From 3a19266843788c17a2fa8d7e3bf9fb55d18f277b Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 4 Apr 2013 16:07:00 -0400 Subject: [PATCH] Fix residual merge conflicts --- .../haplotypecaller/graphs/SeqGraph.java | 6 +-- .../graphs/SharedSequenceMerger.java | 2 +- .../sting/utils/haplotype/EventMap.java | 46 +++++++++---------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java index 97969d098..8c78d8515 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java @@ -350,7 +350,7 @@ public final class SeqGraph extends BaseGraph { protected class MergeDiamonds extends VertexBasedTransformer { @Override protected boolean tryToTransform(final SeqVertex top) { - final List middles = outgoingVerticesOf(top); + final Set middles = outgoingVerticesOf(top); if ( middles.size() <= 1 ) // we can only merge if there's at least two middle nodes return false; @@ -407,7 +407,7 @@ public final class SeqGraph extends BaseGraph { protected class MergeTails extends VertexBasedTransformer { @Override protected boolean tryToTransform(final SeqVertex top) { - final List tails = outgoingVerticesOf(top); + final Set tails = outgoingVerticesOf(top); if ( tails.size() <= 1 ) return false; @@ -495,7 +495,7 @@ public final class SeqGraph extends BaseGraph { protected class MergeHeadlessIncomingSources extends VertexBasedTransformer { @Override boolean tryToTransform(final SeqVertex bottom) { - final List incoming = incomingVerticesOf(bottom); + final Set incoming = incomingVerticesOf(bottom); if ( incoming.size() <= 1 ) return false; diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java index 28734e505..1c53f2332 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java @@ -75,7 +75,7 @@ public class SharedSequenceMerger { if ( graph == null ) throw new IllegalArgumentException("graph cannot be null"); if ( ! graph.vertexSet().contains(v) ) throw new IllegalArgumentException("graph doesn't contain vertex " + v); - final List prevs = graph.incomingVerticesOf(v); + final Set prevs = graph.incomingVerticesOf(v); if ( ! canMerge(graph, v, prevs) ) return false; else { diff --git a/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java b/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java index ab5f23894..752c880b9 100644 --- a/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java +++ b/public/java/src/org/broadinstitute/sting/utils/haplotype/EventMap.java @@ -1,27 +1,27 @@ /* -* Copyright (c) 2012 The Broad Institute -* -* Permission is hereby granted, free of charge, to any person -* obtaining a copy of this software and associated documentation -* files (the "Software"), to deal in the Software without -* restriction, including without limitation the rights to use, -* copy, modify, merge, publish, distribute, sublicense, and/or sell -* copies of the Software, and to permit persons to whom the -* Software is furnished to do so, subject to the following -* conditions: -* -* The above copyright notice and this permission notice shall be -* included in all copies or substantial portions of the Software. -* -* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR -* THE USE OR OTHER DEALINGS IN THE SOFTWARE. -*/ + * Copyright (c) 2012 The Broad Institute + * + * Permission is hereby granted, free of charge, to any person + * obtaining a copy of this software and associated documentation + * files (the "Software"), to deal in the Software without + * restriction, including without limitation the rights to use, + * copy, modify, merge, publish, distribute, sublicense, and/or sell + * copies of the Software, and to permit persons to whom the + * Software is furnished to do so, subject to the following + * conditions: + * + * The above copyright notice and this permission notice shall be + * included in all copies or substantial portions of the Software. + * + * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES + * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, + * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING + * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR + * THE USE OR OTHER DEALINGS IN THE SOFTWARE. + */ package org.broadinstitute.sting.utils.haplotype;