 1L;