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Merge pull request #141 from broadinstitute/md_linkedhashsets 

Use LinkedHashSets in incoming/outgoing vertex functions in BaseGraph
This commit is contained in:
Mark DePristo 2013-04-02 17:42:07 -07:00
parent 95be16dca7 bb42c90f2b
commit 09edee2c97
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
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@ -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));
}

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

@ -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) {