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Use LinkedHashSets in incoming and outgoing vertex functions in BaseGraph 

-- Using a LinkedHashSet changed the md5 for HCTestComplexVariants.
This commit is contained in:
Mark DePristo 2013-04-02 15:31:09 -04:00
parent e7a8e6e8ee
commit bb42c90f2b
2 changed files with 3 additions and 3 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
View File

@ -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 * @return a set of vertices connected by outgoing edges from v
*/ */
public Set<T> outgoingVerticesOf(final T 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) ) { for ( final BaseEdge e : outgoingEdgesOf(v) ) {
s.add(getEdgeTarget(e)); 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 * @return a set of vertices {X} connected X -> v
*/ */
public Set<T> incomingVerticesOf(final T 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) ) { for ( final BaseEdge e : incomingEdgesOf(v) ) {
s.add(getEdgeSource(e)); s.add(getEdgeSource(e));
} }

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test @Test
public void testHaplotypeCallerMultiSampleComplex() { 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) { private void HCTestSymbolicVariants(String bam, String args, String md5) {