Overriding inherited options

[lbergelson]

Tools be able to override the behavior of options they have inherited?

How should this work? Should you be able to change a required field to an optional one? Or only the other way around?

If you override the a field that has an @Option annotation does it effectively replace it?

[droazen]

Am going to address part of this ticket in my next branch by giving tools a way to indicate that particular data sources are required or optional, even when the inherited argument itself is marked as optional. Once this is done, all we probably need to do is change the code that displays the tool arguments to the user so that they take each tools requirements into account when displaying args.

[droazen]

Louis has a solution for this!

[akiezun]

@lbergelson is this solution going in this iteration?

[akiezun]

@lbergelson ping

[lbergelson]

Oh, sorry, I missed that last comment. Yeah this should go in. It's been sitting in local branch, just need to update it.

[lbergelson]

This is not resolved in the general case, but it is resolved in the case of the special BAM, reference, and interval options in walkers. Going to close this. Reopen when it comes up as an issue again.