Package picard.sam.SamErrorMetric
Class IndelErrorCalculator
java.lang.Object
picard.sam.SamErrorMetric.BaseErrorCalculator
picard.sam.SamErrorMetric.IndelErrorCalculator
- All Implemented Interfaces:
BaseCalculator
A calculator that estimates the error rate of the bases it observes for indels only.
-
Field Summary
FieldsModifier and TypeFieldDescriptionprotected long
Total number of deleted basesprotected long
Total number of deletionsprotected long
Total number of inserted basesprotected long
Total number of inserts -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addBase
(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) the function by which new loci are "shown" to the calculatorReturns the metric generated by the observed lociThe suffix that pertains to the implementation of aggregation
-
Field Details
-
nInsertions
protected long nInsertionsTotal number of inserts -
nInsertedBases
protected long nInsertedBasesTotal number of inserted bases -
nDeletions
protected long nDeletionsTotal number of deletions -
nDeletedBases
protected long nDeletedBasesTotal number of deleted bases
-
-
Constructor Details
-
IndelErrorCalculator
public IndelErrorCalculator()
-
-
Method Details
-
addBase
public void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) Description copied from class:BaseErrorCalculator
the function by which new loci are "shown" to the calculator- Specified by:
addBase
in interfaceBaseCalculator
- Overrides:
addBase
in classBaseErrorCalculator
-
getSuffix
The suffix that pertains to the implementation of aggregation -
getMetric
Returns the metric generated by the observed loci
-