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Fix final merge conflicts

This commit is contained in:
Mark DePristo 2013-01-10 20:48:55 -05:00
parent b9a33d3c66
commit 6a91902aa2
2 changed files with 26 additions and 27 deletions
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27
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsOriginal.java
View File

@ -1,3 +1,28 @@
/*
* 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.gatk.traversals; package org.broadinstitute.sting.gatk.traversals;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
@ -232,6 +257,6 @@ public class TraverseActiveRegionsOriginal<M,T> extends TraverseActiveRegions<M,
* Ugly for now but will be cleaned up when we push this functionality more into the engine * Ugly for now but will be cleaned up when we push this functionality more into the engine
*/ */
public T endTraversal( final Walker<M,T> walker, T sum) { public T endTraversal( final Walker<M,T> walker, T sum) {
return processActiveRegions((ActiveRegionWalker<M,T>)walker, sum, Integer.MAX_VALUE, null); return processActiveRegions((ActiveRegionWalker<M, T>) walker, sum, Integer.MAX_VALUE, null);
} }
} }

26
public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIteratorByState.java
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@ -1,5 +1,4 @@
/* /*
<<<<<<< HEAD
* 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
@ -23,31 +22,6 @@
* 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.
*/ */
=======
* 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.
*/
>>>>>>> Create LIBS using new AlignmentStateMachine infrastructure
package org.broadinstitute.sting.utils.locusiterator; package org.broadinstitute.sting.utils.locusiterator;