UmiMetrics (picard 2.18.2 API)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.sam.markduplicates.UmiMetrics

```
public class UmiMetrics
extends htsjdk.samtools.metrics.MetricBase
```
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.

Field Summary

Fields
Modifier and Type	Field	Description
`long`	`DUPLICATE_SETS_IGNORING_UMI`	Number of duplicate sets found before taking UMIs into account
`long`	`DUPLICATE_SETS_WITH_UMI`	Number of duplicate sets found after taking UMIs into account
`double`	`INFERRED_UMI_ENTROPY`	Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.
`long`	`INFERRED_UNIQUE_UMIS`	Number of different inferred UMI sequences derived
`double`	`MEAN_UMI_LENGTH`	Number of bases in each UMI
`long`	`OBSERVED_BASE_ERRORS`	Number of errors inferred by comparing the observed and inferred UMIs
`double`	`OBSERVED_UMI_ENTROPY`	Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.
`long`	`OBSERVED_UNIQUE_UMIS`	Number of different UMI sequences observed
`double`	`PCT_UMI_WITH_N`	The percentage of reads that contain an UMI that contains at least one N
`double`	`UMI_BASE_QUALITIES`	Estimation of Phred scaled quality scores for UMIs

Constructor Summary

Constructors
Constructor	Description
`UmiMetrics()`
`UmiMetrics(double length, int observedUniqueUmis, int inferredUniqueUmis, int observedBaseErrors, int duplicateSetsWithoutUmi, int duplicateSetsWithUmi, double effectiveLengthOfInferredUmis, double effectiveLengthOfObservedUmis, double estimatedBaseQualityOfUmis, double percentUmiWithN)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addUmiObservation(String observedUmi, String inferredUmi)`	Add an observation of a UMI to the metrics
`void`	`addUmiObservationN()`	Add an observation of a UMI containing at least one N to the metrics
`void`	`calculateDerivedFields()`

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
  - MEAN_UMI_LENGTH
```
public double MEAN_UMI_LENGTH
```
    Number of bases in each UMI
  - OBSERVED_UNIQUE_UMIS
```
public long OBSERVED_UNIQUE_UMIS
```
    Number of different UMI sequences observed
  - INFERRED_UNIQUE_UMIS
```
public long INFERRED_UNIQUE_UMIS
```
    Number of different inferred UMI sequences derived
  - OBSERVED_BASE_ERRORS
```
public long OBSERVED_BASE_ERRORS
```
    Number of errors inferred by comparing the observed and inferred UMIs
  - DUPLICATE_SETS_IGNORING_UMI
```
public long DUPLICATE_SETS_IGNORING_UMI
```
    Number of duplicate sets found before taking UMIs into account
  - DUPLICATE_SETS_WITH_UMI
```
public long DUPLICATE_SETS_WITH_UMI
```
    Number of duplicate sets found after taking UMIs into account
  - OBSERVED_UMI_ENTROPY
```
public double OBSERVED_UMI_ENTROPY
```
    Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly.
  - INFERRED_UMI_ENTROPY
```
public double INFERRED_UMI_ENTROPY
```
    Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs. If this is significantly smaller than UMI_LENGTH, it indicates that the UMIs are not distributed uniformly.
  - UMI_BASE_QUALITIES
```
public double UMI_BASE_QUALITIES
```
    Estimation of Phred scaled quality scores for UMIs
  - PCT_UMI_WITH_N
```
public double PCT_UMI_WITH_N
```
    The percentage of reads that contain an UMI that contains at least one N
- Constructor Detail
  - UmiMetrics
```
public UmiMetrics()
```
  - UmiMetrics
```
public UmiMetrics(double length,
                  int observedUniqueUmis,
                  int inferredUniqueUmis,
                  int observedBaseErrors,
                  int duplicateSetsWithoutUmi,
                  int duplicateSetsWithUmi,
                  double effectiveLengthOfInferredUmis,
                  double effectiveLengthOfObservedUmis,
                  double estimatedBaseQualityOfUmis,
                  double percentUmiWithN)
```
- Method Detail
  - calculateDerivedFields
```
public void calculateDerivedFields()
```
  - addUmiObservation
```
public void addUmiObservation(String observedUmi,
                              String inferredUmi)
```
    Add an observation of a UMI to the metrics
    
    Parameters:
    
    observedUmi - String containing the observed UMI
    
    inferredUmi - String containing the UMI inferred after error correcting the observed UMI
  - addUmiObservationN
```
public void addUmiObservationN()
```
    Add an observation of a UMI containing at least one N to the metrics

Class UmiMetrics

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

MEAN_UMI_LENGTH

OBSERVED_UNIQUE_UMIS

INFERRED_UNIQUE_UMIS

OBSERVED_BASE_ERRORS

DUPLICATE_SETS_IGNORING_UMI

DUPLICATE_SETS_WITH_UMI

OBSERVED_UMI_ENTROPY

INFERRED_UMI_ENTROPY

UMI_BASE_QUALITIES

PCT_UMI_WITH_N

Constructor Detail

UmiMetrics

UmiMetrics

Method Detail

calculateDerivedFields

addUmiObservation

addUmiObservationN