[Bioc-devel] viewMedians

Hervé Pagès hpages at fhcrc.org
Sat May 31 02:33:52 CEST 2014

Hi Michael,

On 05/30/2014 11:37 AM, Michael Lawrence wrote:
> Herve,
> How hard do you think it would be to add a viewMedians? It would be nice
> to have a robust average of e.g. coverage. Also, many genotypers
> including GATK summarize non-alt runs using the median. We want to be
> consistent.

Don't know. I didn't implement any of the view* methods for RleViews
objects (they're all implemented in C). My first impression after
having a quick look at the code is that adding RleViews_viewMedians
should not be too hard. Also it feels like there might be opportunity
for more code sharing than what we have right now. Will have to dig
into this a little bit more. Won't happen before a couple of weeks


> Thanks,
> Michael

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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