[Bioperl-pipeline] runnable parameters

[Elia Stupka]

> yup the genewise runnable should do the trick. however its debatable
> how inflated we want the runnable to be..but of course the initial
> design to have runnables as modules is to allow for things like this.

I have a feeling that it should take one optional input and that input is
a simple class that gives it the necessary info... hey wait a minute, that
class is a SeqFeature with subseqfeatures! It's just lots of
starts,ends,strands! So we "just" need to figure how to pass it into the
genewise runnable... we come back to the fact of being able to pass things
in memory, without writing to database... unless of course we don't write
all these starts,ends, strands to GFD temporarily....

> I guess we will pass in the start/end/ info as cigar strings. hm. yup.
> sounding more doable.

Ok, yep, cigar strings is really the way to go, no doubt about
that. Agreed.... :)

> ok..off to bed. good nite!

Nice joke ;)

Elia

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