Fix GATK null allele error when calculating DepthPerAlleleBySample for indels

dpsample_nullallele.patch

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 5d83ddd..928d836 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -87,12 +87,12 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
 
         for ( PileupElement p : pileup ) {
             if ( p.isBeforeInsertion() ) {
-
-                final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false);
-                if ( alleleCounts.containsKey(insertion) ) {
-                    alleleCounts.put(insertion, alleleCounts.get(insertion)+1);
+                if ( p.getEventBases() != null ) {
+                    final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false);
+                    if ( alleleCounts.containsKey(insertion) ) {
+                        alleleCounts.put(insertion, alleleCounts.get(insertion)+1);
+                    }
                 }
-
             } else if ( p.isBeforeDeletionStart() ) {
                 if ( p.getEventLength() == refAllele.length() - 1 ) {
                     // this is indeed the deletion allele recorded in VC
@@ -120,4 +120,4 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
     public List<VCFFormatHeaderLine> getDescriptions() {
         return Arrays.asList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
     }
-}
\ No newline at end of file
+}