Package picard.analysis

Class ChimeraUtil

java.lang.Object
picard.analysis.ChimeraUtil
public class ChimeraUtil extends Object

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static Set<htsjdk.samtools.SamPairUtil.PairOrientation>
    DEFAULT_EXPECTED_ORIENTATIONS
     
    static int
    DEFAULT_INSERT_SIZE_LIMIT
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    ChimeraUtil()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    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.
    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.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • 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 Details

    • ChimeraUtil

      public ChimeraUtil()

  • Method Details

    • 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