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