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Optimize bc_demultiplex #11

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jarondl opened this issue Jun 5, 2017 · 0 comments
Open

Optimize bc_demultiplex #11

jarondl opened this issue Jun 5, 2017 · 0 comments

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@jarondl
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jarondl commented Jun 5, 2017

Embarrassingly, bc_demultiplex can be the most time-consuming step in a pipeline.
We should profile it to check what are the causes for this, and optimize. Ideally, we should benchmark this on real-life data.

After profiling, possible solutions could be:

  • Simple optimizations of inner loops in Python. Sometimes even assigning local variables can make a difference.
  • Stronger optimizations of inner loops - maybe use a C-based package, or Cython
  • Parallelize.

@flo-compbio , @gufranca

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