Package picard.sam.markduplicates.util

Class ReadEndsForMarkDuplicates

java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.util.PhysicalLocationShort
picard.sam.markduplicates.util.ReadEnds
picard.sam.markduplicates.util.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)