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RED memory usage is high on simplex reads #220

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brianwalenz opened this issue Dec 18, 2023 · 0 comments
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RED memory usage is high on simplex reads #220

brianwalenz opened this issue Dec 18, 2023 · 0 comments
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enhancement New feature or request

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@brianwalenz
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Verkko makes RED batches with exactly 20,000 reads in them. for long simplex reads, this exhausts (default) memory limits.

Adding a parameter to set 'red_total' or something like that instead of the hardcoded len=19999 at c4-findErrors.sm line 46 would work. But it's not that much work to do actual partitioning based on read length. Ideally we'd set the max based on red_memory but that's been a headache in canu to get the scaling correct...

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