@DocumentedFeature 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.lang.String |
FILE_EXTENSION |
boolean |
IS_NOVASEQ |
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_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, 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.
|
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(doc="The Illumina run directory of the run for which the lane metrics are to be generated") public java.io.File RUN_DIRECTORY
@Argument(doc="The directory to which the output file will be written") public java.io.File OUTPUT_DIRECTORY
@Argument(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
@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.\nIf not given, will use the RunInfo.xml in the run directory.",
shortName="RS",
optional=true)
public ReadStructure READ_STRUCTURE
@Argument(shortName="EXT",
doc="Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null",
optional=true)
public java.lang.String FILE_EXTENSION
@Argument(doc="Boolean the determines if this run is a NovaSeq run or not. (NovaSeq tile metrics files are in cycle 25 directory.",
optional=true)
public boolean IS_NOVASEQ
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram