[BioC] findOveraps suggestions

[Janet Young]

Thanks Michael,

On Jan 21, 2010, at 1:49 PM, Michael Lawrence wrote:
>
> So, we could go ahead and add that option.
that would be great - thank you.

> Not sure "simplify" would be a good word. Or would we want two  
> separate options, one to remove the obvious self hits and another to  
> remove the redundant hits?

I think keeping the two options separate is probably better?

> Maybe 'ignoreSelf' and then "normalize" or something? Suggestions  
> welcome.

good - I think ignoreSelf is very clear (and you're right, simplify  
isn't so good).  "normalize" makes me think of other things - maybe  
not so good. "ignoreSymmetric" perhaps? (only makes sense if  
query=subject - perhaps there could be a check for that if user tries  
to invoke that option?)

Janet