[Rd] ShortRead::FastqStreamer and parallelization

Cook, Malcolm MEC at stowers.org
Tue Nov 18 18:00:53 CET 2014


I understand ShortRead::FastqStreamer will read chunks in parallel depending on the value of ShortRead:::.set_omp_threads

I see this discussed here:  https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004355.html and nowhere else.

It probably should be documented in ShortRead.

Possibly this has already changed for I am using still R 3.1.0.   I thought I'd check.

Oh, and, in my hands/hardware, the value of this FastqStreamer's use of srapply's parallelization is negligible, at least if the consumer of successive yields is in the main process.  I see that the new bpiterate appears to take advantage of yielding in forked processes, which sounds promising.  Is that the idea?

Looking forward....

Malcolm Cook

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