From bfa966a4e94f440f5eeb5bb338c09dd04198bafb Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 9 Apr 2012 15:50:20 -0400
Subject: [PATCH] Bugfix for OneBPIndel

-- Previously was only including 1 bp insertions in stratification
---
 .../gatk/walkers/varianteval/stratifications/OneBPIndel.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
index fe4f7641f..65633bc2b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
@@ -50,7 +50,7 @@ public class OneBPIndel extends VariantStratifier {
     public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         if (eval != null && eval.isIndel()) {
             for ( int l : eval.getIndelLengths() )
-                if ( l > 1 )
+                if ( Math.abs(l) > 1 )
                     return TWO_PLUS_BP; // someone is too long
             return ONE_BP; // all lengths are one
         } else