Ported small BAM performance test suite to the Google Caliper microbenchmarking suite. Looks promising,
but I'm still not sure that GC is a good long-term solution. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5683 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
00b57c751b
commit
57a4700299
5
ivy.xml
5
ivy.xml
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@ -46,7 +46,7 @@
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<!-- Dependencies for LSF library -->
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<!-- Dependencies for LSF library -->
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<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
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<dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
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<!-- Dependencies for LSF library -->
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<!-- Dependencies for amazon.com S3 support -->
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<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
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<dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.0"/>
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<!-- Scala dependancies -->
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<!-- Scala dependancies -->
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@ -60,6 +60,9 @@
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<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="default"/>
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<dependency org="net.sourceforge.findbugs" name="annotations" rev="1.3.2" conf="default"/>
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<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="default"/>
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<dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="default"/>
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<!-- caliper, for benchmarking -->
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<dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="default" />
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<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
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<!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
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<exclude org="javax.servlet" />
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<exclude org="javax.servlet" />
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<exclude org="javax.jms" />
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<exclude org="javax.jms" />
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@ -1,143 +0,0 @@
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/*
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* Copyright (c) 2011, 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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* 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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package org.broadinstitute.sting.gatk.datasources.reads.performance;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.CommandLineProgram;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.gatk.DownsamplingMethod;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.utils.SimpleTimer;
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import java.io.File;
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/**
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* Basic suite for testing idealized and actual performance of read processing.
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*/
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public class BAMProcessingPerformanceMeter extends CommandLineProgram {
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@Input(fullName = "input_file", shortName = "I", doc = "SAM or BAM file(s)", required = true)
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File samFile;
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@Input(fullName = "reference_file", shortName="R", doc = "Associated FASTA sequence", required = true)
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File referenceFile;
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@Argument(fullName="test_repetitions", shortName = "test_reps", doc="Number of times to repeat each test", required = false)
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int testRepetitions = 5;
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@Argument(fullName="print_frequency", shortName = "pf", doc="Print cumulative time after x # reads", required = false)
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int printFrequency = 100000;
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private void testBAMFileProcessingThroughput(ReadProcessor readProcessor) {
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readProcessor.execute(samFile,referenceFile);
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}
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public int execute() {
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new NoAdditionalProcessing(this));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new IterateOverEachBase(this));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new IterateOverCigarString(this));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new ExtractTag(this,"OQ"));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new InvokeSamLocusIterator(this));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new InvokeLocusIteratorByState(this, GATKArgumentCollection.getDefaultDownsamplingMethod()));
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(new InvokeLocusIteratorByState(this, DownsamplingMethod.NONE));
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GATKWalkerInvoker countReadsInvoker = new GATKWalkerInvoker(this);
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CountReadsPerformanceWalker countReadsWalker = new CountReadsPerformanceWalker(countReadsInvoker);
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countReadsInvoker.setWalker(countReadsWalker);
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(countReadsInvoker);
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GATKWalkerInvoker countBasesInReadInvoker = new GATKWalkerInvoker(this);
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CountBasesInReadPerformanceWalker countBasesInReadWalker = new CountBasesInReadPerformanceWalker(countBasesInReadInvoker);
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countBasesInReadInvoker.setWalker(countBasesInReadWalker);
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for(int i = 0; i < testRepetitions; i++) testBAMFileProcessingThroughput(countBasesInReadInvoker);
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return 0;
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}
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/**
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* Required main method implementation.
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* @param argv Command-line argument text.
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* @throws Exception on error.
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*/
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public static void main(String[] argv) throws Exception {
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int returnCode = 0;
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try {
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BAMProcessingPerformanceMeter instance = new BAMProcessingPerformanceMeter();
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start(instance, argv);
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returnCode = 0;
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}
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catch(Exception ex) {
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returnCode = 1;
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ex.printStackTrace();
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throw ex;
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}
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finally {
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System.exit(returnCode);
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}
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}
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}
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abstract class ReadProcessor {
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private final SimpleTimer timer;
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private final int printFrequency;
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protected int iterations = 0;
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public ReadProcessor(BAMProcessingPerformanceMeter performanceMeter) {
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timer = new SimpleTimer("timer");
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this.printFrequency = performanceMeter.printFrequency;
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}
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public abstract String getTestName();
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public String getIterationType() { return "loci"; }
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public void processRead(final SAMRecord read) { }
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public void execute(File bamFile,File fastaFile) {
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SAMFileReader reader = new SAMFileReader(bamFile);
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startTest();
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for(SAMRecord read: reader) {
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processRead(read);
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updateIterationCount();
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}
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stopTest();
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reader.close();
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}
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protected void startTest() {
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timer.start();
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}
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protected void stopTest() {
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timer.stop();
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printStatus("TEST COMPLETE");
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}
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protected void updateIterationCount() {
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if(++iterations % printFrequency == 0) printStatus("ONGOING");
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}
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private void printStatus(String prefix) {
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System.out.printf("%s: %s printed %d %s in %f seconds.%n",prefix,getTestName(),iterations,getIterationType(),timer.getElapsedTime());
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}
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}
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@ -1,67 +0,0 @@
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/*
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* Copyright (c) 2011, 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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* 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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package org.broadinstitute.sting.gatk.datasources.reads.performance;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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/**
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* Created by IntelliJ IDEA.
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* User: mhanna
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* Date: Feb 25, 2011
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* Time: 10:16:55 AM
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* To change this template use File | Settings | File Templates.
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*/
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class CountBasesInReadPerformanceWalker extends ReadWalker<Integer,Long> {
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private long As;
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private long Cs;
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private long Gs;
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private long Ts;
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private final GATKWalkerInvoker invoker;
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public CountBasesInReadPerformanceWalker(GATKWalkerInvoker walkerInvoker) {
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this.invoker = walkerInvoker;
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}
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
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for(byte base: read.getReadBases()) {
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switch(base) {
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case 'A': As++; break;
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case 'C': Cs++; break;
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case 'G': Gs++; break;
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case 'T': Ts++; break;
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}
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}
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invoker.updateIterationCount();
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return 1;
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}
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public Long reduceInit() { return 0L; }
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public Long reduce(Integer value, Long accum) { return value + accum; }
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}
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@ -1,54 +0,0 @@
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/*
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* Copyright (c) 2011, 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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*
|
|
||||||
* 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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||||||
* 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
|
|
||||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
|
||||||
* 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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package org.broadinstitute.sting.gatk.datasources.reads.performance;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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/**
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* Created by IntelliJ IDEA.
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* User: mhanna
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* Date: Feb 25, 2011
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* Time: 10:16:55 AM
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* To change this template use File | Settings | File Templates.
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*/
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class CountReadsPerformanceWalker extends ReadWalker<Integer,Long> {
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private final GATKWalkerInvoker invoker;
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public CountReadsPerformanceWalker(GATKWalkerInvoker walkerInvoker) {
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this.invoker = walkerInvoker;
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}
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker tracker) {
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invoker.updateIterationCount();
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return 1;
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}
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public Long reduceInit() { return 0L; }
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public Long reduce(Integer value, Long accum) { return value + accum; }
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}
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@ -0,0 +1,114 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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||||||
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* 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
|
||||||
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* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
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||||||
|
* 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,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
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*/
|
||||||
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|
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package org.broadinstitute.sting.gatk.datasources.reads.performance;
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import com.google.caliper.Param;
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import net.sf.picard.filter.FilteringIterator;
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import net.sf.picard.filter.SamRecordFilter;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.commandline.Tags;
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import org.broadinstitute.sting.gatk.DownsamplingMethod;
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import org.broadinstitute.sting.gatk.ReadProperties;
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import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
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import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
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import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
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import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
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import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
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import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.baq.BAQ;
|
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import java.io.File;
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import java.util.Collections;
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import java.util.Iterator;
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||||||
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|
||||||
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/**
|
||||||
|
* Created by IntelliJ IDEA.
|
||||||
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* User: mhanna
|
||||||
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* Date: Apr 22, 2011
|
||||||
|
* Time: 4:02:56 PM
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||||||
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* To change this template use File | Settings | File Templates.
|
||||||
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*/
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public class DownsamplerBenchmark extends ReadProcessingBenchmark {
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@Param
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private String bamFile;
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@Param
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private Integer maxReads;
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@Override
|
||||||
|
public String getBAMFile() { return bamFile; }
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Integer getMaxReads() { return maxReads; }
|
||||||
|
|
||||||
|
@Param
|
||||||
|
private Downsampling downsampling;
|
||||||
|
|
||||||
|
public void timeDownsampling(int reps) {
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
ReadProperties readProperties = new ReadProperties(Collections.<SAMReaderID>singletonList(new SAMReaderID(inputFile,new Tags())),
|
||||||
|
reader.getFileHeader(),
|
||||||
|
false,
|
||||||
|
SAMFileReader.ValidationStringency.SILENT,
|
||||||
|
0,
|
||||||
|
downsampling.create(),
|
||||||
|
new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
|
||||||
|
Collections.<SamRecordFilter>emptyList(),
|
||||||
|
false,
|
||||||
|
false,
|
||||||
|
BAQ.CalculationMode.OFF,
|
||||||
|
BAQ.QualityMode.DONT_MODIFY,
|
||||||
|
null,
|
||||||
|
(byte)0);
|
||||||
|
|
||||||
|
GenomeLocParser genomeLocParser = new GenomeLocParser(reader.getFileHeader().getSequenceDictionary());
|
||||||
|
SampleDataSource sampleDataSource = new SampleDataSource();
|
||||||
|
sampleDataSource.addSamplesFromSAMHeader(reader.getFileHeader());
|
||||||
|
|
||||||
|
// Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out?
|
||||||
|
Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
|
||||||
|
LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource);
|
||||||
|
while(locusIteratorByState.hasNext()) {
|
||||||
|
locusIteratorByState.next().getLocation();
|
||||||
|
}
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private enum Downsampling {
|
||||||
|
NONE {
|
||||||
|
@Override
|
||||||
|
DownsamplingMethod create() { return DownsamplingMethod.NONE; }
|
||||||
|
},
|
||||||
|
PER_SAMPLE {
|
||||||
|
@Override
|
||||||
|
DownsamplingMethod create() { return GATKArgumentCollection.getDefaultDownsamplingMethod(); }
|
||||||
|
};
|
||||||
|
abstract DownsamplingMethod create();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -1,49 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Created by IntelliJ IDEA.
|
|
||||||
* User: mhanna
|
|
||||||
* Date: Feb 25, 2011
|
|
||||||
* Time: 10:16:53 AM
|
|
||||||
* To change this template use File | Settings | File Templates.
|
|
||||||
*/
|
|
||||||
class ExtractTag extends ReadProcessor {
|
|
||||||
private final String tag;
|
|
||||||
|
|
||||||
public ExtractTag(final BAMProcessingPerformanceMeter performanceMeter, final String tag) {
|
|
||||||
super(performanceMeter);
|
|
||||||
this.tag = tag;
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() { return "extract tag"; }
|
|
||||||
public void processRead(final SAMRecord read) {
|
|
||||||
read.getAttribute(tag);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,142 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2011, 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,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
||||||
|
|
||||||
|
import com.google.caliper.Param;
|
||||||
|
import net.sf.picard.filter.SamRecordFilter;
|
||||||
|
import net.sf.samtools.SAMRecord;
|
||||||
|
import org.broadinstitute.sting.commandline.Tags;
|
||||||
|
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||||
|
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
||||||
|
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||||
|
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
||||||
|
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
|
||||||
|
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
|
||||||
|
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
|
||||||
|
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
|
||||||
|
import org.broadinstitute.sting.gatk.walkers.Walker;
|
||||||
|
import org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker;
|
||||||
|
import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker;
|
||||||
|
import org.broadinstitute.sting.utils.classloader.JVMUtils;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.lang.reflect.Field;
|
||||||
|
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.<SamRecordFilter>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 CountReadsWalker(); }
|
||||||
|
},
|
||||||
|
COUNT_BASES_IN_READ {
|
||||||
|
@Override
|
||||||
|
Walker create() { return new CountBasesInReadPerformanceWalker(); }
|
||||||
|
},
|
||||||
|
COUNT_LOCI {
|
||||||
|
@Override
|
||||||
|
Walker create() {
|
||||||
|
CountLociWalker walker = new CountLociWalker();
|
||||||
|
JVMUtils.setFieldValue(JVMUtils.findField(CountLociWalker.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, SAMRecord read, ReadMetaDataTracker 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; }
|
||||||
|
}
|
||||||
|
|
@ -1,85 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.picard.filter.SamRecordFilter;
|
|
||||||
import org.broadinstitute.sting.commandline.Tags;
|
|
||||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
|
||||||
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
|
||||||
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
|
||||||
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
|
|
||||||
import org.broadinstitute.sting.gatk.walkers.Walker;
|
|
||||||
|
|
||||||
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.
|
|
||||||
*/
|
|
||||||
class GATKWalkerInvoker extends ReadProcessor {
|
|
||||||
/**
|
|
||||||
* Walker to run over the existing dataset.
|
|
||||||
*/
|
|
||||||
private Walker<?,?> walker;
|
|
||||||
|
|
||||||
public GATKWalkerInvoker(BAMProcessingPerformanceMeter performanceMeter) {
|
|
||||||
super(performanceMeter);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() { return "GATK-CountReads"; }
|
|
||||||
|
|
||||||
public void setWalker(Walker<?,?> walker) {
|
|
||||||
this.walker = walker;
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void execute(File samFile, File fastaFile) {
|
|
||||||
GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
|
|
||||||
|
|
||||||
// Establish the argument collection
|
|
||||||
GATKArgumentCollection argCollection = new GATKArgumentCollection();
|
|
||||||
argCollection.referenceFile = fastaFile;
|
|
||||||
argCollection.samFiles = Collections.singletonList(samFile.getAbsolutePath());
|
|
||||||
|
|
||||||
engine.setArguments(argCollection);
|
|
||||||
// Bugs in the engine mean that this has to be set twice.
|
|
||||||
engine.setSAMFileIDs(Collections.singletonList(new SAMReaderID(samFile,new Tags())));
|
|
||||||
engine.setFilters(Collections.<SamRecordFilter>emptyList());
|
|
||||||
engine.setReferenceMetaDataFiles(Collections.<RMDTriplet>emptyList());
|
|
||||||
|
|
||||||
// Create the walker
|
|
||||||
engine.setWalker(walker);
|
|
||||||
|
|
||||||
startTest();
|
|
||||||
engine.execute();
|
|
||||||
stopTest();
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,106 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.picard.filter.FilteringIterator;
|
|
||||||
import net.sf.picard.filter.SamRecordFilter;
|
|
||||||
import net.sf.samtools.SAMFileReader;
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
import org.broadinstitute.sting.commandline.Tags;
|
|
||||||
import org.broadinstitute.sting.gatk.DownsamplingMethod;
|
|
||||||
import org.broadinstitute.sting.gatk.ReadProperties;
|
|
||||||
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
|
|
||||||
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
|
|
||||||
import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource;
|
|
||||||
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
|
|
||||||
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
|
|
||||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
|
||||||
import org.broadinstitute.sting.utils.baq.BAQ;
|
|
||||||
|
|
||||||
import java.io.File;
|
|
||||||
import java.util.Collections;
|
|
||||||
import java.util.Iterator;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Created by IntelliJ IDEA.
|
|
||||||
* User: mhanna
|
|
||||||
* Date: Feb 25, 2011
|
|
||||||
* Time: 10:16:54 AM
|
|
||||||
* To change this template use File | Settings | File Templates.
|
|
||||||
*/
|
|
||||||
class InvokeLocusIteratorByState extends ReadProcessor {
|
|
||||||
private final DownsamplingMethod downsamplingMethod;
|
|
||||||
|
|
||||||
public InvokeLocusIteratorByState(final BAMProcessingPerformanceMeter performanceMeter,DownsamplingMethod downsamplingMethod) {
|
|
||||||
super(performanceMeter);
|
|
||||||
this.downsamplingMethod = downsamplingMethod;
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() {
|
|
||||||
if(downsamplingMethod != DownsamplingMethod.NONE)
|
|
||||||
return String.format("invoke locus iterator by state; downsampling by sample to coverage = %d; ",downsamplingMethod.toCoverage);
|
|
||||||
else
|
|
||||||
return String.format("invoke locus iterator by state; no downsampling; ");
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getIterationType() { return "loci"; }
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void execute(File samFile, File fastaFile) {
|
|
||||||
SAMFileReader reader = new SAMFileReader(samFile);
|
|
||||||
ReadProperties readProperties = new ReadProperties(Collections.<SAMReaderID>singletonList(new SAMReaderID(samFile,new Tags())),
|
|
||||||
reader.getFileHeader(),
|
|
||||||
false,
|
|
||||||
SAMFileReader.ValidationStringency.SILENT,
|
|
||||||
0,
|
|
||||||
downsamplingMethod,
|
|
||||||
new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
|
|
||||||
Collections.<SamRecordFilter>emptyList(),
|
|
||||||
false,
|
|
||||||
false,
|
|
||||||
BAQ.CalculationMode.OFF,
|
|
||||||
BAQ.QualityMode.DONT_MODIFY,
|
|
||||||
null,
|
|
||||||
(byte)0);
|
|
||||||
|
|
||||||
GenomeLocParser genomeLocParser = new GenomeLocParser(reader.getFileHeader().getSequenceDictionary());
|
|
||||||
SampleDataSource sampleDataSource = new SampleDataSource();
|
|
||||||
sampleDataSource.addSamplesFromSAMHeader(reader.getFileHeader());
|
|
||||||
|
|
||||||
// Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out?
|
|
||||||
Iterator<SAMRecord> readIterator = new FilteringIterator(reader.iterator(),new UnmappedReadFilter());
|
|
||||||
LocusIteratorByState locusIteratorByState = new LocusIteratorByState(readIterator,readProperties,genomeLocParser,sampleDataSource);
|
|
||||||
startTest();
|
|
||||||
while(locusIteratorByState.hasNext()) {
|
|
||||||
locusIteratorByState.next();
|
|
||||||
updateIterationCount();
|
|
||||||
}
|
|
||||||
stopTest();
|
|
||||||
|
|
||||||
reader.close();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,65 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.samtools.Cigar;
|
|
||||||
import net.sf.samtools.CigarElement;
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Created by IntelliJ IDEA.
|
|
||||||
* User: mhanna
|
|
||||||
* Date: Feb 25, 2011
|
|
||||||
* Time: 10:16:53 AM
|
|
||||||
* To change this template use File | Settings | File Templates.
|
|
||||||
*/
|
|
||||||
class IterateOverCigarString extends ReadProcessor {
|
|
||||||
private long matchMismatches;
|
|
||||||
private long insertions;
|
|
||||||
private long deletions;
|
|
||||||
private long others;
|
|
||||||
|
|
||||||
public IterateOverCigarString(final BAMProcessingPerformanceMeter performanceMeter) {
|
|
||||||
super(performanceMeter);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() { return "iterator over cigar string"; }
|
|
||||||
public void processRead(final SAMRecord read) {
|
|
||||||
Cigar cigar = read.getCigar();
|
|
||||||
for(CigarElement cigarElement: cigar.getCigarElements()) {
|
|
||||||
int elementSize = cigarElement.getLength();
|
|
||||||
while(elementSize > 0) {
|
|
||||||
switch(cigarElement.getOperator()) {
|
|
||||||
case M: matchMismatches++; break;
|
|
||||||
case I: insertions++; break;
|
|
||||||
case D: deletions++; break;
|
|
||||||
default: others++; break;
|
|
||||||
}
|
|
||||||
elementSize--;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,58 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Created by IntelliJ IDEA.
|
|
||||||
* User: mhanna
|
|
||||||
* Date: Feb 25, 2011
|
|
||||||
* Time: 10:16:53 AM
|
|
||||||
* To change this template use File | Settings | File Templates.
|
|
||||||
*/
|
|
||||||
class IterateOverEachBase extends ReadProcessor {
|
|
||||||
private long As;
|
|
||||||
private long Cs;
|
|
||||||
private long Gs;
|
|
||||||
private long Ts;
|
|
||||||
|
|
||||||
public IterateOverEachBase(final BAMProcessingPerformanceMeter performanceMeter) {
|
|
||||||
super(performanceMeter);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() { return "iterate over each base"; }
|
|
||||||
public void processRead(final SAMRecord read) {
|
|
||||||
for(byte base: read.getReadBases()) {
|
|
||||||
switch(base) {
|
|
||||||
case 'A': As++; break;
|
|
||||||
case 'C': Cs++; break;
|
|
||||||
case 'G': Gs++; break;
|
|
||||||
case 'T': Ts++; break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,44 +0,0 @@
|
||||||
/*
|
|
||||||
* Copyright (c) 2011, 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,
|
|
||||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
|
||||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
|
||||||
* OTHER DEALINGS IN THE SOFTWARE.
|
|
||||||
*/
|
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
|
||||||
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Created by IntelliJ IDEA.
|
|
||||||
* User: mhanna
|
|
||||||
* Date: Feb 25, 2011
|
|
||||||
* Time: 10:16:53 AM
|
|
||||||
* To change this template use File | Settings | File Templates.
|
|
||||||
*/
|
|
||||||
class NoAdditionalProcessing extends ReadProcessor {
|
|
||||||
public NoAdditionalProcessing(final BAMProcessingPerformanceMeter performanceMeter) {
|
|
||||||
super(performanceMeter);
|
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getTestName() { return "no additional processing"; }
|
|
||||||
public void processRead(final SAMRecord read) {}
|
|
||||||
}
|
|
||||||
|
|
@ -0,0 +1,100 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2011, 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,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
||||||
|
|
||||||
|
import com.google.caliper.Param;
|
||||||
|
import com.google.caliper.SimpleBenchmark;
|
||||||
|
import net.sf.picard.util.SamLocusIterator;
|
||||||
|
import net.sf.samtools.SAMFileReader;
|
||||||
|
import net.sf.samtools.SAMRecord;
|
||||||
|
import net.sf.samtools.util.CloseableIterator;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.util.Iterator;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Created by IntelliJ IDEA.
|
||||||
|
* User: mhanna
|
||||||
|
* Date: Apr 22, 2011
|
||||||
|
* Time: 3:51:06 PM
|
||||||
|
* To change this template use File | Settings | File Templates.
|
||||||
|
*/
|
||||||
|
public class PicardBaselineBenchmark extends ReadProcessingBenchmark {
|
||||||
|
@Param
|
||||||
|
private String bamFile;
|
||||||
|
|
||||||
|
@Param
|
||||||
|
private Integer maxReads;
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getBAMFile() { return bamFile; }
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Integer getMaxReads() { return maxReads; }
|
||||||
|
|
||||||
|
public void timeDecompressBamFile(int reps) {
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
CloseableIterator<SAMRecord> iterator = reader.iterator();
|
||||||
|
while(iterator.hasNext())
|
||||||
|
iterator.next();
|
||||||
|
iterator.close();
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void timeExtractTag(int reps) {
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
CloseableIterator<SAMRecord> iterator = reader.iterator();
|
||||||
|
while(iterator.hasNext()) {
|
||||||
|
SAMRecord read = iterator.next();
|
||||||
|
read.getAttribute("OQ");
|
||||||
|
}
|
||||||
|
iterator.close();
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void timeSamLocusIterator(int reps) {
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
long loci = 0;
|
||||||
|
|
||||||
|
SamLocusIterator samLocusIterator = new SamLocusIterator(reader);
|
||||||
|
samLocusIterator.setEmitUncoveredLoci(false);
|
||||||
|
Iterator<SamLocusIterator.LocusInfo> workhorseIterator = samLocusIterator.iterator();
|
||||||
|
|
||||||
|
while(workhorseIterator.hasNext()) {
|
||||||
|
SamLocusIterator.LocusInfo locusInfo = workhorseIterator.next();
|
||||||
|
// Use the value of locusInfo to avoid optimization.
|
||||||
|
if(locusInfo != null) loci++;
|
||||||
|
}
|
||||||
|
System.out.printf("Total loci = %d%n",loci);
|
||||||
|
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -24,47 +24,59 @@
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
||||||
|
|
||||||
import net.sf.picard.util.SamLocusIterator;
|
import com.google.caliper.Param;
|
||||||
|
import com.google.caliper.SimpleBenchmark;
|
||||||
import net.sf.samtools.SAMFileReader;
|
import net.sf.samtools.SAMFileReader;
|
||||||
|
import net.sf.samtools.SAMFileWriter;
|
||||||
|
import net.sf.samtools.SAMFileWriterFactory;
|
||||||
|
import net.sf.samtools.SAMRecord;
|
||||||
|
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||||
|
|
||||||
import java.io.File;
|
import java.io.File;
|
||||||
import java.util.Iterator;
|
import java.io.IOException;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Created by IntelliJ IDEA.
|
* Created by IntelliJ IDEA.
|
||||||
* User: mhanna
|
* User: mhanna
|
||||||
* Date: Feb 25, 2011
|
* Date: Apr 22, 2011
|
||||||
* Time: 10:16:54 AM
|
* Time: 4:04:38 PM
|
||||||
* To change this template use File | Settings | File Templates.
|
* To change this template use File | Settings | File Templates.
|
||||||
*/
|
*/
|
||||||
class InvokeSamLocusIterator extends ReadProcessor {
|
public abstract class ReadProcessingBenchmark extends SimpleBenchmark {
|
||||||
public InvokeSamLocusIterator(final BAMProcessingPerformanceMeter performanceMeter) {
|
protected abstract String getBAMFile();
|
||||||
super(performanceMeter);
|
protected abstract Integer getMaxReads();
|
||||||
|
|
||||||
|
protected File inputFile;
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public void setUp() {
|
||||||
|
SAMFileReader fullInputFile = new SAMFileReader(new File(getBAMFile()));
|
||||||
|
|
||||||
|
File tempFile = null;
|
||||||
|
try {
|
||||||
|
tempFile = File.createTempFile("testfile_"+getMaxReads(),".bam");
|
||||||
|
}
|
||||||
|
catch(IOException ex) {
|
||||||
|
throw new ReviewedStingException("Unable to create temporary BAM",ex);
|
||||||
|
}
|
||||||
|
SAMFileWriterFactory factory = new SAMFileWriterFactory();
|
||||||
|
factory.setCreateIndex(true);
|
||||||
|
SAMFileWriter writer = factory.makeBAMWriter(fullInputFile.getFileHeader(),true,tempFile);
|
||||||
|
|
||||||
|
long numReads = 0;
|
||||||
|
for(SAMRecord read: fullInputFile) {
|
||||||
|
if(numReads++ >= getMaxReads())
|
||||||
|
break;
|
||||||
|
writer.addAlignment(read);
|
||||||
|
}
|
||||||
|
|
||||||
|
writer.close();
|
||||||
|
|
||||||
|
inputFile = tempFile;
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public String getTestName() {
|
public void tearDown() {
|
||||||
return String.format("invoke sam locus iterator");
|
inputFile.delete();
|
||||||
}
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public String getIterationType() { return "loci"; }
|
|
||||||
|
|
||||||
@Override
|
|
||||||
public void execute(File samFile, File fastaFile) {
|
|
||||||
SAMFileReader reader = new SAMFileReader(samFile);
|
|
||||||
|
|
||||||
SamLocusIterator samLocusIterator = new SamLocusIterator(reader);
|
|
||||||
samLocusIterator.setEmitUncoveredLoci(false);
|
|
||||||
Iterator<SamLocusIterator.LocusInfo> workhorseIterator = samLocusIterator.iterator();
|
|
||||||
|
|
||||||
startTest();
|
|
||||||
while(workhorseIterator.hasNext()) {
|
|
||||||
SamLocusIterator.LocusInfo locusInfo = workhorseIterator.next();
|
|
||||||
updateIterationCount();
|
|
||||||
}
|
|
||||||
stopTest();
|
|
||||||
|
|
||||||
reader.close();
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -0,0 +1,113 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2011, 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,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.datasources.reads.performance;
|
||||||
|
|
||||||
|
import com.google.caliper.Param;
|
||||||
|
import net.sf.samtools.Cigar;
|
||||||
|
import net.sf.samtools.CigarElement;
|
||||||
|
import net.sf.samtools.SAMFileReader;
|
||||||
|
import net.sf.samtools.SAMRecord;
|
||||||
|
import net.sf.samtools.util.CloseableIterator;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Created by IntelliJ IDEA.
|
||||||
|
* User: mhanna
|
||||||
|
* Date: Apr 22, 2011
|
||||||
|
* Time: 4:01:23 PM
|
||||||
|
* To change this template use File | Settings | File Templates.
|
||||||
|
*/
|
||||||
|
public class TheoreticalMinimaBenchmark extends ReadProcessingBenchmark {
|
||||||
|
@Param
|
||||||
|
private String bamFile;
|
||||||
|
|
||||||
|
@Param
|
||||||
|
private Integer maxReads;
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public String getBAMFile() { return bamFile; }
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public Integer getMaxReads() { return maxReads; }
|
||||||
|
|
||||||
|
public void timeIterateOverEachBase(int reps) {
|
||||||
|
System.out.printf("Processing " + inputFile);
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
CloseableIterator<SAMRecord> iterator = reader.iterator();
|
||||||
|
|
||||||
|
long As=0,Cs=0,Gs=0,Ts=0;
|
||||||
|
while(iterator.hasNext()) {
|
||||||
|
SAMRecord read = iterator.next();
|
||||||
|
for(byte base: read.getReadBases()) {
|
||||||
|
switch(base) {
|
||||||
|
case 'A': As++; break;
|
||||||
|
case 'C': Cs++; break;
|
||||||
|
case 'G': Gs++; break;
|
||||||
|
case 'T': Ts++; break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
System.out.printf("As = %d; Cs = %d; Gs = %d; Ts = %d; total = %d%n",As,Cs,Gs,Ts,As+Cs+Gs+Ts);
|
||||||
|
iterator.close();
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public void timeIterateOverCigarString(int reps) {
|
||||||
|
for(int i = 0; i < reps; i++) {
|
||||||
|
long matchMismatches = 0;
|
||||||
|
long insertions = 0;
|
||||||
|
long deletions = 0;
|
||||||
|
long others = 0;
|
||||||
|
|
||||||
|
SAMFileReader reader = new SAMFileReader(inputFile);
|
||||||
|
CloseableIterator<SAMRecord> iterator = reader.iterator();
|
||||||
|
while(iterator.hasNext()) {
|
||||||
|
SAMRecord read = iterator.next();
|
||||||
|
|
||||||
|
Cigar cigar = read.getCigar();
|
||||||
|
for(CigarElement cigarElement: cigar.getCigarElements()) {
|
||||||
|
int elementSize = cigarElement.getLength();
|
||||||
|
while(elementSize > 0) {
|
||||||
|
switch(cigarElement.getOperator()) {
|
||||||
|
case M: matchMismatches++; break;
|
||||||
|
case I: insertions++; break;
|
||||||
|
case D: deletions++; break;
|
||||||
|
default: others++; break;
|
||||||
|
}
|
||||||
|
elementSize--;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
System.out.printf("Ms = %d; Is = %d; Ds = %d; others = %d; total = %d%n",matchMismatches,insertions,deletions,others,matchMismatches+insertions+deletions+others);
|
||||||
|
|
||||||
|
iterator.close();
|
||||||
|
reader.close();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -11,6 +11,7 @@
|
||||||
<ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
|
<ibiblio name="reflections-repo" m2compatible="true" root="http://reflections.googlecode.com/svn/repo" />
|
||||||
<ibiblio name="java.net" m2compatible="false" root="http://download.java.net/maven/1/" pattern="[organisation]/jars/[artifact]-[revision].[ext]"/>
|
<ibiblio name="java.net" m2compatible="false" root="http://download.java.net/maven/1/" pattern="[organisation]/jars/[artifact]-[revision].[ext]"/>
|
||||||
<ibiblio name="maven2-repository.dev.java.net" m2compatible="true" root="http://download.java.net/maven/2/" />
|
<ibiblio name="maven2-repository.dev.java.net" m2compatible="true" root="http://download.java.net/maven/2/" />
|
||||||
|
<ibiblio name="sonatype" m2compatible="true" root="https://oss.sonatype.org/content/repositories/snapshots" />
|
||||||
</resolvers>
|
</resolvers>
|
||||||
<modules>
|
<modules>
|
||||||
<module organisation="edu.mit.broad" resolver="projects" />
|
<module organisation="edu.mit.broad" resolver="projects" />
|
||||||
|
|
@ -24,5 +25,7 @@
|
||||||
<module organisation="javax.mail" resolver="java.net" />
|
<module organisation="javax.mail" resolver="java.net" />
|
||||||
<module organisation="javax.activation" resolver="java.net" />
|
<module organisation="javax.activation" resolver="java.net" />
|
||||||
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
|
<module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
|
||||||
|
<module organisation="com.google.code.caliper" resolver="sonatype" />
|
||||||
|
<module organisation="com.google.code.gson" revision="1.7-SNAPSHOT" resolver="sonatype" />
|
||||||
</modules>
|
</modules>
|
||||||
</ivysettings>
|
</ivysettings>
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue