Class ReadEndsForMarkDuplicates

All Implemented Interfaces:
Serializable, Cloneable, PhysicalLocation
Direct Known Subclasses:
ReadEndsForMarkDuplicatesWithBarcodes

public class ReadEndsForMarkDuplicates extends ReadEnds implements Cloneable
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
See Also:
  • Field Details

    • SIZE_OF

      protected static final int SIZE_OF
      See Also:
    • score

      public short score
    • read1IndexInFile

      public long read1IndexInFile
    • read2IndexInFile

      public long read2IndexInFile
    • duplicateSetSize

      public int duplicateSetSize
  • Constructor Details

    • ReadEndsForMarkDuplicates

      public ReadEndsForMarkDuplicates()
    • ReadEndsForMarkDuplicates

      public ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates read)
  • Method Details

    • getSizeOf

      public static int getSizeOf()
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • clone

      public ReadEndsForMarkDuplicates clone()
      Overrides:
      clone in class Object
    • isSingleEndReadKnownFragment

      public static boolean isSingleEndReadKnownFragment(htsjdk.samtools.SAMRecord rec)
      This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e. it was not quality trimmed)