From 6e517df5d94141d3badc45f0ec0b7e65828fc158 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@broadinstitute.org>
Date: Wed, 5 Sep 2012 14:33:08 -0400
Subject: [PATCH] fixed a typo in StringText.properties

---
 .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 845fc68a6..5009698e1 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -380,7 +380,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
             allelesToGenotype.removeAll( activeAllelesToGenotype );
         }
 
-        if( !activeRegion.isActive ) { return 0; } // Not active so nothing to do!
+        if( !activeRegion.isActive ) { return 0; } // Not active so nothing to do TODO : YOSSI Write something smart!!
         if( activeRegion.size() == 0 && UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { return 0; } // No reads here so nothing to do!
         if( UG_engine.getUAC().GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES && activeAllelesToGenotype.isEmpty() ) { return 0; } // No alleles found in this region so nothing to do!