Example #1
0
  /**
   * Parse one sample file and integrate it with samples that are already there Fail quickly if we
   * find any errors in the file
   */
  private Collection<Sample> addSamplesFromPedigreeArgument(File sampleFile) {
    final PedReader reader = new PedReader();

    try {
      return reader.parse(sampleFile, getMissingFields(sampleFile), sampleDB);
    } catch (FileNotFoundException e) {
      throw new UserException.CouldNotReadInputFile(sampleFile, e);
    }
  }
Example #2
0
 private Collection<Sample> addSamplesFromPedigreeArgument(final String string) {
   final PedReader reader = new PedReader();
   return reader.parse(string, getMissingFields(string), sampleDB);
 }