picard.sam.SamErrorMetric (picard 2.26.10 API)

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

Package picard.sam.SamErrorMetric