Class ChimeraUtil


  • public class ChimeraUtil
    extends Object
    • Field Detail

      • DEFAULT_INSERT_SIZE_LIMIT

        public static int DEFAULT_INSERT_SIZE_LIMIT
      • DEFAULT_EXPECTED_ORIENTATIONS

        public static Set<htsjdk.samtools.SamPairUtil.PairOrientation> DEFAULT_EXPECTED_ORIENTATIONS
    • Constructor Detail

      • ChimeraUtil

        public ChimeraUtil()
    • Method Detail

      • isChimeric

        public static boolean isChimeric​(htsjdk.samtools.SAMRecord rec,
                                         int maxInsertSize,
                                         Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations)
        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.
        Parameters:
        rec - the read
        maxInsertSize - max insert size to be considered non-chimeric
        expectedOrientations - set of orientations that are not chimeric; must not ne null
        Returns:
        true if this record is part of a chimeric read pair, false otherwise
      • isChimeric

        public static boolean isChimeric​(htsjdk.samtools.SAMRecord r1,
                                         htsjdk.samtools.SAMRecord r2,
                                         int maxInsertSize,
                                         Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations)
        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.
        Parameters:
        r1 - first read of the pair
        r2 - second read of the pair
        maxInsertSize - max insert size to be considered non-chimeric
        expectedOrientations - set of orientations that are not chimeric
        Returns:
        true if this pair is chimeric, false otherwise