Field Detail

• CROSSCHECK_SAMPLES

  @Argument(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the sample level and print out a sample x sample matrix with LOD scores.")
  public boolean CROSSCHECK_SAMPLES

  Deprecated.

• CROSSCHECK_LIBRARIES

  @Argument(doc="Instead of producing the normal comparison of read-groups, roll fingerprints up to the library level and print out a library x library matrix with LOD scores.")
  public boolean CROSSCHECK_LIBRARIES

  Deprecated.

• EXPECT_ALL_READ_GROUPS_TO_MATCH

  @Argument(doc="Expect all read groups\' fingerprints to match, irrespective of their sample names.  By default (with this value set to false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected to match.",
            mutex="EXPECT_ALL_GROUPS_TO_MATCH")
  public boolean EXPECT_ALL_READ_GROUPS_TO_MATCH

  Deprecated.

Constructor Detail

• CrosscheckReadGroupFingerprints

  public CrosscheckReadGroupFingerprints()

  Deprecated.

Method Detail

• customCommandLineValidation

  protected String[] customCommandLineValidation()

  Deprecated.
  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 CrosscheckFingerprints

  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()

  Deprecated.
  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.

  Overrides:

  doWork in class CrosscheckFingerprints

  Returns:

  program exit status.