Package picard.sam.markduplicates.util

Class ReadEndsForMateCigar

java.lang.Object
picard.sam.util.PhysicalLocationInt
picard.sam.util.PhysicalLocationShort
picard.sam.markduplicates.util.ReadEnds
picard.sam.markduplicates.util.ReadEndsForMateCigar
All Implemented Interfaces:
Serializable, PhysicalLocation
public class ReadEndsForMateCigar extends ReadEnds
A class to store individual records for MarkDuplicatesWithMateCigar. This aids in comparing records to determine which need to be compared when we mark duplicates. We also store the original SAMRecord and its ordinal in the input file (in SamRecordWithOrdinal) to access optional tags (mate cigar) and other information.
See Also:

  • Field Details

    • samRecordWithOrdinal

      public htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal

  • Constructor Details

    • ReadEndsForMateCigar

      public ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal, OpticalDuplicateFinder opticalDuplicateFinder, short libraryId)
      Builds a read ends object that represents a single read.

    • ReadEndsForMateCigar

      public ReadEndsForMateCigar(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)
      Creates a shallow copy from the "other"

  • Method Details

    • getSamRecordIndex

      public htsjdk.samtools.util.SamRecordWithOrdinal getSamRecordIndex()
      A number of convenience functions

    • getRecord

      public htsjdk.samtools.SAMRecord getRecord()

    • getRecordReadName

      public String getRecordReadName()

    • isPaired

      public boolean isPaired()
      Overrides:
      isPaired in class ReadEnds

    • getReadEndSetForOpticalDuplicates

      public Set<ReadEnds> getReadEndSetForOpticalDuplicates()
      Gets the read ends for optical duplicate tracking

    • getLocationSet

      public PhysicalLocationForMateCigarSet getLocationSet()

    • removeLocationSet

      public PhysicalLocationForMateCigarSet removeLocationSet()

    • setLocationSet

      public void setLocationSet(PhysicalLocationForMateCigarSet locationSet)