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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 {

46
public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java
View File

@ -1,27 +1,27 @@
/* /*
* Copyright (c) 2012 The Broad Institute * Copyright (c) 2012 The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without * files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use, * restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell * copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the * copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following * Software is furnished to do so, subject to the following
* conditions: * conditions:
* *
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * included in all copies or substantial portions of the Software.
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.utils.haplotype; package org.broadinstitute.sting.utils.haplotype;