public static class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
extends htsjdk.samtools.metrics.MetricBase
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 | Description |
---|---|
PFFailSummaryMetric() |
This ctor is necessary for when reading metrics from file
|
PFFailSummaryMetric(String tile) |
Modifier and Type | Method | Description |
---|---|---|
void |
calculateDerivedFields() |
|
void |
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric) |
Adds the non-calculated fields from the other metric to this one.
|
public 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(String tile)
public PFFailSummaryMetric()
public void merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric metric)
metric
- public void calculateDerivedFields()