IlluminaBasecallingMetrics (PICARD JDK API Documentation)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.illumina.IlluminaBasecallingMetrics

```
public class IlluminaBasecallingMetrics
extends htsjdk.samtools.metrics.MetricBase
```
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis. Averages and means are taken over all tiles.

Field Summary

Fields
Modifier and Type	Field and Description
`java.lang.String`	`LANE` The lane for which the metrics were calculated.
`double`	`MEAN_CLUSTERS_PER_TILE` The mean number of clusters per tile.
`double`	`MEAN_PCT_PF_CLUSTERS_PER_TILE` The mean percentage of pf clusters per tile.
`double`	`MEAN_PF_CLUSTERS_PER_TILE` The mean number of pf clusters per tile.
`java.lang.String`	`MOLECULAR_BARCODE_NAME` The barcode name for which the metrics were calculated.
`java.lang.String`	`MOLECULAR_BARCODE_SEQUENCE_1` The barcode sequence for which the metrics were calculated.
`long`	`PF_BASES` The total number of passing-filter bases assigned to the index.
`long`	`PF_CLUSTERS` The total number of PF clusters assigned to the index.
`long`	`PF_READS` The total number of passing-filter reads assigned to the index.
`double`	`SD_CLUSTERS_PER_TILE` The standard deviation of clusters per tile.
`double`	`SD_PCT_PF_CLUSTERS_PER_TILE` The standard deviation in percentage of pf clusters per tile.
`double`	`SD_PF_CLUSTERS_PER_TILE` The standard deviation in number of pf clusters per tile.
`long`	`TOTAL_BASES` The total number of bases assigned to the index.
`long`	`TOTAL_CLUSTERS` The total number of clusters assigned to the index.
`long`	`TOTAL_READS` The total number of reads assigned to the index.

Constructor Summary

Constructors
Constructor and Description

IlluminaBasecallingMetrics()

Constructors
Constructor and Description
`IlluminaBasecallingMetrics()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method and Description

java.lang.String toString()
- Methods inherited from class htsjdk.samtools.metrics.MetricBase
  equals, hashCode
- Methods inherited from class java.lang.Object
  clone, finalize, getClass, notify, notifyAll, wait, wait, wait

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`toString()`

- Field Detail
  - LANE
```
public java.lang.String LANE
```
    The lane for which the metrics were calculated.
  - MOLECULAR_BARCODE_SEQUENCE_1
```
public java.lang.String MOLECULAR_BARCODE_SEQUENCE_1
```
    The barcode sequence for which the metrics were calculated.
  - MOLECULAR_BARCODE_NAME
```
public java.lang.String MOLECULAR_BARCODE_NAME
```
    The barcode name for which the metrics were calculated.
  - TOTAL_BASES
```
public long TOTAL_BASES
```
    The total number of bases assigned to the index.
  - PF_BASES
```
public long PF_BASES
```
    The total number of passing-filter bases assigned to the index.
  - TOTAL_READS
```
public long TOTAL_READS
```
    The total number of reads assigned to the index.
  - PF_READS
```
public long PF_READS
```
    The total number of passing-filter reads assigned to the index.
  - TOTAL_CLUSTERS
```
public long TOTAL_CLUSTERS
```
    The total number of clusters assigned to the index.
  - PF_CLUSTERS
```
public long PF_CLUSTERS
```
    The total number of PF clusters assigned to the index.
  - MEAN_CLUSTERS_PER_TILE
```
public double MEAN_CLUSTERS_PER_TILE
```
    The mean number of clusters per tile.
  - SD_CLUSTERS_PER_TILE
```
public double SD_CLUSTERS_PER_TILE
```
    The standard deviation of clusters per tile.
  - MEAN_PCT_PF_CLUSTERS_PER_TILE
```
public double MEAN_PCT_PF_CLUSTERS_PER_TILE
```
    The mean percentage of pf clusters per tile.
  - SD_PCT_PF_CLUSTERS_PER_TILE
```
public double SD_PCT_PF_CLUSTERS_PER_TILE
```
    The standard deviation in percentage of pf clusters per tile.
  - MEAN_PF_CLUSTERS_PER_TILE
```
public double MEAN_PF_CLUSTERS_PER_TILE
```
    The mean number of pf clusters per tile.
  - SD_PF_CLUSTERS_PER_TILE
```
public double SD_PF_CLUSTERS_PER_TILE
```
    The standard deviation in number of pf clusters per tile.
- Constructor Detail
  - IlluminaBasecallingMetrics
```
public IlluminaBasecallingMetrics()
```
- Method Detail
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class htsjdk.samtools.metrics.MetricBase

Class IlluminaBasecallingMetrics

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

LANE

MOLECULAR_BARCODE_SEQUENCE_1

MOLECULAR_BARCODE_NAME

TOTAL_BASES

PF_BASES

TOTAL_READS

PF_READS

TOTAL_CLUSTERS

PF_CLUSTERS

MEAN_CLUSTERS_PER_TILE

SD_CLUSTERS_PER_TILE

MEAN_PCT_PF_CLUSTERS_PER_TILE

SD_PCT_PF_CLUSTERS_PER_TILE

MEAN_PF_CLUSTERS_PER_TILE

SD_PF_CLUSTERS_PER_TILE

Constructor Detail

IlluminaBasecallingMetrics

Method Detail

toString