Package picard.illumina
Class CollectIlluminaBasecallingMetrics
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- picard.cmdline.CommandLineProgram
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- picard.illumina.CollectIlluminaBasecallingMetrics
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@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
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Field Summary
Fields Modifier and Type Field Description File
BARCODES_DIR
File
BASECALLS_DIR
File
INPUT
Integer
LANE
File
OUTPUT
String
READ_STRUCTURE
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectIlluminaBasecallingMetrics()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.static void
main(String[] argv)
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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BASECALLS_DIR
@Argument(doc="The Illumina basecalls output directory from which data are read", shortName="B") public File BASECALLS_DIR
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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
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LANE
@Argument(doc="The lane whose data will be read", shortName="L") public Integer 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
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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
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OUTPUT
@Argument(doc="The file to which the collected metrics are written", shortName="O", optional=true) public File OUTPUT
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Method Detail
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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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main
public static void main(String[] argv)
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