From bb42c90f2b8b5de41ecb941597146ccf33c29c7c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 2 Apr 2013 15:31:09 -0400
Subject: [PATCH] Use LinkedHashSets in incoming and outgoing vertex functions
 in BaseGraph

-- Using a LinkedHashSet changed the md5 for HCTestComplexVariants.
---
 .../sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java  | 4 ++--
 ...lotypeCallerComplexAndSymbolicVariantsIntegrationTest.java | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
index 1d294e591..5d591fd5c 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
@@ -348,7 +348,7 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
      * @return a set of vertices connected by outgoing edges from v
      */
     public Set<T> outgoingVerticesOf(final T v) {
-        final Set<T> s = new HashSet<T>();
+        final Set<T> s = new LinkedHashSet<T>();
         for ( final BaseEdge e : outgoingEdgesOf(v) ) {
             s.add(getEdgeTarget(e));
         }
@@ -361,7 +361,7 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
      * @return a set of vertices {X} connected X -> v
      */
     public Set<T> incomingVerticesOf(final T v) {
-        final Set<T> s = new HashSet<T>();
+        final Set<T> s = new LinkedHashSet<T>();
         for ( final BaseEdge e : incomingEdgesOf(v) ) {
             s.add(getEdgeSource(e));
         }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index 9400b3dd2..4204a0634 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "a898b551f78c71befee4d12070d3a788");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "73817d9173b8d9d05dac1f3092871f33");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {