gatk-3.8/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java

/*
 * Copyright (c) 2009 The Broad Institute
 *
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 *
 * The above copyright notice and this permission notice shall be
 * 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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package org.broadinstitute.sting.gatk.contexts;

import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.GATKException;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.exceptions.UserError;
import org.broadinstitute.sting.utils.pileup.*;

import java.util.*;

/**
 * Useful class for storing different AlignmentContexts
 * User: ebanks
 * Modified: chartl (split by read group)
 */
public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {

    // Definitions:
    //   COMPLETE = full alignment context
    //   FORWARD  = reads on forward strand
    //   REVERSE  = reads on forward strand
    //
    public enum StratifiedContextType { COMPLETE, FORWARD, REVERSE }

    private GenomeLoc loc;
    private RBP basePileup = null;

    //
    // accessors
    //
    public GenomeLoc getLocation() { return loc; }

    public StratifiedAlignmentContext(GenomeLoc loc) {
        this(loc,null);
    }

    public StratifiedAlignmentContext(GenomeLoc loc, RBP pileup) {
        this.loc = loc;
        this.basePileup = pileup;
    }

    public AlignmentContext getContext(StratifiedContextType type) {
        switch(type) {
            case COMPLETE:
                return new AlignmentContext(loc,basePileup);
            case FORWARD:
                return new AlignmentContext(loc,basePileup.getPositiveStrandPileup());
            case REVERSE:
                return new AlignmentContext(loc,basePileup.getNegativeStrandPileup());
            default:
                throw new GATKException("Unable to get alignment context for type = " + type);
        }
    }

    /**
     * Splits the given AlignmentContext into a StratifiedAlignmentContext per sample.
     *
     * @param pileup                the original pileup
     *
     * @return a Map of sample name to StratifiedAlignmentContext
     *
     **/
    public static <RBP extends ReadBackedPileup,PE extends PileupElement> Map<String, StratifiedAlignmentContext> splitContextBySample(RBP pileup) {
        return splitContextBySample(pileup, null);
    }

    /**
     * Splits the given AlignmentContext into a StratifiedAlignmentContext per sample.
     *
     * @param pileup                the original pileup
     * @param assumedSingleSample   if not null, any read without a readgroup will be given this sample name
     *
     * @return a Map of sample name to StratifiedAlignmentContext
     *
     **/
    public static <RBP extends ReadBackedPileup> Map<String, StratifiedAlignmentContext> splitContextBySample(RBP pileup, String assumedSingleSample) {

        GenomeLoc loc = pileup.getLocation();
        HashMap<String, StratifiedAlignmentContext> contexts = new HashMap<String, StratifiedAlignmentContext>();

        for(String sampleName: pileup.getSamples()) {
            RBP pileupBySample = (RBP)pileup.getPileupForSample(sampleName);

            // Don't add empty pileups to the split context.
            if(pileupBySample.size() == 0)
                continue;

            if(sampleName != null)
                contexts.put(sampleName,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
            else {
                if(assumedSingleSample == null) {
                    throw new UserError.MalformedBam(pileupBySample.iterator().next().getRead(), "Missing read group for read");
                }
                contexts.put(assumedSingleSample,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
            }
        }

        return contexts;
    }

     /**
     * Splits the given AlignmentContext into a StratifiedAlignmentContext per read group.
     *
     * @param pileup                the original pileup
     * @return a Map of sample name to StratifiedAlignmentContext
     * TODO - support for collapsing or assuming read groups if they are missing
     *
     **/
    public static <RBP extends ReadBackedPileup> Map<String,StratifiedAlignmentContext<RBP>> splitContextByReadGroup(RBP pileup) {
         HashMap<String,StratifiedAlignmentContext<RBP>> contexts = new HashMap<String,StratifiedAlignmentContext<RBP>>();
         for(String readGroupId: pileup.getReadGroups())
             contexts.put(readGroupId,new StratifiedAlignmentContext<RBP>(pileup.getLocation(),(RBP)pileup.getPileupForReadGroup(readGroupId)));
         return contexts;
    }

    public static AlignmentContext joinContexts(Collection<StratifiedAlignmentContext> contexts) {
         
        // validation
        GenomeLoc loc = contexts.iterator().next().getLocation();
        boolean isExtended = contexts.iterator().next().basePileup instanceof ReadBackedExtendedEventPileup;
        for(StratifiedAlignmentContext context: contexts) {
            if(!loc.equals(context.getLocation()))
                throw new GATKException("Illegal attempt to join contexts from different genomic locations");
            if(isExtended != (context.basePileup instanceof ReadBackedExtendedEventPileup))
                throw new GATKException("Illegal attempt to join simple and extended contexts");
        }

        AlignmentContext jointContext;
        if(isExtended) {
            List<ExtendedEventPileupElement> pe = new ArrayList<ExtendedEventPileupElement>();
            for(StratifiedAlignmentContext context: contexts) {
                for(PileupElement pileupElement: context.basePileup)
                    pe.add((ExtendedEventPileupElement)pileupElement);
            }
            jointContext = new AlignmentContext(loc, new ReadBackedExtendedEventPileupImpl(loc,pe));
        }
        else {
            List<PileupElement> pe = new ArrayList<PileupElement>();
            for(StratifiedAlignmentContext context: contexts) {
                for(PileupElement pileupElement: context.basePileup)
                    pe.add(pileupElement);
            }
            jointContext = new AlignmentContext(loc, new ReadBackedPileupImpl(loc,pe));
        }

        return jointContext;
    }
}