[mira_talk] Re: smalt doc additions

  • From: Bastien Chevreux <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sun, 6 Mar 2011 16:09:53 +0100

On Sunday 06 March 2011 15:20:50 Martin Mokrejs wrote:
> > And of course, as in every clipping: rightmost leftlip and leftmost
> > rightclip will win.
> 
> I don't see anything obvious in that logic, I expected that actually the
> leftmost leftclip wins.

So assuming the sequence AAAAAAAAAAA is your adaptor and you have

>someread
AAAAAAAAAAAAAAAACTGACTGTGACTGACTGACTGACTGACTG

and your first method says that the adaptor leftclip should be at position 3

>someread_method1
aaAAAAAAAAAAAAAACTGACTGTGACTGACTGACTGACTGACTG

and the second method says it should be at position 17

>someread_method1
aaaaaaaaaaaaaaaaCTGACTGTGACTGACTGACTGACTGACTG

... you would really want the clip according to method 1 to win? :-)

> > But please do not built upon this behaviour ... I might very well remove
> > it in the future when consolidating the code.
> 
> Hmm, that's bad if it is going to be changed silently. Hope you document
> current approach and then document changes so that people know what is
> going on after they upgrade mira. ;)

It's not documented for a reason: I do not officially support it. I just told 
you because you are doing experiments (not many people do it) and it could be 
you have both files present, which would lead to side-effects which are not 
intended (and therefore not documented).

Therefore I maight also change that behaviour "silently" if I happen to rework 
that portion of MIRA. Regarding the current TODO it will not happen anytime 
soon though.

B.

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