public static boolean validateQualityFormatFlags(CFlags flags,String format){
  if (format.equals(FASTQ_FORMAT)) {
    if (!flags.isSet(CommonFlags.QUALITY_FLAG)) {
      flags.setParseMessage("--" + CommonFlags.QUALITY_FLAG + " is required for \"fastq\" format.");
      return false;
    }
  }
 else {
    if (flags.isSet(CommonFlags.QUALITY_FLAG)) {
      flags.setParseMessage("--" + CommonFlags.QUALITY_FLAG + " is only allowed for \"fastq\" format.");
      return false;
    }
  }
  return true;
}

public static boolean validateQualityFormatFlags ( CFlags flags , String format ) { if ( format . equals ( FASTQ_FORMAT ) ) { if ( ! flags . isSet ( CommonFlags . QUALITY_FLAG ) ) { flags . setParseMessage ( "--" + CommonFlags . QUALITY_FLAG + " is required for \"fastq\" format." ) ; return false ; } } else { if ( flags . isSet ( CommonFlags . QUALITY_FLAG ) ) { flags . setParseMessage ( "--" + CommonFlags . QUALITY_FLAG + " is only allowed for \"fastq\" format." ) ; return false ; } } return true ; }
validates the flags for a quality encoding
