117 lines
4.7 KiB
Java
Executable File
117 lines
4.7 KiB
Java
Executable File
package org.broadinstitute.sting.gatk.traversals;
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import net.sf.samtools.SAMRecord;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.WalkerManager;
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import org.broadinstitute.sting.gatk.datasources.providers.*;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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/*
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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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/**
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* @author aaron
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* @version 1.0
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* @date Apr 24, 2009
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* <p/>
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* Class TraverseReads
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* <p/>
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* This class handles traversing by reads in the new shardable style
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*/
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public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,ReadShardDataProvider> {
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/** our log, which we want to capture anything from this class */
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protected static Logger logger = Logger.getLogger(TraverseReads.class);
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/** descriptor of the type */
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private static final String READS_STRING = "reads";
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/**
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* Traverse by reads, given the data and the walker
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*
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* @param walker the walker to traverse with
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* @param dataProvider the provider of the reads data
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* @param sum the value of type T, specified by the walker, to feed to the walkers reduce function
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* @return the reduce variable of the read walker
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*/
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public T traverse(ReadWalker<M,T> walker,
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ReadShardDataProvider dataProvider,
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T sum) {
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logger.debug(String.format("TraverseReads.traverse Covered dataset is %s", dataProvider));
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if( !dataProvider.hasReads() )
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throw new IllegalArgumentException("Unable to traverse reads; no read data is available.");
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boolean needsReferenceBasesP = WalkerManager.isRequired(walker, DataSource.REFERENCE_BASES);
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ReadView reads = new ReadView(dataProvider);
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ReadReferenceView reference = new ReadReferenceView(dataProvider);
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// get the reference ordered data
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ReadBasedReferenceOrderedView rodView = new ReadBasedReferenceOrderedView(dataProvider);
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// while we still have more reads
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for (SAMRecord read : reads) {
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// an array of characters that represent the reference
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char[] refSeq = null;
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// get the array of characters for the reference sequence, since we're a mapped read
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if (needsReferenceBasesP && !read.getReadUnmappedFlag() && dataProvider.hasReference())
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refSeq = reference.getReferenceBases(read);
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// update the number of reads we've seen
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TraversalStatistics.nRecords++;
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TraversalStatistics.nReads++;
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// if the read is mapped, create a metadata tracker
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ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;
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final boolean keepMeP = walker.filter(refSeq, read);
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if (keepMeP) {
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M x = walker.map(refSeq, read, tracker); // the tracker can be null
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sum = walker.reduce(x, sum);
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}
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printProgress(READS_STRING,
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(read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) ?
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null :
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GenomeLocParser.createGenomeLoc(read.getReferenceIndex(),read.getAlignmentStart()));
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}
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return sum;
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}
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/**
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* Temporary override of printOnTraversalDone.
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* TODO: Add some sort of TE.getName() function once all TraversalEngines are ported.
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* @param sum Result of the computation.
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*/
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public void printOnTraversalDone( T sum ) {
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printOnTraversalDone(READS_STRING, sum );
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}
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}
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