Field Detail

• BASECALLS_DIR

  @Argument(doc="The basecalls directory. ",
            shortName="B")
  public 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 File BARCODES_DIR

• LANE

  @Argument(doc="Lane number. ",
            shortName="L")
  public 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 File OUTPUT_PREFIX

• RUN_BARCODE

  @Argument(doc="The barcode of the run.  Prefixed to read names.")
  public 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 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 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 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 File MULTIPLEX_PARAMS

• ADAPTERS_TO_CHECK

  @Deprecated
  @Argument(doc="Deprecated (No longer used). Which adapters to look for in the read.",
            optional=true)
  public 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 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 Integer FIRST_TILE

• TILE_LIMIT

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

• MAX_READS_IN_RAM_PER_TILE

  @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.")
  public int MAX_READS_IN_RAM_PER_TILE

• 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 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.

• main

  public static void main​(String[] args)