ChimeraUtil.java

/*
 * The MIT License
 *
 * Copyright (c) 2016 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
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 * THE SOFTWARE.
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package picard.analysis;

import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTag;
import htsjdk.samtools.SamPairUtil;
import htsjdk.samtools.SamPairUtil.PairOrientation;

import java.util.EnumSet;
import java.util.Set;

public class ChimeraUtil {
    public static int DEFAULT_INSERT_SIZE_LIMIT = 100000;
    public static Set<PairOrientation> DEFAULT_EXPECTED_ORIENTATIONS = EnumSet.of(PairOrientation.FR);

    /**
     * Checks whether the given read is part of a chimeric pair.
     * Note that this method returns false if the read is unpaired or if either end of the pair is unmapped.
     *
     * @param rec                    the read
     * @param maxInsertSize          max insert size to be considered non-chimeric
     * @param expectedOrientations   set of orientations that are not chimeric; must not ne null
     * @return true if this record is part of a chimeric read pair, false otherwise
     */
    public static boolean isChimeric(final SAMRecord rec, final int maxInsertSize, final Set<PairOrientation> expectedOrientations) {
        return isMappedPair(rec) &&                                               // the read pair needs to be mapped and...
                (Math.abs(rec.getInferredInsertSize()) > maxInsertSize ||         //    either far apart on the same contig
                !rec.getReferenceIndex().equals(rec.getMateReferenceIndex()) ||   //    or on different contigs
                !matchesExpectedOrientations(rec, expectedOrientations));         //    or in unexpected orientations
    }

    /**
     * Checks whether the given read is part of a chimeric pair.
     * Note that this method returns false if either end of the pair is unmapped.
     *
     * @param r1                     first read of the pair
     * @param r2                     second read of the pair
     * @param maxInsertSize          max insert size to be considered non-chimeric
     * @param expectedOrientations   set of orientations that are not chimeric
     * @return true if this pair is chimeric, false otherwise
     */
    public static boolean isChimeric(final SAMRecord r1, final SAMRecord r2, final int maxInsertSize, final Set<PairOrientation> expectedOrientations) {
        return isMappedPair(r1) &&                                                  // the read pair needs to be mapped and...
                (Math.abs(r1.getInferredInsertSize()) > maxInsertSize ||            //    either far apart on the same contig
                        !r1.getReferenceIndex().equals(r2.getReferenceIndex()) ||   //    or on different contigs
                        !matchesExpectedOrientations(r1, expectedOrientations) ||   //    or in unexpected orientations
                        r2.getAttribute(SAMTag.SA.toString()) != null);                             //      (another check for an unexpected orientation here)
    }

    private static boolean isMappedPair(final SAMRecord rec) {
        return rec.getReadPairedFlag() && !rec.getReadUnmappedFlag() && !rec.getMateUnmappedFlag();
    }

    private static boolean matchesExpectedOrientations(final SAMRecord rec, final Set<PairOrientation> expectedOrientations) {
        return expectedOrientations.contains(SamPairUtil.getPairOrientation(rec)) && rec.getAttribute(SAMTag.SA.toString()) == null;
    }
}