Performance tweak - Githubissues

alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.

http://biorxiv.org/content/early/2014/12/12/006015

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Performance tweak #38

Closed ttdtrang closed 3 years ago

ttdtrang commented 8 years ago

I try to speed up the code a bit by

Reduce type casting
Use .Internal call in heavily used sprintf whenever possible
Replace nested if elses
Enable parallelization (will cause additional dependency)

These changes result in significant speedup when one performs a large simulation (e.g. thousands of samples).

alyssafrazee commented 8 years ago

Hey @ttdtrang, thanks for the PR. We're looking in to these changes (but are a bit crunched due to the release cycle right now) and will get back to you! Sorry for the delay.

alyssafrazee commented 7 years ago

Hi again, sorry (again) for the delay.

Could you be a bit more specific about the speedups you're seeing here? e.g., can you put some benchmarking results in here?

I'll try to get to this over the holiday break, but given the size of the change it will likely involve writing a test suite, which is going to take some time unfortunately.

Thanks for your patience!

ttdtrang commented 7 years ago

Hi Alyssa,

I'm thinking about doing benchmark tests too, but haven't had a chance to sit down to it. I'll let you know as soon as I have some!

Bests, Trang