/*
* 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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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils.fragments;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;
import htsjdk.samtools.SAMFileHeader;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
import org.broadinstitute.gatk.utils.sam.ArtificialSAMUtils;
import java.util.ArrayList;
import java.util.List;
/**
* Caliper microbenchmark of fragment pileup
*/
public class FragmentUtilsBenchmark extends SimpleBenchmark {
List<ReadBackedPileup> pileups;
@Param({"0", "4", "30", "150", "1000"})
int pileupSize; // set automatically by framework
@Param({"200", "400"})
int insertSize; // set automatically by framework
@Override protected void setUp() {
final int nPileupsToGenerate = 100;
pileups = new ArrayList<ReadBackedPileup>(nPileupsToGenerate);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
GenomeLocParser genomeLocParser;
genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 50);
final int readLen = 100;
for ( int pileupN = 0; pileupN < nPileupsToGenerate; pileupN++ ) {
ReadBackedPileup rbp = ArtificialSAMUtils.createReadBackedPileup(header, loc, readLen, insertSize, pileupSize);
pileups.add(rbp);
}
}
// public void timeOriginal(int rep) {
// run(rep, FragmentUtils.FragmentMatchingAlgorithm.ORIGINAL);
// }
public void timeSkipNonOverlapping(int rep) {
int nFrags = 0;
for ( int i = 0; i < rep; i++ ) {
for ( ReadBackedPileup rbp : pileups )
nFrags += FragmentUtils.create(rbp).getOverlappingPairs().size();
}
}
public static void main(String[] args) {
com.google.caliper.Runner.main(FragmentUtilsBenchmark.class, args);
}
}