From cd9bf1bfc35a9cf18aa4c9b4e521bc09f8c22dd2 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Tue, 10 Apr 2012 00:22:40 -0400
Subject: [PATCH] Changing IndelSummary eval module so that PostCallingQC.scala
 can run with MIXED-record VCFs.

---
 .../gatk/walkers/varianteval/evaluators/IndelSummary.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
index 786b7296b..c22f82969 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
@@ -207,7 +207,9 @@ public class IndelSummary extends VariantEvaluator implements StandardEval {
 
                 break;
             default:
-                throw new UserException.BadInput("Unexpected variant context type: " + eval);
+                // TODO - MIXED, SYMBOLIC, and MNP records are skipped over
+                //throw new UserException.BadInput("Unexpected variant context type: " + eval);
+                break;
         }
 
         return;