diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index a96262c96..49c131ce2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -150,12 +150,14 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                 // case 1: current insertion is prefix of indel in hash map
                                 consensusIndelStrings.put(s, cnt + 1);
                                 foundKey = true;
+                                break;
                             } else if (indelString.startsWith(s)) {
                                 // case 2: indel stored in hash table is prefix of current insertion
                                 // In this case, new bases are new key.
                                 consensusIndelStrings.remove(s);
                                 consensusIndelStrings.put(indelString, cnt + 1);
                                 foundKey = true;
+                                break;
                             }
                         }
                         if (!foundKey)
@@ -170,6 +172,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                 // case 1: current insertion is suffix of indel in hash map
                                 consensusIndelStrings.put(s, cnt + 1);
                                 foundKey = true;
+                                break;
                             } else if (indelString.endsWith(s)) {
                                 // case 2: indel stored in hash table is suffix of current insertion
                                 // In this case, new bases are new key.
@@ -177,6 +180,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                 consensusIndelStrings.remove(s);
                                 consensusIndelStrings.put(indelString, cnt + 1);
                                 foundKey = true;
+                                break;
                             }
                         }
                         if (!foundKey)