allowdangling option in obo2obo

[Chris Mungall]

at some point the defaults for allowdangling in obo2obo switched back
to disallow. For example

z.obo:

> [Term]
> id: a
> intersection_of: b
> intersection_of: r c
>
> [Term]
> id: b
>


[1] obo2obo -o out.obo z.obo
-- complains

[2] obo2obo -allowdangling -o out.obo z.obo
-- silently drops an intersection_of tag, completely changing the
semantics of the file - bad!!!

[3] obo2obo -allowdangling -o -allowdangling out.obo z.obo
-- desirable behavior, but requires unwieldy command line

I think [1] is fine. [2] is terrible - we need to prevent lone
intersection links further upstream, and in addition, obo2obo should
never silently drop things by default. silent loss should always be a
non-default behavior a user explicitly asks for

[3] is the correct command line to use when the user knows that there
are dangling references. Here it should only be necessary to specify
allow dangling once.



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[Amina Abdulla]

Thanks for pointing that out Chris. I've removed the discrepancy.
allowdangling will be default true for obo2obo and false for all other
OE load/save operations.
That solves [1]

[2]: fixed - was silently dropping one of the intersection_of tags

[3]: not required from now on