[Bioperl-pipeline] runnable parameters

[shawnh@worf.fugu-sg.org]

> 
> No I agree with you, go ahead with your idea, sorry for the "intrusion"
> 

ok will give it a shot. everything is up for review once we get the annotation
pipeline thru.

> > But then again mapping maybe something worth generalizing into a data
> > monger. 
> 
> No it is already generalised in CoordinateMapper, so you are already
> reusing a reusable component. And of course you are doing mapping only if
> those arguments are being passed right? So it's clean for those who
> "just" want to run genewise, which anyway in reality never happens.
> 
> Just another separate point. If we want to create a miniseq around the
> blast hit (which is the case for human and could be the case for other
> organisms) where would that be handled? I guess it's just an option in the
> InputCreate you have already, so instead of min_start to max_end, it would
> go over the features, and create the miniseq right? But what about

hmm. maybe we can talk about this tomorrow. You are talking about in-memory stuff?

cuz input_create, sets up the inputs to be fetched for the next analysis. Unless,
we store the mini-seqs. But we can pass the mini-seqs in memory, but of course there is
the issue of batch failures.

> "de-mini-seq'ing" in your design where runnable has parameters, would you
> pass in a long cigar-style string, i.e. an array of start-ends?

What do u mean de-mini-seq ing? to combine the exons in to a transcript ?