Class CrosscheckReadGroupFingerprints


@Deprecated public class CrosscheckReadGroupFingerprints extends CrosscheckFingerprints
Deprecated.
6/6/2017 Use CrosscheckFingerprints instead.
Program to check that all read groups within the set of BAM files appear to come from the same individual.
  • Field Details

    • 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 Details

    • CrosscheckReadGroupFingerprints

      public CrosscheckReadGroupFingerprints()
      Deprecated.
  • Method Details

    • 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.