java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric

Enclosing class:

CollectHiSeqXPfFailMetrics
```
public static class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
extends htsjdk.samtools.metrics.MetricBase
```
Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF. Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)

Field Summary

Fields
Modifier and Type	Field	Description
`double`	`PCT_PF_FAIL_EMPTY`	The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
`double`	`PCT_PF_FAIL_MISALIGNED`	The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
`double`	`PCT_PF_FAIL_POLYCLONAL`	The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
`double`	`PCT_PF_FAIL_READS`	The fraction of PF_READS
`double`	`PCT_PF_FAIL_UNKNOWN`	The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
`int`	`PF_FAIL_EMPTY`	The number of non-PF reads in this tile that are deemed empty.
`int`	`PF_FAIL_MISALIGNED`	The number of non-PF reads in this tile that are deemed "misaligned".
`int`	`PF_FAIL_POLYCLONAL`	The number of non-PF reads in this tile that are deemed multiclonal.
`int`	`PF_FAIL_READS`	The number of non-PF reads in this tile.
`int`	`PF_FAIL_UNKNOWN`	The number of non-PF reads in this tile that have not been classified.
`int`	`READS`	The total number of reads examined
`String`	`TILE`	The Tile that is described by this metric.

Constructor Summary

Constructors
Constructor Description

PFFailSummaryMetric()
This ctor is necessary for when reading metrics from file

PFFailSummaryMetric(String tile)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calculateDerivedFields()`
`void`	`merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric)`	Adds the non-calculated fields from the other metric to this one.

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
  - TILE
```
public String TILE
```
    The Tile that is described by this metric. Can be a string (like "All") to mean some marginal over tiles. *
  - READS
```
public int READS
```
    The total number of reads examined
  - PF_FAIL_READS
```
public int PF_FAIL_READS
```
    The number of non-PF reads in this tile.
  - PCT_PF_FAIL_READS
```
public double PCT_PF_FAIL_READS
```
    The fraction of PF_READS
  - PF_FAIL_EMPTY
```
public int PF_FAIL_EMPTY
```
    The number of non-PF reads in this tile that are deemed empty.
  - PCT_PF_FAIL_EMPTY
```
public double PCT_PF_FAIL_EMPTY
```
    The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
  - PF_FAIL_POLYCLONAL
```
public int PF_FAIL_POLYCLONAL
```
    The number of non-PF reads in this tile that are deemed multiclonal.
  - PCT_PF_FAIL_POLYCLONAL
```
public double PCT_PF_FAIL_POLYCLONAL
```
    The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
  - PF_FAIL_MISALIGNED
```
public int PF_FAIL_MISALIGNED
```
    The number of non-PF reads in this tile that are deemed "misaligned".
  - PCT_PF_FAIL_MISALIGNED
```
public double PCT_PF_FAIL_MISALIGNED
```
    The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
  - PF_FAIL_UNKNOWN
```
public int PF_FAIL_UNKNOWN
```
    The number of non-PF reads in this tile that have not been classified.
  - PCT_PF_FAIL_UNKNOWN
```
public double PCT_PF_FAIL_UNKNOWN
```
    The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
- Constructor Detail
  - PFFailSummaryMetric
```
public PFFailSummaryMetric(String tile)
```
  - PFFailSummaryMetric
```
public PFFailSummaryMetric()
```
    This ctor is necessary for when reading metrics from file
- Method Detail
  - merge
```
public void merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric)
```
    Adds the non-calculated fields from the other metric to this one.
    
    Parameters:
    
    metric -
  - calculateDerivedFields
```
public void calculateDerivedFields()
```

Constructor	Description
`PFFailSummaryMetric()`	This ctor is necessary for when reading metrics from file
`PFFailSummaryMetric(String tile)`

Class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric

Field Summary

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

TILE

READS

PF_FAIL_READS

PCT_PF_FAIL_READS

PF_FAIL_EMPTY

PCT_PF_FAIL_EMPTY

PF_FAIL_POLYCLONAL

PCT_PF_FAIL_POLYCLONAL

PF_FAIL_MISALIGNED

PCT_PF_FAIL_MISALIGNED

PF_FAIL_UNKNOWN

PCT_PF_FAIL_UNKNOWN

Constructor Detail

PFFailSummaryMetric

PFFailSummaryMetric

Method Detail

merge

calculateDerivedFields