picard.sam.SamErrorMetric

Class ReadBaseStratification.NsInReadStratifier

java.lang.Object

picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier

All Implemented Interfaces:

ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Integer>

Enclosing class:

ReadBaseStratification

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

Stratify by the number of Ns found in the read. This is particularly useful for data that has been consensus-called (a process that can add 'N' bases when there is no consensus)

Constructor Summary

Constructors

Constructor and Description
NsInReadStratifier()

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 sam)

Methods inherited from class java.lang.Object

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

Constructor Detail

NsInReadStratifier

public NsInReadStratifier()

Method Detail

stratify

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

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>>