Package picard.illumina

Class CollectIlluminaLaneMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.CollectIlluminaLaneMetrics

@DocumentedFeature
public class CollectIlluminaLaneMetrics
extends CommandLineProgram

Command-line wrapper around CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector	Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.

Field Summary

Fields

Modifier and Type	Field	Description
String	FILE_EXTENSION
File	OUTPUT_DIRECTORY
String	OUTPUT_PREFIX
ReadStructure	READ_STRUCTURE
File	RUN_DIRECTORY

Fields inherited from class picard.cmdline.CommandLineProgram

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

Constructor Summary

Constructors

Constructor	Description
CollectIlluminaLaneMetrics()

Method Summary

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

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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 Details

RUN_DIRECTORY

@Argument(doc="The Illumina run directory of the run for which the lane metrics are to be generated")
public File RUN_DIRECTORY

OUTPUT_DIRECTORY

@Argument(doc="The directory to which the output file will be written")
public File OUTPUT_DIRECTORY

OUTPUT_PREFIX

@Argument(doc="The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied",
          shortName="O")
public String OUTPUT_PREFIX

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.\nIf not given, will use the RunInfo.xml in the run directory.",
          shortName="RS",
          optional=true)
public ReadStructure READ_STRUCTURE

FILE_EXTENSION

@Argument(doc="Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null",
          shortName="EXT",
          optional=true)
public String FILE_EXTENSION

Constructor Details

CollectIlluminaLaneMetrics

public CollectIlluminaLaneMetrics()

Method Details

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.