java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.MergeableMetricBase
  - - picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics

Direct Known Subclasses:

CollectQualityYieldMetrics.QualityYieldMetricsFlow

Enclosing class:

CollectQualityYieldMetrics
```
@DocumentedFeature(groupName="Metrics",
                   summary="Metrics")
public static class CollectQualityYieldMetrics.QualityYieldMetrics
extends MergeableMetricBase
```
A set of metrics used to describe the general quality of a BAM file

Nested Class Summary
- Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
  MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

Field Summary

Fields
Modifier and Type	Field	Description
`long`	`PF_BASES`	The total number of bases in all PF reads
`long`	`PF_Q20_BASES`	The number of bases in PF reads that achieve quality score 20 or higher
`long`	`PF_Q20_EQUIVALENT_YIELD`	The sum of quality scores of all bases in PF reads divided by 20
`long`	`PF_Q30_BASES`	The number of bases in PF reads that achieve quality score 30 or higher
`long`	`PF_READS`	The number of reads that are PF - pass filter
`long`	`Q20_BASES`	The number of bases in all reads that achieve quality score 20 or higher
`long`	`Q20_EQUIVALENT_YIELD`	The sum of quality scores of all bases divided by 20
`long`	`Q30_BASES`	The number of bases in all reads that achieve quality score 30 or higher
`int`	`READ_LENGTH`	The average read length of all the reads
`long`	`TOTAL_BASES`	The total number of bases in all reads
`long`	`TOTAL_READS`	The total number of reads in the input file
`protected boolean`	`useOriginalQualities`

Constructor Summary

Constructors
Constructor Description

QualityYieldMetrics()

QualityYieldMetrics(boolean useOriginalQualities)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calculateDerivedFields()`	Placeholder method that will calculate the derived fields from the other ones.
`MergeableMetricBase`	`merge(MergeableMetricBase other)`	Merge another metric into this one

Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, mergeIfCan

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
  - TOTAL_READS
```
public long TOTAL_READS
```
    The total number of reads in the input file
  - PF_READS
```
public long PF_READS
```
    The number of reads that are PF - pass filter
  - READ_LENGTH
```
public int READ_LENGTH
```
    The average read length of all the reads
  - TOTAL_BASES
```
public long TOTAL_BASES
```
    The total number of bases in all reads
  - PF_BASES
```
public long PF_BASES
```
    The total number of bases in all PF reads
  - Q20_BASES
```
public long Q20_BASES
```
    The number of bases in all reads that achieve quality score 20 or higher
  - PF_Q20_BASES
```
public long PF_Q20_BASES
```
    The number of bases in PF reads that achieve quality score 20 or higher
  - Q30_BASES
```
public long Q30_BASES
```
    The number of bases in all reads that achieve quality score 30 or higher
  - PF_Q30_BASES
```
public long PF_Q30_BASES
```
    The number of bases in PF reads that achieve quality score 30 or higher
  - Q20_EQUIVALENT_YIELD
```
public long Q20_EQUIVALENT_YIELD
```
    The sum of quality scores of all bases divided by 20
  - PF_Q20_EQUIVALENT_YIELD
```
public long PF_Q20_EQUIVALENT_YIELD
```
    The sum of quality scores of all bases in PF reads divided by 20
  - useOriginalQualities
```
protected final boolean useOriginalQualities
```
- Constructor Detail
  - QualityYieldMetrics
```
public QualityYieldMetrics()
```
  - QualityYieldMetrics
```
public QualityYieldMetrics(boolean useOriginalQualities)
```
- Method Detail
  - calculateDerivedFields
```
public void calculateDerivedFields()
```
    Description copied from class: MergeableMetricBase
    
    Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
    
    Overrides:
    
    calculateDerivedFields in class MergeableMetricBase
  - merge
```
public MergeableMetricBase merge(MergeableMetricBase other)
```
    Description copied from class: MergeableMetricBase
    
    Merge another metric into this one
    
    Overrides:
    
    merge in class MergeableMetricBase
    
    Parameters:
    
    other - metric to merge into this one.

Constructor	Description
`QualityYieldMetrics()`
`QualityYieldMetrics(boolean useOriginalQualities)`

Class CollectQualityYieldMetrics.QualityYieldMetrics

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

Field Summary

Constructor Summary

Method Summary

Methods inherited from class picard.analysis.MergeableMetricBase

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

TOTAL_READS

PF_READS

READ_LENGTH

TOTAL_BASES

PF_BASES

Q20_BASES

PF_Q20_BASES

Q30_BASES

PF_Q30_BASES

Q20_EQUIVALENT_YIELD

PF_Q20_EQUIVALENT_YIELD

useOriginalQualities

Constructor Detail

QualityYieldMetrics

QualityYieldMetrics

Method Detail

calculateDerivedFields

merge