# Package picard.sam.SamErrorMetric

package picard.sam.SamErrorMetric

Related Packages
Package
Description
picard.sam
picard.sam.markduplicates
picard.sam.util
Class
Description
BaseCalculator
An interface that can take a collection of bases (provided as `SamLocusIterator.RecordAndOffset` and `SamLocusAndReferenceIterator.SAMLocusAndReference`) and generates a `ErrorMetric` from them.
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.Consensus
Types of consensus reads as determined by the number of duplicates used from first and second strands.
ReadBaseStratification.ConsensusStratifier
Stratify by tags used during duplex and single index consensus calling.
ReadBaseStratification.CycleBin
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
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.LongShortHomopolymer
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.PairOrientation
An enum for holding a reads read-pair's Orientation (i.e.
ReadBaseStratification.PairStratifier<T extends Comparable<T>, R extends Comparable<R>>
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
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
ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>
The main interface for a stratifier.
SimpleErrorCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.