sshash
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jermp
A compressed, associative, exact, and weighted dictionary for k-mers.
Hi @jermp ! This is a continuation of my work that I mentioned in #35. With this change, I rewrite current implementation of `kmer_t` in a full-fledged structure that handles...
As per the title, try to avoid that. So annoying. Perhaps a simple linear search over the buckets' thresholds is fast anyway since these are supposed to be very few.
Hi @jermp! I'm currently working on adopting SSHash in MetaGraph, as we want to see if we can improve our performance using it as an internal structure for indexing and...
The output is described here: https://github.com/COMBINE-lab/cuttlefish#cuttlefish-1-output. We want to parse the `.cf_seg` files output by Cuttlefish1 to build the unitigs from a reference dBG.
Store the minimizer's absolute positions rather than those of super-kmers. Align the query kmer to the minimizer's position at query time. This will simplify the code logic avoiding the scan...
Continuing from #22 > >The problem is, that doesn’t work with this code. We immediately get an illegal instruction error. You can see this, e.g. if you pull down the...
**Even if set**, users should be notified about suitable values for m. As documented in the papers, m should be chosen >= log_4(N)+1, where N is the cumulative length (num....