picard.illumina

Class CheckIlluminaDirectory

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.CheckIlluminaDirectory

@DocumentedFeature
public class CheckIlluminaDirectory
extends CommandLineProgram

Program to check a lane of an Illumina output directory. This program checks that files exist, are non-zero in length, for every tile/cycle and specified data type. If NO data type is specified then the default data types used by IlluminaBasecallsToSam are used.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	BASECALLS_DIR
java.util.Set<IlluminaDataType>	DATA_TYPES
java.lang.Boolean	FAKE_FILES
java.util.List<java.lang.Integer>	LANES
java.lang.Boolean	LINK_LOCS Deprecated. It is no longer necessary to create locs file symlinks.
java.lang.String	READ_STRUCTURE
java.util.List<java.lang.Integer>	TILE_NUMBERS

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

Constructor Summary

Constructors

Constructor and Description
CheckIlluminaDirectory()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BASECALLS_DIR

@Argument(doc="The basecalls output directory. ",
          shortName="B")
public java.io.File BASECALLS_DIR

DATA_TYPES

@Argument(doc="The data types that should be checked for each tile/cycle.  If no values are provided then the data types checked are those required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes).  These data types vary slightly depending on whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam.  If this option is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the individual records of the files themselves are spurious.",
          shortName="DT",
          optional=true)
public java.util.Set<IlluminaDataType> DATA_TYPES

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. Note:  If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run.",
          shortName="RS")
public java.lang.String READ_STRUCTURE

LANES

@Argument(doc="The number of the lane(s) to check. ",
          shortName="L",
          minElements=1)
public java.util.List<java.lang.Integer> LANES

TILE_NUMBERS

@Argument(doc="The number(s) of the tile(s) to check. ",
          shortName="T",
          optional=true)
public java.util.List<java.lang.Integer> TILE_NUMBERS

FAKE_FILES

@Argument(doc="A flag to determine whether or not to create fake versions of the missing files.",
          shortName="F",
          optional=true)
public java.lang.Boolean FAKE_FILES

LINK_LOCS

@Deprecated
 @Argument(doc="A flag to create symlinks to the loc file for the X Ten for each tile. @deprecated It is no longer necessary to create locs file symlinks.",
          shortName="X",
          optional=true)
public java.lang.Boolean LINK_LOCS

Deprecated. It is no longer necessary to create locs file symlinks.

Constructor Detail

CheckIlluminaDirectory

public CheckIlluminaDirectory()

Method Detail

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 class CommandLineProgram

Returns:

program exit status.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.