Package picard.illumina
Class CollectIlluminaBasecallingMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.illumina.CollectIlluminaBasecallingMetrics
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
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Field Summary
FieldsModifier and TypeFieldDescriptionFields 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected 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
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Field Details
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BASECALLS_DIR
@Argument(doc="The Illumina basecalls output directory from which data are read", shortName="B") public 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 File BARCODES_DIR -
LANE
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INPUT
@Argument(doc="The file containing barcodes to expect from the run - barcodeData.#", shortName="I", optional=true) public 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 String READ_STRUCTURE -
OUTPUT
@Argument(doc="The file to which the collected metrics are written", shortName="O", optional=true) public File OUTPUT
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Constructor Details
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CollectIlluminaBasecallingMetrics
public CollectIlluminaBasecallingMetrics()
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Method Details
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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 classCommandLineProgram
- Returns:
- program exit status.
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