338 lines
15 KiB
Java
Executable File
338 lines
15 KiB
Java
Executable File
/*
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* Copyright (c) 2009 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 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;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.picard.reference.ReferenceSequenceFileFactory;
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import net.sf.picard.filter.SamRecordFilter;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.executive.MicroScheduler;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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public class GenomeAnalysisEngine {
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// our instance of this genome analysis toolkit; it's used by other classes to extract the traversal engine
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// TODO: public static without final tends to indicate we're thinking about this the wrong way
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public static GenomeAnalysisEngine instance;
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// our traversal engine
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private TraversalEngine engine = null;
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// our argument collection
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private GATKArgumentCollection argCollection;
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/** Collection of output streams used by the walker. */
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private OutputTracker outputTracker = null;
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/** our log, which we want to capture anything from this class */
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private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);
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/** our walker manager */
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private final WalkerManager walkerManager;
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/** plugin path for the walker manager. */
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public final String pluginPathName = null;
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/**
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* our constructor, where all the work is done
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* <p/>
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* legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
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* new MicroScheduler class we'll be able to delete that function.
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*
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*/
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public GenomeAnalysisEngine() {
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// make sure our instance variable points to this analysis engine
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instance = this;
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walkerManager = new WalkerManager(pluginPathName);
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}
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/**
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* Actually run the GATK with the specified walker.
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* @param args the argument collection, where we get all our setup information from
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* @param my_walker Walker to run over the dataset. Must not be null.
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*/
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public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
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// validate our parameters
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if (args == null) {
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throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can be null.");
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}
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// validate our parameters
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if (my_walker == null)
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throw new StingException("The walker passed to GenomeAnalysisEngine can be null.");
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// save our argument parameter
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this.argCollection = args;
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// our reference ordered data collection
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List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
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//
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// please don't use these in the future, use the new syntax <- if we're not using these please remove them
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//
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if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile);
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if (argCollection.HAPMAPFile != null)
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bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
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if (argCollection.HAPMAPChipFile != null)
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bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
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// TODO: The ROD iterator currently does not understand multiple intervals file. Fix this by cleaning the ROD system.
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if (argCollection.intervals != null && argCollection.intervals.size() == 1) {
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bindConvenienceRods("interval", "Intervals", argCollection.intervals.get(0).replaceAll(",", ""));
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}
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// parse out the rod bindings
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ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);
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// Validate the walker inputs against the walker.
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validateInputsAgainstWalker(my_walker, argCollection, rods);
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// create the output streams
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initializeOutputStreams(my_walker);
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// our microscheduler, which is in charge of running everything
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MicroScheduler microScheduler = null;
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microScheduler = createMicroscheduler(my_walker, rods);
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// Prepare the sort ordering w.r.t. the sequence dictionary
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if (argCollection.referenceFile != null) {
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final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
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GenomeLocParser.setupRefContigOrdering(refFile);
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}
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logger.info("Strictness is " + argCollection.strictnessLevel);
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// perform validation steps that are common to all the engines
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genericEngineSetup();
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GenomeLocSortedSet locs = null;
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if (argCollection.intervals != null) {
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locs = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
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}
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// excute the microscheduler, storing the results
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return microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
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}
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/**
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* Retrieves an instance of the walker based on the walker name.
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* @param walkerName Name of the walker. Must not be null. If the walker cannot be instantiated, an exception will be thrown.
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* @return An instance of the walker.
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*/
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public Walker<?,?> getWalkerByName( String walkerName ) {
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try {
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return walkerManager.createWalkerByName(walkerName);
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} catch (InstantiationException ex) {
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throw new StingException("Unable to instantiate walker.", ex);
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}
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catch (IllegalAccessException ex) {
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throw new StingException("Unable to access walker", ex);
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}
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}
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/**
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* setup a microscheduler
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*
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* @param my_walker our walker of type LocusWalker
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* @param rods the reference order data
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*
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* @return a new microscheduler
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*/
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private MicroScheduler createMicroscheduler(Walker my_walker, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
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// the mircoscheduler to return
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MicroScheduler microScheduler = null;
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// we need to verify different parameter based on the walker type
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if (my_walker instanceof LocusWalker || my_walker instanceof LocusWindowWalker) {
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// create the MicroScheduler
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microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
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engine = microScheduler.getTraversalEngine();
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} else if (my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker) {
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if (argCollection.referenceFile == null)
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Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
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microScheduler = MicroScheduler.create(my_walker, extractSourceInfo(my_walker,argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
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engine = microScheduler.getTraversalEngine();
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} else {
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Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));
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}
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return microScheduler;
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}
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/** commands that get executed for each engine, regardless of the type */
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private void genericEngineSetup() {
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engine.setMaximumIterations(argCollection.maximumEngineIterations);
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engine.initialize();
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}
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/**
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* setup the interval regions, from either the interval file of the genome region string
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*
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* @param intervals the list of intervals to parse
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*
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* @return a list of genomeLoc representing the interval file
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*/
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public static List<GenomeLoc> parseIntervalRegion(final List<String> intervals) {
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List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
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for (String interval : intervals) {
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if (new File(interval).exists()) {
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locs.addAll(GenomeLocParser.intervalFileToList(interval));
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} else {
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locs.addAll(GenomeLocParser.parseGenomeLocs(interval));
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}
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}
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return locs;
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}
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/**
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* Bundles all the source information about the reads into a unified data structure.
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*
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* @param walker The walker for which to extract info.
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* @param argCollection The collection of arguments passed to the engine.
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*
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* @return The reads object providing reads source info.
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*/
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private Reads extractSourceInfo( Walker walker, GATKArgumentCollection argCollection ) {
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List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
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filters.addAll( WalkerManager.getReadFilters(walker) );
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if( argCollection.filterZeroMappingQualityReads != null && argCollection.filterZeroMappingQualityReads )
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filters.add( new ZeroMappingQualityReadFilter() );
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return new Reads( argCollection.samFiles,
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argCollection.strictnessLevel,
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argCollection.downsampleFraction,
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argCollection.downsampleCoverage,
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!argCollection.unsafe,
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filters );
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}
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private void validateInputsAgainstWalker(Walker walker,
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GATKArgumentCollection arguments,
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List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
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String walkerName = WalkerManager.getWalkerName(walker.getClass());
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// Check what the walker says is required against what was provided on the command line.
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if (WalkerManager.isRequired(walker, DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0))
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throw new ArgumentException(String.format("Walker %s requires reads but none were provided. If this is incorrect, alter the walker's @Requires annotation.", walkerName));
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if (WalkerManager.isRequired(walker, DataSource.REFERENCE) && arguments.referenceFile == null)
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throw new ArgumentException(String.format("Walker %s requires a reference but none was provided. If this is incorrect, alter the walker's @Requires annotation.", walkerName));
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// Check what the walker says is allowed against what was provided on the command line.
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if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS))
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throw new ArgumentException(String.format("Walker %s does not allow reads but reads were provided. If this is incorrect, alter the walker's @Allows annotation", walkerName));
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if (arguments.referenceFile != null && !WalkerManager.isAllowed(walker, DataSource.REFERENCE))
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throw new ArgumentException(String.format("Walker %s does not allow a reference but one was provided. If this is incorrect, alter the walker's @Allows annotation", walkerName));
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// Check to make sure that all required metadata is present.
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List<RMD> allRequired = WalkerManager.getRequiredMetaData(walker);
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for (RMD required : allRequired) {
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boolean found = false;
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for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods) {
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if (rod.matches(required.name(), required.type()))
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found = true;
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}
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if (!found)
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throw new ArgumentException(String.format("Unable to find reference metadata (%s,%s)", required.name(), required.type()));
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}
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// Check to see that no forbidden rods are present.
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for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods) {
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if (!WalkerManager.isAllowed(walker, rod))
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throw new ArgumentException(String.format("Walker does not allow access to metadata: %s. If this is correct, change the @Allows metadata", rod.getName()));
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}
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}
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/**
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* Default to 5 (based on research by Alec Wysoker)
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*
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* @return the BAM compression
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*/
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public int getBAMCompression() {
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return (argCollection.BAMcompression == null ||
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argCollection.BAMcompression < 1 ||
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argCollection.BAMcompression > 8) ? 5 : argCollection.BAMcompression;
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}
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/**
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* Convenience function that binds RODs using the old-style command line parser to the new style list for
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* a uniform processing.
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*
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* @param name the name of the rod
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* @param type its type
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* @param file the file to load the rod from
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*/
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private void bindConvenienceRods(final String name, final String type, final String file) {
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argCollection.RODBindings.add(Utils.join(",", new String[]{name, type, file}));
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}
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/**
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* Initialize the output streams as specified by the user.
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*
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* @param walker the walker to initialize output streams for
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*/
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private void initializeOutputStreams(Walker walker) {
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outputTracker = (argCollection.outErrFileName != null) ? new OutputTracker(argCollection.outErrFileName, argCollection.outErrFileName)
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: new OutputTracker(argCollection.outFileName, argCollection.errFileName);
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walker.initializeOutputStreams(outputTracker);
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}
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/**
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* Gets the output tracker. Tracks data available to a given walker.
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*
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* @return The output tracker.
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*/
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public OutputTracker getOutputTracker() {
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return outputTracker;
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}
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public TraversalEngine getEngine() {
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return this.engine;
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}
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/**
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* Gets the collection of GATK main application arguments for enhanced walker validation.
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*
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* @return the GATK argument collection
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*/
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public GATKArgumentCollection getArguments() {
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return this.argCollection;
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}
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}
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