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Some optimizations to tree intersection #46

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@dcjones dcjones commented Oct 5, 2018

Here's some progress on reducing overhead in the tree intersection iterator. My test case is finding all intersections between RNA-Seq reads and annotated transcripts in a dataset with ~18 million such intersections. With this I was able to improve run time from 46 seconds to 6.7 seconds.

Don't ask me to explain why storing the state in nullables works better than Union{Nothing, ...}. The compiler works in mysterious ways. 🤷‍♂️

@StefanKarpinski
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Please do report any cases that you encounter like this where Union{Nothing, ...} doesn't have the performance it should so that we can investigate and improve the compiler to fix it!

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codecov bot commented Oct 5, 2018

Codecov Report

Merging #46 into master will decrease coverage by 0.47%.
The diff coverage is 82.75%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #46      +/-   ##
==========================================
- Coverage   97.65%   97.18%   -0.48%     
==========================================
  Files           3        3              
  Lines         596      603       +7     
==========================================
+ Hits          582      586       +4     
- Misses         14       17       +3
Impacted Files Coverage Δ
src/IntervalTrees.jl 97.14% <82.75%> (-0.55%) ⬇️

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