public static class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
extends htsjdk.samtools.metrics.MetricBase
Modifier and Type | Field and 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
|
java.lang.String |
TILE
The Tile that is described by this metric.
|
Constructor and Description |
---|
PFFailSummaryMetric()
This ctor is necessary for when reading metrics from file
|
PFFailSummaryMetric(java.lang.String tile) |
Modifier and Type | Method and Description |
---|---|
void |
calculateDerivedFields() |
void |
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric)
Adds the non-calculated fields from the other metric to this one.
|
public java.lang.String TILE
public int READS
public int PF_FAIL_READS
public double PCT_PF_FAIL_READS
public int PF_FAIL_EMPTY
public double PCT_PF_FAIL_EMPTY
public int PF_FAIL_POLYCLONAL
public double PCT_PF_FAIL_POLYCLONAL
public int PF_FAIL_MISALIGNED
public double PCT_PF_FAIL_MISALIGNED
public int PF_FAIL_UNKNOWN
public double PCT_PF_FAIL_UNKNOWN
public PFFailSummaryMetric(java.lang.String tile)
public PFFailSummaryMetric()
public void merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric)
metric
- public void calculateDerivedFields()