[Bioperl-l] Trace files and trace points

[Jason Stajich]

Way cool stuff Aaron.  I think this will be very very useful.  I like the
idea of Seq::Trace object.  When you get to thinking about building one,
can you send out a list of methods you think it would need - this is
mostly for my edification about how one might want to design a trace
object.

-jason

On Wed, 10 Jul 2002, Aaron J Mackey wrote:

>
> So the other large chunk of data in a trace file besides the quality
> values are the trace point data.  Chad's scf.pm module is storing them in
> the io object (not in the Seq object itself) (which of course makes
> writing an SCF file with peak info a bit difficult - maybe I've
> misunderstood something there).  Regardless, do we want to just trash this
> info for now, put it in a data field of the seq object, or make a
> Seq::Trace object to hold them (and potentially do interesting stuff with
> it?) ... we don't have to answer this immediately, but until we do, 'ctf'
> format output won't work (as it requires trace info).
>
> And, I've found that the io_lib routines don't write 'abi' or 'alf'
> (multi-seq abi format) formats (and also no 'ctf' unless trace info is
> available, as I said above).  Everything else is ready to go, just putting
> finishing touches on make test (100 tests!) and whatnot.
>
> -Aaron
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu