picard.illumina

Class IlluminaBasecallsToFastq

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.IlluminaBasecallsToFastq

@DocumentedFeature
public class IlluminaBasecallsToFastq
extends CommandLineProgram

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	IlluminaBasecallsToFastq.ReadNameFormat Simple switch to control the read name format to emit.

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<IlluminaUtil.IlluminaAdapterPair>	ADAPTERS_TO_CHECK Deprecated.
boolean	APPLY_EAMSS_FILTER
java.io.File	BARCODES_DIR
java.io.File	BASECALLS_DIR
boolean	COMPRESS_OUTPUTS
java.lang.Integer	FIRST_TILE
java.lang.String	FLOWCELL_BARCODE
java.lang.Boolean	FORCE_GC
boolean	IGNORE_UNEXPECTED_BARCODES
boolean	INCLUDE_NON_PF_READS
java.lang.Integer	LANE
java.lang.String	MACHINE_NAME
int	MAX_READS_IN_RAM_PER_TILE Deprecated.
int	MINIMUM_QUALITY
java.io.File	MULTIPLEX_PARAMS
java.lang.Integer	NUM_PROCESSORS
java.io.File	OUTPUT_PREFIX
IlluminaBasecallsToFastq.ReadNameFormat	READ_NAME_FORMAT
java.lang.String	READ_STRUCTURE
java.lang.String	RUN_BARCODE
java.lang.Boolean	SORT
java.lang.Integer	TILE_LIMIT

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
IlluminaBasecallsToFastq()

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

checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, 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 directory. ",
          shortName="B")
public java.io.File BASECALLS_DIR

BARCODES_DIR

@Argument(doc="The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR. ",
          shortName="BCD",
          optional=true)
public java.io.File BARCODES_DIR

LANE

@Argument(doc="Lane number. ",
          shortName="L")
public java.lang.Integer LANE

OUTPUT_PREFIX

@Argument(doc="The prefix for output FASTQs.  Extensions as described above are appended.  Use this option for a non-barcoded run, or for a barcoded run in which it is not desired to demultiplex reads into separate files by barcode.",
          shortName="O",
          mutex="MULTIPLEX_PARAMS")
public java.io.File OUTPUT_PREFIX

RUN_BARCODE

@Argument(doc="The barcode of the run.  Prefixed to read names.")
public java.lang.String RUN_BARCODE

MACHINE_NAME

@Argument(doc="The name of the machine on which the run was sequenced; required if emitting Casava1.8-style read name headers",
          optional=true)
public java.lang.String MACHINE_NAME

FLOWCELL_BARCODE

@Argument(doc="The barcode of the flowcell that was sequenced; required if emitting Casava1.8-style read name headers",
          optional=true)
public java.lang.String FLOWCELL_BARCODE

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.",
          shortName="RS")
public java.lang.String READ_STRUCTURE

MULTIPLEX_PARAMS

@Argument(doc="Tab-separated file for creating all output FASTQs demultiplexed by barcode for a lane with single IlluminaBasecallsToFastq invocation.  The columns are OUTPUT_PREFIX, and BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster (optional).  Row with BARCODE_1 set to \'N\' is used to specify an output_prefix for no barcode match.",
          mutex="OUTPUT_PREFIX")
public java.io.File MULTIPLEX_PARAMS

ADAPTERS_TO_CHECK

@Deprecated
 @Argument(doc="Deprecated (No longer used). Which adapters to look for in the read.",
          optional=true)
public java.util.List<IlluminaUtil.IlluminaAdapterPair> ADAPTERS_TO_CHECK

Deprecated.

NUM_PROCESSORS

@Argument(doc="The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, then the number of cores used will be the number available on the machine less NUM_PROCESSORS.")
public java.lang.Integer NUM_PROCESSORS

FIRST_TILE

@Argument(doc="If set, this is the first tile to be processed (used for debugging).  Note that tiles are not processed in numerical order.",
          optional=true)
public java.lang.Integer FIRST_TILE

TILE_LIMIT

@Argument(doc="If set, process no more than this many tiles (used for debugging).",
          optional=true)
public java.lang.Integer TILE_LIMIT

APPLY_EAMSS_FILTER

@Argument(doc="Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of reads and convert their quality scores to Q2.")
public boolean APPLY_EAMSS_FILTER

FORCE_GC

@Argument(doc="If true, call System.gc() periodically.  This is useful in cases in which the -Xmx value passed is larger than the available memory.")
public java.lang.Boolean FORCE_GC

SORT

@Argument(doc="If true, the output records are sorted by read name. Otherwise they are output in the same order that the data was produced on the sequencer (ordered by tile and position).")
public java.lang.Boolean SORT

MAX_READS_IN_RAM_PER_TILE

@Deprecated
 @Argument(doc="Configure SortingCollections to store this many records before spilling to disk. For an indexed run, each SortingCollection gets this value/number of indices. Deprecated: use `MAX_RECORDS_IN_RAM`")
public int MAX_READS_IN_RAM_PER_TILE

Deprecated.

MINIMUM_QUALITY

@Argument(doc="The minimum quality (after transforming 0s to 1s) expected from reads.  If qualities are lower than this value, an error is thrown.The default of 2 is what the Illumina\'s spec describes as the minimum, but in practice the value has been observed lower.")
public int MINIMUM_QUALITY

INCLUDE_NON_PF_READS

@Argument(doc="Whether to include non-PF reads",
          shortName="NONPF",
          optional=true)
public boolean INCLUDE_NON_PF_READS

IGNORE_UNEXPECTED_BARCODES

@Argument(doc="Whether to ignore reads whose barcodes are not found in MULTIPLEX_PARAMS.  Useful when outputting FASTQs for only a subset of the barcodes in a lane.",
          shortName="INGORE_UNEXPECTED")
public boolean IGNORE_UNEXPECTED_BARCODES

READ_NAME_FORMAT

@Argument(doc="The read name header formatting to emit.  Casava1.8 formatting has additional information beyond Illumina, including: the passing-filter flag value for the read, the flowcell name, and the sequencer name.")
public IlluminaBasecallsToFastq.ReadNameFormat READ_NAME_FORMAT

COMPRESS_OUTPUTS

@Argument(shortName="GZIP",
          doc="Compress output FASTQ files using gzip and append a .gz extension to the file names.")
public boolean COMPRESS_OUTPUTS

Constructor Detail

IlluminaBasecallsToFastq

public IlluminaBasecallsToFastq()

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.