gatk-3.8/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

/*
 * Copyright (c) 2009 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.
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package org.broadinstitute.sting.gatk;

import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.ArgumentException;

import java.util.ArrayList;
import java.util.List;
import java.io.File;

public class GenomeAnalysisEngine {

    // our instance of this genome analysis toolkit; it's used by other classes to extract the traversal engine
    // TODO: public static without final tends to indicate we're thinking about this the wrong way
    public static GenomeAnalysisEngine instance;

    // our traversal engine
    private TraversalEngine engine = null;

    // the level of debugging we're using
    public boolean DEBUGGING = false;

    // our argument collection
    private final GATKArgumentCollection argCollection;

    /** Collection of output streams used by the walker. */
    private OutputTracker outputTracker = null;

    /** our log, which we want to capture anything from this class */
    private static Logger logger = Logger.getLogger(GenomeAnalysisEngine.class);

    /** the return value from our walker */
    private Object walkerReturn = null;

    /**
     * our constructor, where all the work is done
     * <p/>
     * legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
     * new MicroScheduler class we'll be able to delete that function.
     *
     * @param args      the argument collection, where we get all our setup information from
     * @param my_walker the walker we're running with
     */
    public GenomeAnalysisEngine(GATKArgumentCollection args, Walker my_walker) {

        // validate our parameters
        if (args == null || my_walker == null) {
            throw new StingException("Neither the GATKArgumentCollection or the Walker passed to GenomeAnalysisEngine can be null.");
        }

        // save our argument parameter
        this.argCollection = args;

        // make sure our instance variable points to this analysis engine
        instance = this;

        // our reference ordered data collection
        List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();

        //
        // please don't use these in the future, use the new syntax <- if we're not using these please remove them
        //
        if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile);
        if (argCollection.HAPMAPFile != null)
            bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
        if (argCollection.HAPMAPChipFile != null)
            bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
        if ( argCollection.intervals != null )
            bindConvenienceRods("interval", "Intervals", argCollection.intervals.replaceAll(",", ""));

        // parse out the rod bindings
        ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);

        // Validate the walker inputs against the walker.
        validateInputsAgainstWalker(my_walker, argCollection, rods);

        // create the output streams
        initializeOutputStreams( my_walker );

        // our microscheduler, which is in charge of running everything
        MicroScheduler microScheduler = null;

        // if we're a read or a locus walker, we use the new system.  Right now we have complicated
        // branching based on the input data, but this should disapear when all the traversals are switched over
        if (my_walker instanceof LocusWalker || my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker) {
            microScheduler = createMicroscheduler(my_walker, rods);
        } else { // we have an old style traversal, once we're done return
            legacyTraversal(my_walker, rods);
            return;
        }

        // Prepare the sort ordering w.r.t. the sequence dictionary
        if (argCollection.referenceFile != null) {
            final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
            GenomeLocParser.setupRefContigOrdering(refFile);
        }

        // Determine the validation stringency.  Default to ValidationStringency.STRICT.
        ValidationStringency strictness = getValidationStringency();

        logger.info("Strictness is " + strictness);

        // perform validation steps that are common to all the engines
        genericEngineSetup();

        // parse out any genomic location they've provided
        //List<GenomeLoc> locationsList = setupIntervalRegion();
        List<GenomeLoc> locationsList = engine.getLocations();        
        GenomeLocSortedSet locs = null;
        if (locationsList != null)
            locs = GenomeLocSortedSet.createSetFromList(locationsList);

        // excute the microscheduler, storing the results
        walkerReturn = microScheduler.execute(my_walker, locs, argCollection.maximumEngineIterations);
    }


    /**
     * this is to accomdate the older style traversals, that haven't been converted over to the new system.  Putting them
     * into their own function allows us to deviate in the two behaviors so the new style traversals aren't limited to what
     * the old style does.  As traversals are converted, this function should disappear.
     *
     * @param my_walker the walker to run
     * @param rods the rod tracks to associate with
     */
    private void legacyTraversal(Walker my_walker, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
        if (my_walker instanceof LocusWindowWalker) {
            this.engine = new TraverseByLocusWindows(argCollection.samFiles, argCollection.referenceFile, rods);
        } else {
            throw new RuntimeException("Unexpected walker type: " + my_walker);
        }

        // Prepare the sort ordering w.r.t. the sequence dictionary
        if (argCollection.referenceFile != null) {
            final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
            GenomeLocParser.setupRefContigOrdering(refFile);
        }

        // Determine the validation stringency.  Default to ValidationStringency.STRICT.
        ValidationStringency strictness = getValidationStringency();

        logger.info("Strictness is " + strictness);
        genericEngineSetup();

        // store the results of the walker run
        walkerReturn = engine.traverse(my_walker);

    }

    /**
     * setup a microscheduler
     *
     * @param my_walker our walker of type LocusWalker
     * @param rods      the reference order data
     * @return a new microscheduler
     */
    private MicroScheduler createMicroscheduler(Walker my_walker, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
        // the mircoscheduler to return
        MicroScheduler microScheduler = null;

        // we need to verify different parameter based on the walker type
        if (my_walker instanceof LocusWalker) {
            // create the MicroScheduler
            if( argCollection.walkAllLoci )
                Utils.scareUser("Argument --all_loci is deprecated.  Please annotate your walker with @By(DataSource.REFERENCE) to perform a by-reference traversal.");
            microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
            engine = microScheduler.getTraversalEngine();
        }
        else if (my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker) {
            if (argCollection.referenceFile == null)
                Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
            microScheduler = MicroScheduler.create(my_walker, extractSourceInfoFromArguments(argCollection), argCollection.referenceFile, rods, argCollection.numberOfThreads);
            engine = microScheduler.getTraversalEngine();
        } else {
            Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));    
        }

        return microScheduler;
    }


    /**
     * commands that get executed for each engine, regardless of the type
     */
    private void genericEngineSetup() {
        Reads sourceInfo = extractSourceInfoFromArguments(argCollection);

        engine.setStrictness(sourceInfo.getValidationStringency());

        engine.setMaxReads(argCollection.maximumEngineIterations);
        engine.setFilterZeroMappingQualityReads(argCollection.filterZeroMappingQualityReads);

        // we default interval files over the genome region string
        if (argCollection.intervals != null) {
            engine.setLocation(parseIntervalRegion(argCollection.intervals, false));
        }

        engine.setReadFilters(sourceInfo);

        engine.setThreadedIO(argCollection.enabledThreadedIO);
        engine.setWalkOverAllSites(argCollection.walkAllLoci);
        engine.initialize();
    }

    /**
     * setup the interval regions, from either the interval file of the genome region string
     *
     * @return a list of genomeLoc representing the interval file
     */
    public static List<GenomeLoc> parseIntervalRegion(final String intervalsString, boolean quiet ) {
        List<GenomeLoc> locs = null;
        if ( intervalsString != null) {
            if (new File(intervalsString).exists()) {
                if (! quiet) logger.info("Intervals argument specifies a file.  Loading intervals from file.");
                locs = GenomeLocParser.intervalFileToList(intervalsString);
            } else {
                if (! quiet) logger.info("Intervals argument does not specify a file.  Trying to parse it as a simple string.");
                locs = GenomeLocParser.parseGenomeLocs(intervalsString);
            }
        }
        return locs;
    }

    /**
     * Bundles all the source information about the reads into a unified data structure.
     * @param argCollection The collection of arguments passed to the engine.
     * @return The reads object providing reads source info.
     */
    private Reads extractSourceInfoFromArguments( GATKArgumentCollection argCollection ) {
        return new Reads( argCollection.samFiles,
                          getValidationStringency(),
                          argCollection.downsampleFraction,
                          argCollection.downsampleCoverage,
                          argCollection.maximumReadSorts,
                          !argCollection.unsafe,
                          argCollection.filterZeroMappingQualityReads );
    }

    private void validateInputsAgainstWalker(Walker walker,
                                             GATKArgumentCollection arguments,
                                             List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
        String walkerName = WalkerManager.getWalkerName(walker.getClass());

        // Check what the walker says is required against what was provided on the command line.
        if( WalkerManager.isRequired(walker,DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0) )
            throw new ArgumentException(String.format("Walker %s requires reads but none were provided.  If this is incorrect, alter the walker's @Requires annotation.",walkerName));
        if( WalkerManager.isRequired(walker,DataSource.REFERENCE) && arguments.referenceFile == null )
            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));

        // Check what the walker says is allowed against what was provided on the command line.
        if( (arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker,DataSource.READS) )
            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));
        if( arguments.referenceFile != null && !WalkerManager.isAllowed(walker,DataSource.REFERENCE) )
            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));

        // Check to make sure that all required metadata is present.
        List<RMD> allRequired = WalkerManager.getRequiredMetaData(walker);
        for( RMD required: allRequired ) {
            boolean found = false;
            for( ReferenceOrderedData<? extends ReferenceOrderedDatum> rod: rods ) {
                if( rod.matches(required.name(),required.type()) )
                    found = true;
            }
            if( !found )
                throw new ArgumentException(String.format("Unable to find reference metadata (%s,%s)",required.name(),required.type()));
        }

        // Check to see that no forbidden rods are present.
        for( ReferenceOrderedData<? extends ReferenceOrderedDatum> rod: rods ) {
            if( !WalkerManager.isAllowed(walker,rod) )
                throw new ArgumentException(String.format("Walker does not allow access to metadata: %s.  If this is correct, change the @Allows metadata",rod.getName()));
        }
    }

    /**
     * Default to ValidationStringency.STRICT.
     *
     * @return the validation stringency
     */
    private ValidationStringency getValidationStringency() {
        ValidationStringency strictness = ValidationStringency.SILENT;
        try {
            strictness = Enum.valueOf(ValidationStringency.class, argCollection.strictnessLevel.toUpperCase().trim());
        }
        catch (IllegalArgumentException ex) {
            logger.debug("Unable to parse strictness from command line.  Assuming SILENT");
        }
        return strictness;
    }

    /**
     * Default to 5 (based on research by Alec Wysoker)
     *
     * @return the BAM compression
     */
    public int getBAMCompression() {
        return (argCollection.BAMcompression == null ||
                argCollection.BAMcompression < 1     ||
                argCollection.BAMcompression > 8) ? 5 : argCollection.BAMcompression;
    }

    /**
     * Convenience function that binds RODs using the old-style command line parser to the new style list for
     * a uniform processing.
     *
     * @param name
     * @param type
     * @param file
     */
    private void bindConvenienceRods(final String name, final String type, final String file) {
        argCollection.RODBindings.add(Utils.join(",", new String[]{name, type, file}));
    }


    /** Initialize the output streams as specified by the user. */
    private void initializeOutputStreams( Walker walker ) {
        outputTracker = (argCollection.outErrFileName != null) ? new OutputTracker(argCollection.outErrFileName, argCollection.outErrFileName)
                : new OutputTracker(argCollection.outFileName, argCollection.errFileName);
        walker.initializeOutputStreams(outputTracker);
    }

    /**
     * Gets the output tracker.  Tracks data available to a given walker.
     *
     * @return The output tracker.
     */
    public OutputTracker getOutputTracker() {
        return outputTracker;
    }

    /**
     * This function is deprecated in the new traversal engines, if you need to get the header
     * please get the engine and then use the getHeader function
     *
     * @return
     */
    @Deprecated
    public SAMFileReader getSamReader() {
        return this.engine.getSamReader();
    }

    public TraversalEngine getEngine() {
        return this.engine;
    }

    /** Gets the collection of GATK main application arguments for enhanced walker validation. */
    public GATKArgumentCollection getArguments() {
        return this.argCollection;
    }

    /**
     * Get's the return value of the walker
     *
     * @return an Object representing the return value of the walker
     */
    public Object getWalkerReturn() {
        return walkerReturn;
    }

}