82 lines
3.4 KiB
Java
82 lines
3.4 KiB
Java
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/*
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* Copyright (c) 2012 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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import com.google.caliper.Param;
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import com.google.caliper.SimpleBenchmark;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
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import java.io.File;
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/**
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* Caliper microbenchmark of genome loc parser
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*/
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public class GenomeLocParserBenchmark extends SimpleBenchmark {
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private IndexedFastaSequenceFile seq;
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private final int ITERATIONS = 1000000;
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@Param({"NEW", "NONE"})
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GenomeLocParser.ValidationLevel validationLevel; // set automatically by framework
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@Param({"true", "false"})
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boolean useContigIndex; // set automatically by framework
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@Override protected void setUp() throws Exception {
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seq = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"));
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}
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//
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// public void timeSequentialCreationFromGenomeLoc(int rep) {
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// final GenomeLocParser genomeLocParser = new GenomeLocParser(seq.getSequenceDictionary(), validationLevel);
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// GenomeLoc last = genomeLocParser.createGenomeLoc("1", 1, 1);
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// for ( int i = 0; i < rep; i++ ) {
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// for ( int j = 1; j < ITERATIONS; j++ ) {
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// if ( useContigIndex )
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// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getContigIndex(), last.getStart() + 1);
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// else
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// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getStart() + 1);
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// }
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// }
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// }
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//
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// public void timeSequentialCreationFromGenomeLocOriginal(int rep) {
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// final GenomeLocParserOriginal genomeLocParser = new GenomeLocParserOriginal(seq.getSequenceDictionary());
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// GenomeLoc last = genomeLocParser.createGenomeLoc("1", 1, 1);
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// for ( int i = 0; i < rep; i++ ) {
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// for ( int j = 1; j < ITERATIONS; j++ ) {
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// if ( useContigIndex )
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// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getContigIndex(), last.getStart() + 1);
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// else
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// last = genomeLocParser.createGenomeLoc(last.getContig(), last.getStart() + 1);
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// }
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// }
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// }
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public static void main(String[] args) {
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com.google.caliper.Runner.main(GenomeLocParserBenchmark.class, args);
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}
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}
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