public class CollectIlluminaBasecallingMetrics extends CommandLineProgram
Modifier and Type | Field and Description |
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File |
BASECALLS_DIR |
File |
INPUT |
Integer |
LANE |
File |
OUTPUT |
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(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 File BASECALLS_DIR
@Option(doc="The file containing barcodes to expect from the run - barcodeData.#", shortName="I", optional=true) public 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 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 \"36T8B8S28T\" then, before being converted to SAM records those bases will be split into 4 reads where read one consists of 36 cycles of template, read two consists of 8 cycles of barcode, read three will be an 8 base read of skipped cycles and read four is another 28 cycle template read. The read consisting of skipped cycles would NOT be included in output SAM/BAM file read groups.", shortName="RS") public String READ_STRUCTURE
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
public static void main(String[] argv)