Package picard.illumina
Class IlluminaBasecallingMetrics
- java.lang.Object
-
- htsjdk.samtools.metrics.MetricBase
-
- picard.illumina.IlluminaBasecallingMetrics
-
@DocumentedFeature(groupName="Metrics", summary="Metrics") 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 Description 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.String
MOLECULAR_BARCODE_NAME
The barcode name for which the metrics were calculated.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 Description IlluminaBasecallingMetrics()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
toString()
-
-
-
Field Detail
-
LANE
public String LANE
The lane for which the metrics were calculated.
-
MOLECULAR_BARCODE_SEQUENCE_1
public String MOLECULAR_BARCODE_SEQUENCE_1
The barcode sequence for which the metrics were calculated.
-
MOLECULAR_BARCODE_NAME
public 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.
-
-
Method Detail
-
toString
public String toString()
- Overrides:
toString
in classhtsjdk.samtools.metrics.MetricBase
-
-