public class CollectIlluminaBasecallingMetrics extends CommandLineProgram
Modifier and Type | Field and Description |
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java.io.File |
BASECALLS_DIR |
java.io.File |
INPUT |
java.lang.Integer |
LANE |
java.io.File |
OUTPUT |
java.lang.String |
READ_STRUCTURE |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectIlluminaBasecallingMetrics() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The Illumina basecalls output directory from which data are read", shortName="B") public java.io.File BASECALLS_DIR
@Option(doc="The file containing barcodes to expect from the run - barcodeData.#", shortName="I", optional=true) public java.io.File INPUT
@Option(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
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
public static void main(java.lang.String[] argv)