`ctleptop` replaces gaps with Ns

[averagehat]

I'm not convinced this is correct behaviour. In particular this may get interpreted as an ambiguous base when it is not. Probably the gap should just be left as it is.

[averagehat]

It looks like ctleptop then marks these Ns as GAPFOUND. But this conflates "true" Ns with gaps.

[InaMBerry]

Hi Michael,
I don't remember exactly why we had gaps replaced by Ns but I know gaps were messing things up and at the time what I needed from MAAPs was not affected by the replacement. However, I know you and I talked about adding things to MAAPs and this might have to be adjusted. I think we need to sit down and go through everything, that will help make the correct decision regarding gaps and other things as well. When it comes to the output it is just the numbering of amino acids that is messed up, it is something you noticed long time ago. But it is something we can discuss later as well. When I come back from Thailand I should have more time and we can get going on this properly.

Thanks for your help!
Ina

[averagehat]

Okay, good deal Ina, I'd forgotten some of that. I forgot that you're in
Thailand next week! Have a fruitful trip.

Mike

On Thu, Mar 17, 2016 at 10:00 AM, InaMBerry notifications@github.com
wrote:

Hi Michael,
I don't remember exactly why we had gaps replaced by Ns but I know gaps
were messing things up and at the time what I needed from MAAPs was not
affected by the replacement. However, I know you and I talked about adding
things to MAAPs and this might have to be adjusted. I think we need to sit
down and go through everything, that will help make the correct decision
regarding gaps and other things as well. When it comes to the output it is
just the numbering of amino acids that is messed up, it is something you
noticed long time ago. But it is something we can discuss later as well.
When I come back from Thailand I should have more time and we can get going
on this properly.

Thanks for your help!
Ina

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