feat: Reduce kmer spacing for short sequences#1242
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corneliusroemer wants to merge 1 commit intomasterfrom
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feat: Reduce kmer spacing for short sequences#1242corneliusroemer wants to merge 1 commit intomasterfrom
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This is a good heuristic to avoid lack of seed matching in short sequences If default kmer spacing is 50, a sequence of 180bp gets only 3 kmers which is not robust
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This is a good heuristic to avoid lack of seed matching in short sequences (~1% of RSV A is only ~200bp long)
If default kmer spacing is 50, a sequence of 180bp gets only 3 kmers which is not robust
I put the parameter adjustment next to the other short-sequence heuristic but this means we have to make params mutable. Might be better to bury the parameter adjustment further up or down the stack. Thoughts @ivan-aksamentov?
We may or may not want to expose the const
MIN_KMER_NUMas a CLI arg. I don't think it's necessary for user to adjust so we can get away with hard coding it for now, I think.See https://neherlab.slack.com/archives/C015PFP5V44/p1693408681322229