[Bioperl-l] Bio::Tools::Primer3.pm bug: code or doc, you decide???

Brian Osborne brian_osborne at cognia.com
Sun Jun 12 18:35:28 EDT 2005


You're presenting a good argument that it's the code that should change.

Brian O.

On 6/12/05 6:09 PM, "George Hartzell" <hartzell at kestrel.alerce.com> wrote:

> The pod for Bio::Tools::Primer3::number_of_results says for Function:
>    "Retrieve the number of primers returned from Primer3"
> and for it's Notes:, it says
>    "Returns the maximum number of primers returned from Primer3."
> In fact, it's returning the maximum offset of the array of results,
> also known as one *less* than the number of results that primer3
> returned....  (see Bio::Tools::Primer3::_separate() and it's use of
> $maxlocation and $self->{'maximum_primers_returned'}).
> Given the method's *name*, I figured it'd tell me how many primers I'd
> gotten back from primer3.
> Given the method's Function doc, ditto....
> Given the method's Notes, it's a bit fuzzier, but it still evokes a
> count.
> I'd like to fix *something*, so that I'll feel better about wasting an
> hour walking the primer3 C code and pestering the authors about an off
> by one bug.....
> So, should I change the method to add one, or change the documentation
> to specify that it's the maximum offset into the results array (even
> though the names then misleading).
> I'd rather fix the code, but *I* don't have to be backward
> compatible....
> Comments?
> g.
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