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. -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html