picard.sam.SamErrorMetric

Class ReadBaseStratification.CigarOperatorsInReadStratifier

java.lang.Object

picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier

All Implemented Interfaces:

ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>

Enclosing class:

ReadBaseStratification

public static class ReadBaseStratification.CigarOperatorsInReadStratifier
extends java.lang.Object

Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.

Constructor Summary

Constructors

Constructor and Description
CigarOperatorsInReadStratifier(htsjdk.samtools.CigarOperator op)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getSuffix()
T	stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
java.lang.Integer	stratify(htsjdk.samtools.SAMRecord samRecord)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CigarOperatorsInReadStratifier

public CigarOperatorsInReadStratifier(htsjdk.samtools.CigarOperator op)

Method Detail

stratify

public java.lang.Integer stratify(htsjdk.samtools.SAMRecord samRecord)

getSuffix

public java.lang.String getSuffix()

stratify

public T stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset,
                  htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)

Specified by:

stratify in interface ReadBaseStratification.RecordAndOffsetStratifier<T extends java.lang.Comparable<T>>