Field Detail

• TARGETS

  @Argument(shortName="T",
            doc="The file with design parameters and targets")
  public File TARGETS

• DESIGN_NAME

  @Argument(doc="The name of the bait design")
  public String DESIGN_NAME

• LEFT_PRIMER

  @Argument(doc="The left amplification primer to prepend to all baits for synthesis")
  public String LEFT_PRIMER

• RIGHT_PRIMER

  @Argument(doc="The right amplification primer to prepend to all baits for synthesis")
  public String RIGHT_PRIMER

• DESIGN_STRATEGY

  @Argument(doc="The design strategy to use to layout baits across each target")
  public BaitDesigner.DesignStrategy DESIGN_STRATEGY

• BAIT_SIZE

  @Argument(doc="The length of each individual bait to design")
  public int BAIT_SIZE

• MINIMUM_BAITS_PER_TARGET

  @Argument(doc="The minimum number of baits to design per target.")
  public int MINIMUM_BAITS_PER_TARGET

• BAIT_OFFSET

  @Argument(doc="The desired offset between the start of one bait and the start of another bait for the same target.")
  public int BAIT_OFFSET

• PADDING

  @Argument(doc="Pad the input targets by this amount when designing baits. Padding is applied on both sides in this amount.")
  public int PADDING

• REPEAT_TOLERANCE

  @Argument(doc="Baits that have more than REPEAT_TOLERANCE soft or hard masked bases will not be allowed")
  public int REPEAT_TOLERANCE

• POOL_SIZE

  @Argument(doc="The size of pools or arrays for synthesis. If no pool files are desired, can be set to 0.")
  public int POOL_SIZE

• FILL_POOLS

  @Argument(doc="If true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained")
  public boolean FILL_POOLS

• DESIGN_ON_TARGET_STRAND

  @Argument(doc="If true design baits on the strand of the target feature, if false always design on the + strand of the genome.")
  public boolean DESIGN_ON_TARGET_STRAND

• MERGE_NEARBY_TARGETS

  @Argument(doc="If true merge targets that are \'close enough\' that designing against a merged target would be more efficient.")
  public boolean MERGE_NEARBY_TARGETS

• OUTPUT_AGILENT_FILES

  @Argument(doc="If true also output .design.txt files per pool with one line per bait sequence")
  public boolean OUTPUT_AGILENT_FILES

• OUTPUT_DIRECTORY

  @Argument(shortName="O",
            optional=true,
            doc="The output directory. If not provided then the DESIGN_NAME will be used as the output directory")
  public File OUTPUT_DIRECTORY

Constructor Detail

• BaitDesigner

  public BaitDesigner()

Method Detail

• requiresReference

  protected boolean requiresReference()

  Overrides:

  requiresReference in class CommandLineProgram

• getMaskedBaseCount

  public static int getMaskedBaseCount​(byte[] bases,
                                       int from,
                                       int until)

  Returns the total of soft or hard masked bases in the interval of bases.

• main

  public static void main​(String[] args)

  Stock main method.

• 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.

• doWork

  protected int doWork()

  Main method that coordinates the checking of inputs, designing of baits and then the writing out of all necessary files.

  Specified by:

  doWork in class CommandLineProgram

  Returns: