[Bioc-devel] readGAlignmentPairs Fails if Used Inside mclapply Loop

Dario Strbenac dstr7320 at uni.sydney.edu.au
Tue Dec 13 02:00:21 CET 2016


I fixed the suggested test case, since the command didn't specify the connection and produced an error. It appears to work without a problem. 

> bamFile <- mappedReadsGenome[2]
> length(serialize(readGAlignmentPairs(bamFile, strandMode=2), NULL))
[1] 1329295005

I also tried mc.cores = 2 and it also resulted in an error. Each of the files has 30 to 40 million mappings, so I wouldn't expect them to be too big. I'll stick to bplapply.

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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