From 92d8aa3d4c20f4f58a15121f5deb8236e090f6da Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 21 May 2012 09:38:52 -0400
Subject: [PATCH] Don't exception out in these VE modules if the VCF has
 records that aren't just SNPs or indels

---
 .../walkers/varianteval/evaluators/MultiallelicSummary.java | 4 ++--
 .../gatk/walkers/varianteval/evaluators/VariantSummary.java | 6 ++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
index 7efb1d823..09c8687eb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
@@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@@ -113,7 +112,8 @@ public class MultiallelicSummary extends VariantEvaluator implements StandardEva
                 }
                 break;
             default:
-                throw new UserException.BadInput("Unexpected variant context type: " + eval);
+                //throw new UserException.BadInput("Unexpected variant context type: " + eval);
+                break;
         }
 
         return;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
index 8766bb14e..cb19df13e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
@@ -35,7 +35,6 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -186,7 +185,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
             case SYMBOLIC:
                 return Type.CNV;
             default:
-                throw new UserException.BadInput("Unexpected variant context type: " + vc);
+                //throw new UserException.BadInput("Unexpected variant context type: " + vc);
+                return null;
         }
     }
 
@@ -211,6 +211,8 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
             return;
 
         final Type type = getType(eval);
+        if ( type == null )
+            return;
 
         TypeSampleMap titvTable = null;