@DocumentedFeature public class CollectIlluminaBasecallingMetrics extends CommandLineProgram
| Modifier and Type | Field | Description |
|---|---|---|
File |
BARCODES_DIR |
|
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, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
CollectIlluminaBasecallingMetrics() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(doc="The Illumina basecalls output directory from which data are read",
shortName="B")
public File BASECALLS_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
@Argument(doc="The lane whose data will be read",
shortName="L")
public Integer LANE
@Argument(doc="The file containing barcodes to expect from the run - barcodeData.#",
shortName="I",
optional=true)
public File INPUT
@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
@Argument(doc="The file to which the collected metrics are written",
shortName="O",
optional=true)
public File OUTPUT
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgrampublic static void main(String[] argv)