380 lines
17 KiB
Java
380 lines
17 KiB
Java
/*
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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.variant.variantcontext;
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import com.google.caliper.Param;
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import com.google.caliper.SimpleBenchmark;
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import org.broad.tribble.Feature;
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import org.broad.tribble.FeatureCodec;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.variant.vcf.VCFCodec;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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/**
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* Caliper microbenchmark of parsing a VCF file
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*/
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public class VariantContextBenchmark extends SimpleBenchmark {
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@Param({"/Users/depristo/Desktop/broadLocal/localData/ALL.chr20.merged_beagle_mach.20101123.snps_indels_svs.genotypes.vcf"})
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String vcfFile;
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@Param({"1000"})
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int linesToRead; // set automatically by framework
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@Param({"100"})
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int nSamplesToTake; // set automatically by framework
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@Param({"10"})
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int dupsToMerge; // set automatically by framework
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@Param
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Operation operation; // set automatically by framework
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private String INPUT_STRING;
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public enum Operation {
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READ,
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SUBSET_TO_SAMPLES,
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GET_TYPE,
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GET_ID,
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GET_GENOTYPES,
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GET_ATTRIBUTE_STRING,
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GET_ATTRIBUTE_INT,
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GET_N_SAMPLES,
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GET_GENOTYPES_FOR_SAMPLES,
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GET_GENOTYPES_IN_ORDER_OF_NAME,
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CALC_GENOTYPE_COUNTS,
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MERGE
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}
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private GenomeLocParser b37GenomeLocParser;
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@Override protected void setUp() {
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// TODO -- update for new tribble interface
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// try {
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// ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.b37KGReference));
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// b37GenomeLocParser = new GenomeLocParser(seq);
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// } catch ( FileNotFoundException e) {
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// throw new RuntimeException(e);
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// }
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//
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// // read it into a String so that we don't try to benchmark IO issues
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// try {
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// FileInputStream s = new FileInputStream(new File(vcfFile));
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// AsciiLineReader lineReader = new AsciiLineReader(s);
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// int counter = 0;
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// StringBuffer sb = new StringBuffer();
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// while (counter++ < linesToRead ) {
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// String line = lineReader.readLine();
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// if ( line == null )
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// break;
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// sb.append(line + "\n");
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// }
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// s.close();
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// INPUT_STRING = sb.toString();
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// } catch (IOException e) {
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// throw new RuntimeException(e);
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// }
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}
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private interface FunctionToBenchmark<T extends Feature> {
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public void run(T vc);
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}
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private <T extends Feature> void runBenchmark(FeatureCodec<T> codec, FunctionToBenchmark<T> func) {
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// TODO -- update for new Tribble interface
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// try {
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// InputStream is = new ByteArrayInputStream(INPUT_STRING.getBytes());
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// AsciiLineReader lineReader = new AsciiLineReader(is);
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// codec.readHeader(lineReader);
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//
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// int counter = 0;
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// while (counter++ < linesToRead ) {
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// String line = lineReader.readLine();
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// if ( line == null )
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// break;
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//
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// T vc = codec.decode(line);
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// func.run(vc);
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// }
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// } catch (Exception e) {
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// System.out.println("Benchmarking run failure because of " + e.getMessage());
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// }
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}
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public void timeV14(int rep) {
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for ( int i = 0; i < rep; i++ ) {
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FunctionToBenchmark<VariantContext> func = getV14FunctionToBenchmark();
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FeatureCodec<VariantContext> codec = new VCFCodec();
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runBenchmark(codec, func);
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}
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}
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public FunctionToBenchmark<VariantContext> getV14FunctionToBenchmark() {
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switch ( operation ) {
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case READ:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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; // empty operation
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}
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};
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case SUBSET_TO_SAMPLES:
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return new FunctionToBenchmark<VariantContext>() {
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Set<String> samples;
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public void run(final VariantContext vc) {
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if ( samples == null )
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samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
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VariantContext sub = vc.subContextFromSamples(samples);
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sub.getNSamples();
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}
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};
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case GET_TYPE:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getType();
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}
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};
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case GET_ID:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getID();
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}
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};
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case GET_GENOTYPES:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getGenotypes().size();
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}
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};
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case GET_GENOTYPES_FOR_SAMPLES:
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return new FunctionToBenchmark<VariantContext>() {
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Set<String> samples;
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public void run(final VariantContext vc) {
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if ( samples == null )
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samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
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vc.getGenotypes(samples).size();
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}
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};
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case GET_ATTRIBUTE_STRING:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getAttribute("AN", null);
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}
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};
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case GET_ATTRIBUTE_INT:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getAttributeAsInt("AC", 0);
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}
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};
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case GET_N_SAMPLES:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getNSamples();
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}
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};
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case GET_GENOTYPES_IN_ORDER_OF_NAME:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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; // TODO - TEST IS BROKEN
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// int n = 0;
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// for ( final Genotype g: vc.getGenotypesOrderedByName() ) n++;
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}
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};
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case CALC_GENOTYPE_COUNTS:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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vc.getHetCount();
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}
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};
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case MERGE:
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return new FunctionToBenchmark<VariantContext>() {
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public void run(final VariantContext vc) {
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List<VariantContext> toMerge = new ArrayList<VariantContext>();
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for ( int i = 0; i < dupsToMerge; i++ ) {
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GenotypesContext gc = GenotypesContext.create(vc.getNSamples());
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for ( final Genotype g : vc.getGenotypes() ) {
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gc.add(new GenotypeBuilder(g).name(g.getSampleName()+"_"+i).make());
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}
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toMerge.add(new VariantContextBuilder(vc).genotypes(gc).make());
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}
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VariantContextUtils.simpleMerge(toMerge, null,
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VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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VariantContextUtils.GenotypeMergeType.UNSORTED,
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true, false, "set", false, true);
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}
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};
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default: throw new IllegalArgumentException("Unexpected operation " + operation);
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}
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}
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// --------------------------------------------------------------------------------
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//
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// V13
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//
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// In order to use this, you must move the v13 version from archive and uncomment
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//
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// git mv private/archive/java/src/org/broadinstitute/sting/utils/variantcontext/v13 public/java/test/org/broadinstitute/sting/utils/variantcontext/v13
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//
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// --------------------------------------------------------------------------------
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// public void timeV13(int rep) {
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// for ( int i = 0; i < rep; i++ ) {
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// FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> func = getV13FunctionToBenchmark();
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// FeatureCodec<org.broadinstitute.variant.variantcontext.v13.VariantContext> codec = new org.broadinstitute.variant.variantcontext.v13.VCFCodec();
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// runBenchmark(codec, func);
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// }
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// }
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//
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// public FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> getV13FunctionToBenchmark() {
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// switch ( operation ) {
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// case READ:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// ; // empty operation
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// }
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// };
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// case SUBSET_TO_SAMPLES:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// List<String> samples;
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// if ( samples == null )
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// samples = new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake);
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// org.broadinstitute.variant.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values());
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// sub.getNSamples();
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// }
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// };
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//
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// case GET_TYPE:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getType();
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// }
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// };
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// case GET_ID:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getID();
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// }
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// };
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// case GET_GENOTYPES:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getGenotypes().size();
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// }
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// };
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//
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// case GET_GENOTYPES_FOR_SAMPLES:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// Set<String> samples;
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// if ( samples == null )
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// samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
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// vc.getGenotypes(samples).size();
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// }
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// };
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//
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// case GET_ATTRIBUTE_STRING:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getExtendedAttribute("AN", null);
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// }
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// };
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//
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// case GET_ATTRIBUTE_INT:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getAttributeAsInt("AC", 0);
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// }
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// };
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//
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// case GET_N_SAMPLES:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getNSamples();
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// }
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// };
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//
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// case GET_GENOTYPES_IN_ORDER_OF_NAME:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// ; // TODO - TEST IS BROKEN
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// //vc.getGenotypesOrderedByName();
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// }
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// };
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//
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// case CALC_GENOTYPE_COUNTS:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// vc.getHetCount();
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// }
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// };
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//
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// case MERGE:
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// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
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// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
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// List<org.broadinstitute.variant.variantcontext.v13.VariantContext> toMerge = new ArrayList<org.broadinstitute.variant.variantcontext.v13.VariantContext>();
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//
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// for ( int i = 0; i < dupsToMerge; i++ ) {
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// Map<String, org.broadinstitute.variant.variantcontext.v13.Genotype> gc = new HashMap<String, org.broadinstitute.variant.variantcontext.v13.Genotype>();
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// for ( final org.broadinstitute.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) {
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// String name = g.getSampleName()+"_"+i;
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// gc.put(name, new org.broadinstitute.variant.variantcontext.v13.Genotype(name,
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// g.getAlleles(), g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased(), g.getLikelihoods().getAsVector()));
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// toMerge.add(org.broadinstitute.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc));
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// }
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// }
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//
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// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser,
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// toMerge, null,
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// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
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// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED,
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// true, false, "set", false, true);
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// }
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// };
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//
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// default: throw new IllegalArgumentException("Unexpected operation " + operation);
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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(VariantContextBenchmark.class, args);
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}
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}
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