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

George Hartzell hartzell at kestrel.alerce.com
Sun Jun 12 18:09:52 EDT 2005

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

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



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