Package picard.illumina
Class CollectIlluminaLaneMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.illumina.CollectIlluminaLaneMetrics
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@DocumentedFeature public class CollectIlluminaLaneMetrics extends CommandLineProgram
Command-line wrapper aroundCollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
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Nested Class Summary
Nested Classes Modifier and Type Class 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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Field Summary
Fields Modifier and Type Field Description String
FILE_EXTENSION
boolean
IS_NOVASEQ
File
OUTPUT_DIRECTORY
String
OUTPUT_PREFIX
ReadStructure
READ_STRUCTURE
File
RUN_DIRECTORY
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Fields inherited from class picard.cmdline.CommandLineProgram
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
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Constructor Summary
Constructors Constructor Description CollectIlluminaLaneMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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RUN_DIRECTORY
@Argument(doc="The Illumina run directory of the run for which the lane metrics are to be generated") public File RUN_DIRECTORY
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OUTPUT_DIRECTORY
@Argument(doc="The directory to which the output file will be written") public File OUTPUT_DIRECTORY
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OUTPUT_PREFIX
@Argument(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
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READ_STRUCTURE
@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
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FILE_EXTENSION
@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 String FILE_EXTENSION
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IS_NOVASEQ
@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
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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