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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
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:
@flo-compbio , @gufranca
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