picard.analysis

Class RrbsCpgDetailMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.metrics.MultilevelMetrics

picard.analysis.RrbsCpgDetailMetrics

public final class RrbsCpgDetailMetrics
extends MultilevelMetrics

Holds information about CpG sites encountered for RRBS processing QC

Author:

jgentry

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.Integer	CONVERTED_SITES Number of times this CpG site was converted (TG for + strand, CA for - strand)
java.lang.Double	PCT_CONVERTED CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
java.lang.Integer	POSITION Position within the sequence of the CpG site
java.lang.String	SEQUENCE_NAME Sequence the CpG is seen in
java.lang.Integer	TOTAL_SITES Number of times this CpG site was encountered

Fields inherited from class picard.metrics.MultilevelMetrics

LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors

Constructor and Description
RrbsCpgDetailMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

SEQUENCE_NAME

public java.lang.String SEQUENCE_NAME

Sequence the CpG is seen in

POSITION

public java.lang.Integer POSITION

Position within the sequence of the CpG site

TOTAL_SITES

public java.lang.Integer TOTAL_SITES

Number of times this CpG site was encountered

CONVERTED_SITES

public java.lang.Integer CONVERTED_SITES

Number of times this CpG site was converted (TG for + strand, CA for - strand)

PCT_CONVERTED

public java.lang.Double PCT_CONVERTED

CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)

Constructor Detail

RrbsCpgDetailMetrics

public RrbsCpgDetailMetrics()