From 525cf331f4e6568479582c44f7c7b8912cdf7773 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 13 Nov 2012 11:52:47 -0500
Subject: [PATCH 1/3] Don't catch a User Error and re-throw as a Reviewed
 Exception.  That makes Eric unhappy.

---
 .../sting/gatk/io/storage/VariantContextWriterStorage.java      | 2 --
 1 file changed, 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 31f6d5954..8e4633869 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -198,8 +198,6 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
 
             source.close();
             file.delete(); // this should be last to aid in debugging when the process fails
-        } catch (UserException e) {
-            throw new ReviewedStingException("BUG: intermediate file " + file + " is malformed, got error while reading", e);
         } catch (IOException e) {
             throw new UserException.CouldNotReadInputFile(file, "Error reading file in VCFWriterStorage: ", e);
         }

From c7335c99023dd1f68afda8a5d43396af77a470b2 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 13 Nov 2012 11:53:12 -0500
Subject: [PATCH 2/3] Having a malformed GATK report is a User Error

---
 .../broadinstitute/sting/gatk/report/GATKReportVersion.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
index b5a5e0443..b51fb17f0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.report;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 
 public enum GATKReportVersion {
     /**
@@ -91,6 +92,6 @@ public enum GATKReportVersion {
         if (header.startsWith("#:GATKReport.v1.1"))
             return GATKReportVersion.V1_1;
 
-        throw new ReviewedStingException("Unknown GATK report version in header: " + header);
+        throw new UserException.BadInput("The GATK report has an unknown/unsupported version in the header: " + header);
     }
 }

From ba41f65759724b650d8996185bc4761f50bda466 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 13 Nov 2012 11:53:39 -0500
Subject: [PATCH 3/3] Protect against NPEs in SelectVariants by checking for
 missing Genotypes

---
 .../sting/gatk/walkers/variantutils/SelectVariants.java      | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index d1b7cb96f..d28fe34d6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -659,7 +659,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         return (g !=null && !g.isHomRef() && (g.isCalled() || (g.isFiltered() && !EXCLUDE_FILTERED)));
     }
 
-    private boolean haveSameGenotypes(Genotype g1, Genotype g2) {
+    private boolean haveSameGenotypes(final Genotype g1, final Genotype g2) {
+        if ( g1 == null || g2 == null )
+            return false;
+
         if ((g1.isCalled() && g2.isFiltered()) ||
                 (g2.isCalled() && g1.isFiltered()) ||
                 (g1.isFiltered() && g2.isFiltered() && EXCLUDE_FILTERED))