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, java.lang.String fileExtension, htsjdk.samtools.ValidationStringency validationStringency, boolean isNovaSeq) 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, htsjdk.samtools.ValidationStringency validationStringency, boolean isNovaSeq) 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, java.lang.String fileExtension)
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, java.lang.String fileExtension, boolean isNovaSeq)

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,
                                                                                                  htsjdk.samtools.ValidationStringency validationStringency,
                                                                                                  boolean isNovaSeq)

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,
                                      java.lang.String fileExtension,
                                      htsjdk.samtools.ValidationStringency validationStringency,
                                      boolean isNovaSeq)

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,
                                               java.lang.String fileExtension,
                                               boolean isNovaSeq)

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,
                                            java.lang.String fileExtension)