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Look into converting sequences into bit strings #22
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The majority of the execution time is spent bootstrapping (eg: 151 seconds out of 164 seconds on Windows, using |
Ok but won't bootstrapping the match/mismatch binary vector instead of sequences speed things up considerably? |
Also try replacing |
Yes, that would. Using I also found using random.choices to pre-compute a list of random numbers, and slicing the list at each window could increase performance. Using
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I think using the match/mismatch binary vector and |
Two options:
Computing number of differences should be attainable by a fast bitwise operator.
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