Field Detail

• OUTPUT

  @Argument(doc="Output SAM file containing only the sequence dictionary. By default it will use the base name of the input reference with the .dict extension",
            shortName="O",
            optional=true)
  public File OUTPUT

• GENOME_ASSEMBLY

  @Argument(shortName="AS",
            doc="Put into AS field of sequence dictionary entry if supplied",
            optional=true)
  public String GENOME_ASSEMBLY

• URI

  @Argument(shortName="UR",
            doc="Put into UR field of sequence dictionary entry.  If not supplied, input reference file is used",
            optional=true)
  public String URI

• SPECIES

  @Argument(shortName="SP",
            doc="Put into SP field of sequence dictionary entry",
            optional=true)
  public String SPECIES

• TRUNCATE_NAMES_AT_WHITESPACE

  @Argument(doc="Make sequence name the first word from the > line in the fasta file.  By default the entire contents of the > line is used, excluding leading and trailing whitespace.")
  public boolean TRUNCATE_NAMES_AT_WHITESPACE

• NUM_SEQUENCES

  @Argument(doc="Stop after writing this many sequences.  For testing.")
  public int NUM_SEQUENCES

Constructor Detail

• CreateSequenceDictionary

  public CreateSequenceDictionary()

Method Detail

• main

  public static void main​(String[] argv)

• makeSequenceDictionary

  @Deprecated
  public htsjdk.samtools.SAMSequenceDictionary makeSequenceDictionary​(File referenceFile)

  Deprecated.
  Read all the sequences from the given reference file, and convert into SAMSequenceRecords

  Parameters:

  referenceFile - fasta or fasta.gz

  Returns:

  SAMSequenceRecords containing info from the fasta, plus from cmd-line arguments.

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Use reference filename to create URI to go into header if URI was not passed on cmd line.

  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.

• makeReferenceArgumentCollection

  protected ReferenceArgumentCollection makeReferenceArgumentCollection()

  Overrides:

  makeReferenceArgumentCollection in class CommandLineProgram

• doWork

  protected int doWork()

  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.