On Thu, Jul 1, 2010 at 9:06 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > > On Donnerstag 01 Juli 2010 Sven Klages wrote: >> Hmm, I surely miss something, why not simply: >> [...] >> in the traceinfo XML file? This is a common situation in the finishing >> process >> of a project, that there are more than one read of the same template in the >> same direction (due to failures in sequencing or suboptimal sequence >> quality). > > You can do that, but then MIRA will not be able to use the template > information (and complain bitterly about this in the log file). > > The reason is pretty dumb: internally MIRA uses read pairs, and the data > structures are not able to cope with more that two reads. I did think at some > time to change this, but I had the impression that the cost/benefit ratio of > implementing these changes simply didn't work out. > > Now that we might soon get PacBio data with their strobed reads > however I fear I'll need to revisit that decision (at least for long dark > inserts). A short term solution would be to keep the current pair limitation, but automatically group a set with multiple forward and reverse reads into as many pairs as possible, with the rest treated as singletons. However, probably not worth the effort if you are already thinking about PacBio strobed reads etc. Thank you for the clarifications. Peter -- 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