4b7bfb284adc01c987fa7bf11f4fdbd510be79cc,java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java,ArgumentParser,addArgumentSource,#Object#,341

Before Change


            String shortName = (arg.shortName().length() != 0) ? arg.shortName() : fullName.substring(0,1);
            if(shortName.length() != 1)
                throw new IllegalArgumentException("Invalid short name: " + shortName);
            String description = arg.required() ? "(Required Flag) " + arg.doc() : arg.doc();

            // TODO: Handle flags, handle lists
            OptionBuilder ob = OptionBuilder.withLongOpt(fullName).withArgName(fullName).hasArg();

After Change


                throw new IllegalArgumentException("Can't have an array of flags.");

            String description = arg.doc();
            if( arg.required() )
                description = (isFlag ? "(Required Flag) " : "(Required Option) ") + description;

            OptionBuilder ob = OptionBuilder.withLongOpt(fullName);