Improve performance by caching k-mer abundance query results #276
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standage
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Codecov Report
@@ Coverage Diff @@
## master #276 +/- ##
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+ Coverage 97.54% 97.55% +<.01%
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Files 47 47
Lines 2937 2941 +4
Branches 511 511
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+ Hits 2865 2869 +4
Misses 45 45
Partials 27 27
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Related to #208, this pull request uses the
lru_cachedecorator to cache results from every invocation ofkmer_is_interestingfunction. With a sufficiently large cache, a k-mer (especially repetitive k-mers) in multiple nearby reads should require only a single invocation of the command. Subsequent invocations with the same arguments will pull from the lru_cache instead of re-executing the command.Preliminary results aren't too promising. The cost of caching results doesn't seem to compensate for the savings gained by avoiding repeat calls.