public class CollectIlluminaLaneMetrics extends CommandLineProgram
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
.Modifier and Type | Class | Description |
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static class |
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector |
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
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Modifier and Type | Field | Description |
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File |
OUTPUT_DIRECTORY |
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String |
OUTPUT_PREFIX |
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ReadStructure |
READ_STRUCTURE |
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File |
RUN_DIRECTORY |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
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CollectIlluminaLaneMetrics() |
Modifier and Type | Method | Description |
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protected int |
doWork() |
Do the work after command line has been parsed.
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static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(doc="The Illumina run directory of the run for which the lane metrics are to be generated") public File RUN_DIRECTORY
@Option(doc="The directory to which the output file will be written") public File OUTPUT_DIRECTORY
@Option(doc="The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied", shortName="O") public String OUTPUT_PREFIX
@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.\nIf not given, will use the RunInfo.xml in the run directory.", shortName="RS", optional=true) public ReadStructure READ_STRUCTURE
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
public static void main(String[] args)