[Bioc-devel] ShortReadQ class and memory usage

Mike Smith grimbough at gmail.com
Mon Mar 30 18:04:53 CEST 2015

Hi all,

I was wondering if anyone could explain the memory usage behaviour I see
when subsetting a ShortReadQ object.

If I create a ShortReadQ with 500 reads, each of length 200bp it uses
~230Kb of memory.  If I do the same, but store 50,000 reads the memory
usage goes up to ~21.5Mb - this seems entirely reasonable.  However, if I
then create a third object by subsetting the first 500 reads from the
larger ShortReadQ it comes in at ~19.5Mb, which seems less understandable.
I was hoping for some insight into why this might be.

I've put some code in a Gist here that can run this example:



Mike Smith
Research Associate
Statistics & Computational Biology Laboratory
Cambridge University

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