[BioC] how to deal with a 30G fastq file

[Steve Lianoglou]

Hi Martin,

Just wanted to say:

On Wed, Oct 5, 2011 at 11:39 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

>  fq = FastqStreamer(<...>)
>  while (length(res <- yield(fq)))
>      # work, e.g., filter

That's really cool!

Then some navel gazing:

Have you thought about "inverting" this flow? Like, run the while loop
in "C-land" but pass an R expression/block/something in and have it be
evaluated within each iteration of the C/while loop?

I'm guessing calling an R function from within C code is costly, but
"while" loops in R are also slow (compared to while loops in C), so I
wonder which would win in the long run.

Just curious -- sorry if I missed some previous discussion on this topic.

Anyway, like I said -- this is really cool already.

Thanks,

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact