Package picard.sam.SamErrorMetric
Class OverlappingReadsErrorCalculator
- java.lang.Object
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- picard.sam.SamErrorMetric.BaseErrorCalculator
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- picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
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- All Implemented Interfaces:
BaseCalculator
public class OverlappingReadsErrorCalculator extends BaseErrorCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth. This calculator only includes bases that have been read twice in the same template (once from each read) and thus only includes bases that arise from the overlapping part of the reads. Over those bases the Calculator distinguishes between whether the two reads agree with each other but differ from the reference (indicative of a difference between the template and the reference, and when one of the reads agrees with the reference but the other does not which indicates that there might have been a sequencing error in that read.
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Constructor Summary
Constructors Constructor Description OverlappingReadsErrorCalculator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
The function by which new loci are "shown" to the calculatorOverlappingErrorMetric
getMetric()
Returns the metric generated by the observed lociString
getSuffix()
The suffix that pertains to the implementation of aggregation
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Method Detail
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addBase
public void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
The function by which new loci are "shown" to the calculator- Specified by:
addBase
in interfaceBaseCalculator
- Overrides:
addBase
in classBaseErrorCalculator
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getSuffix
public String getSuffix()
The suffix that pertains to the implementation of aggregation
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getMetric
public OverlappingErrorMetric getMetric()
Returns the metric generated by the observed loci
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