Field Detail

• INPUT

  @Argument(doc="Input SAM/BAM file to split",
            shortName="I")
  public File INPUT

• SPLIT_TO_N_READS

  @Argument(shortName="N_READS",
            doc="Split to have approximately N reads per output file. The actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).",
            mutex="SPLIT_TO_N_FILES")
  public int SPLIT_TO_N_READS

• SPLIT_TO_N_FILES

  @Argument(shortName="N_FILES",
            doc="Split to N files.",
            mutex="SPLIT_TO_N_READS")
  public int SPLIT_TO_N_FILES

• TOTAL_READS_IN_INPUT

  @Argument(shortName="TOTAL_READS",
            doc="Total number of reads in the input file. If this is not provided, the input will be read twice, the first time to get a count of the total reads.",
            optional=true)
  public long TOTAL_READS_IN_INPUT

• OUTPUT

  @Argument(shortName="O",
            doc="Directory in which to output the split BAM files.")
  public File OUTPUT

• OUT_PREFIX

  @Argument(shortName="OUT_PREFIX",
            doc="Output files will be named <OUT_PREFIX>_N.bam, where N enumerates the output file.")
  public String OUT_PREFIX

Constructor Detail

• SplitSamByNumberOfReads

  public SplitSamByNumberOfReads()

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.