[Bioperl-l] Bio::FeatureIO::gff bug?

Sendu Bala bix at sendu.me.uk
Mon Sep 24 09:20:33 EDT 2007


Chris Fields wrote:
> It looks like the first is a cut-and-paste revision of the second, so I 
> would say the second independent if block is redundant.

I agree. I'll make that change.


> Should we be printing output in _initialize()?  I would think any output 
> would be handled in a write_* method of some sort and not in a common 
> method used for initializing both input and output stream data.  What 
> happens here if you use '-fh' and want output redirected to STDOUT?

I think the problem is that the method is write_feature(), which can be 
called many times for a single output file, but the version should only 
be printed once at the very start of the file.

I suppose it just needs better capturing of when we're intending to 
write... Hmmm... didn't I fix a method related to that?...

Yes, yes I did:
Bio::Root::IO->mode
;)

Any objections to me replacing the if clause with one using that method?


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