Package picard.sam.SamErrorMetric
package picard.sam.SamErrorMetric
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ClassDescriptionAn interface that can take a collection of bases (provided as
SamLocusIterator.RecordAndOffsetandSamLocusAndReferenceIterator.SAMLocusAndReference) and generates aErrorMetricfrom them.BaseErrorAggregation<CALCULATOR extends BaseCalculator>An interface and implementations for classes that apply aRecordAndOffsetStratifierto put bases into various "bins" and then compute anErrorMetricon these bases using aBaseErrorCalculator.An error metric for the errors in bases.Program to collect error metrics on bases stratified in various ways.Created by farjoun on 6/26/18.A calculator that estimates the error rate of the bases it observes for indels only.Metric to be used for InDel errorsAn error metric for the errors invovling bases in the overlapping region of a read-pair.A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.Classes, methods, and enums that deal with the stratification of read bases and reference information.Stratifies into quintiles of read cycle.Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.Types of consensus reads as determined by the number of duplicates used from first and second strands.Stratify by tags used during duplex and single index consensus calling.An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintilesStratifies base into their read's tile which is parsed from the read-name.Stratifies base into their read's X coordinate which is parsed from the read-name.Stratifies base into their read's Y coordinate which is parsed from the read-name.A stratifier that uses GC (of the read) to stratify.Stratifies according to the length of an insertion or deletion.Stratifies according to the number of indel bases (from CIGAR string) that the read has.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).Stratifies according to the overall mismatches (fromSAMTag.NM) that the read has against the reference, NOT including the current base.Stratify by the number of Ns found in the read.An enum for holding a reads read-pair's Orientation (i.e.A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.An enum to hold information about the "properness" of a read pairAn enum for holding the direction for a read (positive strand or negative strandAn enum to hold the ordinality of a readReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>The main interface for a stratifier.A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.