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);