From 6bf18899dffa4a601d5a5810a783b390fbab0733 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 7 Dec 2011 09:02:49 -0500
Subject: [PATCH] Fix for variant summary -- now treats all 50 bp deletions or
 insertions as CNVs

---
 .../gatk/walkers/varianteval/evaluators/VariantSummary.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 b74af9f91..1e33ccc21 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
@@ -184,7 +184,7 @@ public class VariantSummary extends VariantEvaluator implements StandardEval {
                 return Type.SNP;
             case INDEL:
                 for ( int l : vc.getIndelLengths() )
-                    if ( l > MAX_INDEL_LENGTH )
+                    if ( Math.abs(l) > MAX_INDEL_LENGTH )
                         return Type.CNV;
                 return Type.INDEL;
             case SYMBOLIC: