[Bioc-devel] String Matching in Parallel

Dario Strbenac dstr7320 at uni.sydney.edu.au
Mon Sep 5 04:00:07 CEST 2016


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 ?

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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