public class CollectIlluminaLaneMetrics extends CommandLineProgram
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector.| Modifier and Type | Class and Description |
|---|---|
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 and Description |
|---|---|
java.io.File |
OUTPUT_DIRECTORY |
java.lang.String |
OUTPUT_PREFIX |
ReadStructure |
READ_STRUCTURE |
java.io.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 and Description |
|---|
CollectIlluminaLaneMetrics() |
| Modifier and Type | Method and Description |
|---|---|
protected int |
doWork()
Do the work after command line has been parsed.
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static void |
main(java.lang.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 java.io.File RUN_DIRECTORY
@Option(doc="The directory to which the output file will be written") public java.io.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 java.lang.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 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 ReadStructure READ_STRUCTURE
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgrampublic static void main(java.lang.String[] args)