# Package picard.sam.SamErrorMetric

- Interface Summary
  Interface | Description
  --- | ---
  BaseCalculator | An interface that can take a collection of bases (provided as `SamLocusIterator.RecordAndOffset` and `SamLocusAndReferenceIterator.SAMLocusAndReference`) and generates a `ErrorMetric` from them.
  ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>> | The main interface for a stratifier.

- Class Summary
  Class | Description
  --- | ---
  BaseErrorAggregation<CALCULATOR extends BaseCalculator> | An interface and implementations for classes that apply a `RecordAndOffsetStratifier` to put bases into various "bins" and then compute an `ErrorMetric` on these bases using a `BaseErrorCalculator`.
  BaseErrorCalculator |
  BaseErrorMetric | An error metric for the errors in bases.
  CollectSamErrorMetrics | Program to collect error metrics on bases stratified in various ways.
  ErrorMetric | Created by farjoun on 6/26/18.
  IndelErrorCalculator | A calculator that estimates the error rate of the bases it observes for indels only.
  IndelErrorMetric | Metric to be used for InDel errors
  OverlappingErrorMetric | An error metric for the errors invovling bases in the overlapping region of a read-pair.
  OverlappingReadsErrorCalculator | A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
  ReadBaseStratification | Classes, methods, and enums that deal with the stratification of read bases and reference information.
  ReadBaseStratification.BinnedReadCycleStratifier | Stratifies into quintiles of read cycle.
  ReadBaseStratification.CigarOperatorsInReadStratifier | Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
  ReadBaseStratification.CollectionStratifier | A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
  ReadBaseStratification.ConsensusStratifier | Stratify by tags used during duplex and single index consensus calling.
  ReadBaseStratification.FlowCellTileStratifier | Stratifies base into their read's tile which is parsed from the read-name.
  ReadBaseStratification.FlowCellXStratifier | Stratifies base into their read's X coordinate which is parsed from the read-name.
  ReadBaseStratification.FlowCellYStratifier | Stratifies base into their read's Y coordinate which is parsed from the read-name.
  ReadBaseStratification.GCContentStratifier | A stratifier that uses GC (of the read) to stratify.
  ReadBaseStratification.IndelLengthStratifier | Stratifies according to the length of an insertion or deletion.
  ReadBaseStratification.IndelsInReadStratifier | Stratifies according to the number of indel bases (from CIGAR string) that the read has.
  ReadBaseStratification.LongShortHomopolymerStratifier | Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
  ReadBaseStratification.MismatchesInReadStratifier | Stratifies according to the overall mismatches (from `SAMTag.NM`) that the read has against the reference, NOT including the current base.
  ReadBaseStratification.NsInReadStratifier | Stratify by the number of Ns found in the read.
  ReadBaseStratification.PairStratifier<T extends Comparable<T>,​R extends Comparable<R>> | A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
  SimpleErrorCalculator | A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.

- Enum Summary
  Enum | Description
  --- | ---
  ReadBaseStratification.Consensus | Types of consensus reads as determined by the number of duplicates used from first and second strands.
  ReadBaseStratification.CycleBin | An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
  ReadBaseStratification.LongShortHomopolymer |
  ReadBaseStratification.PairOrientation | An enum for holding a reads read-pair's Orientation (i.e.
  ReadBaseStratification.ProperPaired | An enum to hold information about the "properness" of a read pair
  ReadBaseStratification.ReadDirection | An enum for holding the direction for a read (positive strand or negative strand
  ReadBaseStratification.ReadOrdinality | An enum to hold the ordinality of a read