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Fix residual merge conflicts

This commit is contained in:
Mark DePristo 2013-04-04 16:07:00 -04:00
parent 9c7a35f73f
commit 3a19266843
3 changed files with 27 additions and 27 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
View File

@ -350,7 +350,7 @@ public final class SeqGraph extends BaseGraph<SeqVertex> {
protected class MergeDiamonds extends VertexBasedTransformer { protected class MergeDiamonds extends VertexBasedTransformer {
@Override @Override
protected boolean tryToTransform(final SeqVertex top) { protected boolean tryToTransform(final SeqVertex top) {
final List<SeqVertex> middles = outgoingVerticesOf(top); final Set<SeqVertex> middles = outgoingVerticesOf(top);
if ( middles.size() <= 1 ) if ( middles.size() <= 1 )
// we can only merge if there's at least two middle nodes // we can only merge if there's at least two middle nodes
return false; return false;
@ -407,7 +407,7 @@ public final class SeqGraph extends BaseGraph<SeqVertex> {
protected class MergeTails extends VertexBasedTransformer { protected class MergeTails extends VertexBasedTransformer {
@Override @Override
protected boolean tryToTransform(final SeqVertex top) { protected boolean tryToTransform(final SeqVertex top) {
final List<SeqVertex> tails = outgoingVerticesOf(top); final Set<SeqVertex> tails = outgoingVerticesOf(top);
if ( tails.size() <= 1 ) if ( tails.size() <= 1 )
return false; return false;
@ -495,7 +495,7 @@ public final class SeqGraph extends BaseGraph<SeqVertex> {
protected class MergeHeadlessIncomingSources extends VertexBasedTransformer { protected class MergeHeadlessIncomingSources extends VertexBasedTransformer {
@Override @Override
boolean tryToTransform(final SeqVertex bottom) { boolean tryToTransform(final SeqVertex bottom) {
final List<SeqVertex> incoming = incomingVerticesOf(bottom); final Set<SeqVertex> incoming = incomingVerticesOf(bottom);
if ( incoming.size() <= 1 ) if ( incoming.size() <= 1 )
return false; return false;

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
View File

@ -75,7 +75,7 @@ public class SharedSequenceMerger {
if ( graph == null ) throw new IllegalArgumentException("graph cannot be null"); if ( graph == null ) throw new IllegalArgumentException("graph cannot be null");
if ( ! graph.vertexSet().contains(v) ) throw new IllegalArgumentException("graph doesn't contain vertex " + v); if ( ! graph.vertexSet().contains(v) ) throw new IllegalArgumentException("graph doesn't contain vertex " + v);
final List<SeqVertex> prevs = graph.incomingVerticesOf(v); final Set<SeqVertex> prevs = graph.incomingVerticesOf(v);
if ( ! canMerge(graph, v, prevs) ) if ( ! canMerge(graph, v, prevs) )
return false; return false;
else { else {