From f2ef8d1d2342cd4b6d80283587d6db7931d146ec Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Fri, 17 Feb 2012 17:15:53 -0500
Subject: [PATCH] Reverting last commit until I learn how to effectively
 replicate and debug pipeline test failures, and until I also learn how to
 effectively remove a kep from a HashMap that's being iterated on

---
 .../IndelGenotypeLikelihoodsCalculationModel.java    | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

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 6321ef1f6..fe2086d47 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
@@ -152,13 +152,15 @@ 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)
@@ -174,7 +176,8 @@ 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.
@@ -182,6 +185,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                                 consensusIndelStrings.remove(s);
                                 consensusIndelStrings.put(indelString,cnt+1);
                                 foundKey = true;
+                                break;
                             }
                         }
                         if (!foundKey)
@@ -229,7 +233,9 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                 maxAlleleCnt = curCnt;
                 bestAltAllele = s;
             }
-        }
+//            if (DEBUG)
+//                System.out.format("Key:%s, number: %d\n",s,consensusIndelStrings.get(s)  );
+        }         //gdebug-
 
         if (maxAlleleCnt <  minIndelCountForGenotyping)
             return aList;