Field Detail

• BARCODE_SEQUENCE_COLUMN

  public static final String BARCODE_SEQUENCE_COLUMN

  Column header for the first barcode sequence (preferred).

  See Also:

  Constant Field Values

• BARCODE_SEQUENCE_1_COLUMN

  public static final String BARCODE_SEQUENCE_1_COLUMN

  Column header for the first barcode sequence.

  See Also:

  Constant Field Values

• BARCODE_NAME_COLUMN

  public static final String BARCODE_NAME_COLUMN

  Column header for the barcode name.

  See Also:

  Constant Field Values

• LIBRARY_NAME_COLUMN

  public static final String LIBRARY_NAME_COLUMN

  Column header for the library name.

  See Also:

  Constant Field Values

• BASECALLS_DIR

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

• OUTPUT_DIR

  @Argument(doc="Where to write _barcode.txt files.  By default, these are written to BASECALLS_DIR.",
            optional=true)
  public File OUTPUT_DIR

• LANE

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

• 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

• BARCODE

  @Argument(doc="Barcode sequence.  These must be unique, and all the same length.  This cannot be used with reads that have more than one barcode; use BARCODE_FILE in that case. ",
            mutex="BARCODE_FILE")
  public List<String> BARCODE

• BARCODE_FILE

  @Argument(doc="Tab-delimited file of barcode sequences, barcode name and, optionally, library name.  Barcodes must be unique and all the same length.  Column headers must be \'barcode_sequence\' (or \'barcode_sequence_1\'), \'barcode_sequence_2\' (optional), \'barcode_name\', and \'library_name\'.",
            mutex="BARCODE")
  public File BARCODE_FILE

• METRICS_FILE

  @Argument(doc="Per-barcode and per-lane metrics written to this file.",
            shortName="M")
  public File METRICS_FILE

• MAX_MISMATCHES

  @Argument(doc="Maximum mismatches for a barcode to be considered a match.")
  public int MAX_MISMATCHES

• MIN_MISMATCH_DELTA

  @Argument(doc="Minimum difference between number of mismatches in the best and second best barcodes for a barcode to be considered a match.")
  public int MIN_MISMATCH_DELTA

• MAX_NO_CALLS

  @Argument(doc="Maximum allowable number of no-calls in a barcode read before it is considered unmatchable.")
  public int MAX_NO_CALLS

• MINIMUM_BASE_QUALITY

  @Argument(shortName="Q",
            doc="Minimum base quality. Any barcode bases falling below this quality will be considered a mismatch even in the bases match.")
  public int MINIMUM_BASE_QUALITY

• 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

• COMPRESS_OUTPUTS

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

• NUM_PROCESSORS

  @Argument(doc="Run this many PerTileBarcodeExtractors 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 int NUM_PROCESSORS

Constructor Detail

• ExtractIlluminaBarcodes

  public ExtractIlluminaBarcodes()

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.

• finalizeMetrics

  public static void finalizeMetrics​(Map<String,ExtractIlluminaBarcodes.BarcodeMetric> barcodeToMetrics,
                                     ExtractIlluminaBarcodes.BarcodeMetric noMatchMetric)

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Validate that POSITION >= 1, and that all BARCODEs are the same length and unique

  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[] argv)