picard.illumina

Class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector

java.lang.Object

picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector

Enclosing class:

CollectIlluminaLaneMetrics

public static class CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
extends java.lang.Object

Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.

Constructor Summary

Constructors

Constructor and Description
IlluminaLaneMetricsCollector()

Method Summary

Modifier and Type	Method and Description
static void	collectLaneMetrics(java.io.File runDirectory, java.io.File outputDirectory, java.lang.String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile, ReadStructure readStructure) Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
static java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>>	readLaneTiles(java.io.File illuminaRunDirectory, ReadStructure readStructure) Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
static java.io.File	writeLaneMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles, java.io.File outputDirectory, java.lang.String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile)
static java.io.File	writePhasingMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles, java.io.File outputDirectory, java.lang.String outputPrefix, htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IlluminaLaneMetricsCollector

public IlluminaLaneMetricsCollector()

Method Detail

readLaneTiles

public static java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> readLaneTiles(java.io.File illuminaRunDirectory,
                                                                                                  ReadStructure readStructure)

Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.

collectLaneMetrics

public static void collectLaneMetrics(java.io.File runDirectory,
                                      java.io.File outputDirectory,
                                      java.lang.String outputPrefix,
                                      htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile,
                                      htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile,
                                      ReadStructure readStructure)

Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files

writePhasingMetrics

public static java.io.File writePhasingMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles,
                                               java.io.File outputDirectory,
                                               java.lang.String outputPrefix,
                                               htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> phasingMetricsFile)

writeLaneMetrics

public static java.io.File writeLaneMetrics(java.util.Map<java.lang.Integer,? extends java.util.Collection<Tile>> laneTiles,
                                            java.io.File outputDirectory,
                                            java.lang.String outputPrefix,
                                            htsjdk.samtools.metrics.MetricsFile<htsjdk.samtools.metrics.MetricBase,java.lang.Comparable<?>> laneMetricsFile)