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Consider use of cython for distance parsing #9

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johnlees opened this issue Apr 11, 2018 · 1 comment
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Consider use of cython for distance parsing #9

johnlees opened this issue Apr 11, 2018 · 1 comment
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I think mash dist commands when used with lots of threads are faster than we process their output, which increases memory use. Perhaps writing the parsing section in cython would improve speed and memory here.
@johnlees johnlees added the code Changes to the coding implementation label Apr 11, 2018
@johnlees johnlees self-assigned this Apr 11, 2018
@johnlees johnlees mentioned this issue May 6, 2018
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johnlees commented May 7, 2018

Use tmp files (via command line option) to then http://www.blopig.com/blog/2016/08/processing-large-files-using-python/ to parse multithreaded

ccoulombe pushed a commit to ccoulombe/PopPUNK that referenced this issue Oct 28, 2022
@johnlees
Fix regression parameters
b65888f 
Closes bacpop#9
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