Fields, Christopher J | 29 Oct 04:04 2012

Re: Bio::DB::Fasta changes

On Oct 28, 2012, at 9:50 PM, Florent Angly <florent.angly <at>> wrote:

> Hi Chris,
> I have done a bunch of work on Bio::DB::Fasta and associated modules lately, with the goal of making them
more useful and less redundant. There was no intentional change of interface that would make it backward
incompatible and all bioperl tests passed fine. In fact, if I recall correctly, I even added more tests
because I noticed some holes in test coverage.

More tests never hurt (well, unless we're adding a ton of files to the repository).

> I suspect that this bug report you cited unveiled a corner case that was not covered by the tests. I'll
assign the bug to myself and investigate.

Okay.  I just want to ensure that everything for this particular module is covered for the GMOD folks.


> Florent
> On 29/10/12 08:24, Fields, Christopher J wrote:
>> There have been a number of significant changes to Bio::DB::Fasta recently that haven't been discussed
on the bioperl list.  In particular, much of the code has been moved to Bio::DB::IndexedBase.  At the moment
some of these changes are breaking compatibility with other tools (namely MAKER, see:  In the latter case I would consider this a significant
API change that needs to be addressed.
>> Generally, whenever we make significant changes to modules these should always be run on a branch first
(see recent changes to Bio::Tree), and we should at least discuss this on-list prior to merging with
master.  I do think we should start that discussion now and decide what to do, e.g. roll back changes and push
these to a branch, allow these to stay in master with revisions, etc.
>> chris