[Bioc-devel] String Matching in Parallel

Martin Morgan martin.morgan at roswellpark.org
Tue Sep 6 15:13:15 CEST 2016

On 09/04/2016 10:00 PM, Dario Strbenac wrote:
> Hello,
> Functions such as vmatchPattern and vmatchPDict naturally lend
> themselves to being parallelised. Could they be enhanced to accept a
> BiocParallelParam object ? Or, is there no significant performance
> difference using them as-is and having the bplapply loop surrounding
> them and repeatedly calling DNAString (it's odd that vmatchPattern -
> for searching BSgenome objects - requires a DNAString for the
> pattern, rather than a DNAStringSet) or DNAStringSet ?

fwiw, and until there is direct support for this, probably one wants to 
look at bpvec() rather than bplapply() to parallelize these. Also, one 
would _not_ want to parallelize on the argument that becomes the  PDict, 
because this part of the calculation scales favorably with number of 


> -------------------------------------- Dario Strbenac University of
> Sydney Camperdown NSW 2050 Australia
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