[WIP] Experiment compacting counttables into a nodetable given a max abundance criterion#1874
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standage wants to merge 1 commit into
Open
[WIP] Experiment compacting counttables into a nodetable given a max abundance criterion#1874standage wants to merge 1 commit into
standage wants to merge 1 commit into
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Scenario: I want to query some big ol' counttables, and my k-mers of interest are those that are abundance <= X. Rather than keeping several of these big counttables in memory at once, I'd like to be able to initialize and update a nodetable (with the same number of buckets) to indicate which k-mers satisfy the given criterion. That way I only have to keep one counttable in memory at a time.
This PR introduces two new methods for nodetables:
compose_init, andcompose_update. These methods do bit flipping directly on the byte array.The build is currently failing. I'm guessing there's an issue at the C++ level, and maybe at the Cython level as well. This could really benefit from a preliminary review from @luizirber or @camillescott.
make clean diff-coveror the CodeCov report that is automaticallygenerated following a successful CI build.)
changes were made?
CHANGELOG.md? Seekeepachangelog for more details.