org.broadinstitute.hellbender.utils.read.Fragment Maven / Gradle / Ivy

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package org.broadinstitute.hellbender.utils.read;

import htsjdk.samtools.util.Locatable;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.utils.SimpleInterval;
import org.broadinstitute.hellbender.utils.Utils;

import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;

/**
 * All available evidence coming from a single biological fragment.  Either one read or a read pair.
 */
public class Fragment implements Locatable {

    private final SimpleInterval interval;

    private final List reads;

    private static final Logger logger = LogManager.getLogger(Fragment.class);



    public Fragment(final GATKRead read) {
        reads = Collections.singletonList(read);
        interval = new SimpleInterval(read.getAssignedContig(), Math.min(read.getStart(), read.getEnd()), Math.max(read.getStart(), read.getEnd()));
    }

    public Fragment(final Pair pair) {
        reads = Arrays.asList(pair.getLeft(), pair.getRight());
        final int start = Math.min(pair.getLeft().getStart(), pair.getRight().getStart());
        final int end = Math.max(pair.getLeft().getEnd(), pair.getRight().getEnd());
        interval = new SimpleInterval(pair.getLeft().getAssignedContig(), Math.min(start, end), Math.max(start, end));
    }

    public static Fragment create(final List reads) {
        Utils.validateArg(reads.size() <= 2, "Cannot construct fragment from more than two reads");
        Utils.validateArg(!reads.isEmpty(), "Need one or two reads to construct a fragment");
        return reads.size() == 1 ? new Fragment(reads.get(0)) : new Fragment(ImmutablePair.of(reads.get(0), reads.get(1)));
    }

    public static Fragment createAndAvoidFailure(final List reads) {
        if (reads.size() <= 2) {
            return create(reads);
        } else {
            final List nonSupplementaryReads = reads.stream()
                    .filter(read -> !(read.isDuplicate() || read.isSecondaryAlignment() || read.isSupplementaryAlignment()))
                    .collect(Collectors.toList());
            if (nonSupplementaryReads.size() > 2) {
                logger.warn("More than two reads with the same name found.  Using two reads randomly to combine as a fragment.");
                return create(nonSupplementaryReads.subList(0,2));
            }
            //If there are no nonsupplementary reads, try supplementary/secondary/duplicate reads instead
            else if(nonSupplementaryReads.isEmpty())
            {
                return create(reads.subList(0,1));
            }
            return create(nonSupplementaryReads);
        }
    }

    public List getReads() {
        return reads;
    }

    @Override
    public String getContig() {
        return interval.getContig();
    }

    @Override
    public int getStart() {
        return interval.getStart();
    }

    @Override
    public int getEnd() {
        return interval.getEnd();
    }
}