kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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Option to store and load pickle of interval forest in varfilter module #340

Closed standage closed 5 years ago

standage commented 5 years ago

The vast majority of time in the varfilter module is spent populating the index. Unlike some other components that are based on reference data, one or two reference indexes can be stored and used in a variety of contexts regardless of ksize and other parameters.

The varfilter module should have an option to store a pickle of the index and load it again later.