Class ReadBaseStratification.IndelsInReadStratifier

java.lang.Object
picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
All Implemented Interfaces:
ReadBaseStratification.RecordAndOffsetStratifier<Integer>
Enclosing class:
ReadBaseStratification

public static class ReadBaseStratification.IndelsInReadStratifier extends Object
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
  • Constructor Details

    • IndelsInReadStratifier

      public IndelsInReadStratifier()
  • Method Details

    • stratify

      public Integer stratify(htsjdk.samtools.SAMRecord samRecord)
      Returns the number of bases associated with I and D CIGAR elements.
      Parameters:
      samRecord - The read to investigate
      Returns:
      The number of bases associated with I and D CIGAR elements, or null if the evaluation of either operation caused an error
    • getSuffix

      public String getSuffix()
    • stratify

      public Integer stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
      Specified by:
      stratify in interface ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>