/*
* 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,
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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package org.broadinstitute.gatk.engine.datasources.reads;
import com.google.caliper.Param;
import org.broadinstitute.gatk.utils.commandline.Tags;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.filters.ReadFilter;
import org.broadinstitute.gatk.engine.filters.UnmappedReadFilter;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
import org.broadinstitute.gatk.engine.walkers.ReadWalker;
import org.broadinstitute.gatk.engine.walkers.Walker;
import org.broadinstitute.gatk.tools.walkers.qc.CountLoci;
import org.broadinstitute.gatk.tools.walkers.qc.CountReads;
import org.broadinstitute.gatk.utils.classloader.JVMUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.io.File;
import java.util.Collections;
/**
* Created by IntelliJ IDEA.
* User: mhanna
* Date: Feb 25, 2011
* Time: 10:16:54 AM
* To change this template use File | Settings | File Templates.
*/
public class GATKWalkerBenchmark extends ReadProcessingBenchmark {
@Param
private String bamFile;
@Param
private Integer maxReads;
@Param
private String referenceFile;
@Param
private WalkerType walkerType;
@Override
public String getBAMFile() { return bamFile; }
@Override
public Integer getMaxReads() { return maxReads; }
@Override
public void setUp() {
super.setUp();
}
public void timeWalkerPerformance(final int reps) {
for(int i = 0; i < reps; i++) {
GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
// Establish the argument collection
GATKArgumentCollection argCollection = new GATKArgumentCollection();
argCollection.referenceFile = new File(referenceFile);
argCollection.samFiles = Collections.singletonList(inputFile.getAbsolutePath());
engine.setArguments(argCollection);
// Bugs in the engine mean that this has to be set twice.
engine.setSAMFileIDs(Collections.singletonList(new SAMReaderID(inputFile,new Tags())));
engine.setFilters(Collections.<ReadFilter>singletonList(new UnmappedReadFilter()));
engine.setReferenceMetaDataFiles(Collections.<RMDTriplet>emptyList());
// Create the walker
engine.setWalker(walkerType.create());
engine.execute();
}
}
private enum WalkerType {
COUNT_READS {
@Override
Walker create() { return new CountReads(); }
},
COUNT_BASES_IN_READ {
@Override
Walker create() { return new CountBasesInReadPerformanceWalker(); }
},
COUNT_LOCI {
@Override
Walker create() {
CountLoci walker = new CountLoci();
JVMUtils.setFieldValue(JVMUtils.findField(CountLoci.class,"out"),walker,System.out);
return walker;
}
};
abstract Walker create();
}
}
class CountBasesInReadPerformanceWalker extends ReadWalker<Integer,Long> {
private long As;
private long Cs;
private long Gs;
private long Ts;
public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
for(byte base: read.getReadBases()) {
switch(base) {
case 'A': As++; break;
case 'C': Cs++; break;
case 'G': Gs++; break;
case 'T': Ts++; break;
}
}
return 1;
}
public Long reduceInit() { return 0L; }
public Long reduce(Integer value, Long accum) { return value + accum; }
}