Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- 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_READSdouble
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 examinedString
TILE
The Tile that is described by this metric.
-
Constructor Summary
Constructors Constructor Description PFFailSummaryMetric()
This ctor is necessary for when reading metrics from filePFFailSummaryMetric(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.
-
-
-
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()
-
-