picard.illumina

Class CollectIlluminaBasecallingMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.CollectIlluminaBasecallingMetrics

@DocumentedFeature
public class CollectIlluminaBasecallingMetrics
extends CommandLineProgram

A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect. Outputs metrics:

• Mean Clusters Per Tile
• Standard Deviation of Clusters Per Tile
• Mean Pf Clusters Per Tile
• Standard Deviation of Pf Clusters Per Tile
• Mean Percentage of Pf Clusters Per Tile
• Standard Deviation of Percentage of Pf Clusters Per Tile

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	BARCODES_DIR
java.io.File	BASECALLS_DIR
java.io.File	INPUT
java.lang.Integer	LANE
java.io.File	OUTPUT
java.lang.String	READ_STRUCTURE

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectIlluminaBasecallingMetrics()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

BASECALLS_DIR

@Argument(doc="The Illumina basecalls output directory from which data are read",
          shortName="B")
public java.io.File BASECALLS_DIR

BARCODES_DIR

@Argument(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ",
          shortName="BCD",
          optional=true)
public java.io.File BARCODES_DIR

LANE

@Argument(doc="The lane whose data will be read",
          shortName="L")
public java.lang.Integer LANE

INPUT

@Argument(doc="The file containing barcodes to expect from the run - barcodeData.#",
          shortName="I",
          optional=true)
public java.io.File INPUT

READ_STRUCTURE

@Argument(doc="A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the  data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip).  E.g. If the input data consists of 80 base clusters and we provide a read structure of \"28T8M8B8S28T\" then the sequence may be split up into four reads:\n* read one with 28 cycles (bases) of template\n* read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode)\n* read three with 8 cycles (bases) of sample barcode\n* 8 cycles (bases) skipped.\n* read four with 28 cycles (bases) of template\nThe skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein.",
          shortName="RS")
public java.lang.String READ_STRUCTURE

OUTPUT

@Argument(doc="The file to which the collected metrics are written",
          shortName="O",
          optional=true)
public java.io.File OUTPUT

Constructor Detail

CollectIlluminaBasecallingMetrics

public CollectIlluminaBasecallingMetrics()

Method Detail

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.