82 lines
2.9 KiB
Java
Executable File
82 lines
2.9 KiB
Java
Executable File
/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import java.util.Iterator;
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/**
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* Prints out all of the RODs in the input data set. Data is rendered using the toString() method
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* of the given ROD.
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*/
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public class PrintRODsWalker extends RodWalker<Integer, Integer> {
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/**
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* Initialize the number of loci processed to zero.
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*
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* @return 0
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*/
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public Integer reduceInit() { return 0; }
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/**
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return 1 if the locus was successfully processed, 0 if otherwise
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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Iterator<GATKFeature> rods = tracker.getAllRods().iterator();
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while ( rods.hasNext() ) {
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Object rod = rods.next().getUnderlyingObject();
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if (VariantContextAdaptors.canBeConvertedToVariantContext(rod) )
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out.println(rod.toString());
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}
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return 1;
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}
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/**
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* Increment the number of rods processed.
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*
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* @param value result of the map.
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* @param sum accumulator for the reduce.
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* @return the new number of rods processed.
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*/
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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public void onTraversalDone(Integer result) {}
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} |