Daniel Baker

I think it's Diamond is compiling from source by specifying architecture, e.g., https://github.com/bbuchfink/diamond/blob/master/Dockerfile#L11, which is simply using cmake and building for bare x86-64 (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/diamond/build.sh). I'll work with bioconda again for...

Hi alienzj -- Thanks for the report! I'll give it a look. The flags should help. I'm not surprised that 512 failed, since your machine doesn't have avx512 support. In...

`dashing hll` simply computes the cardinality of all sequences provided to it, which I don't think is what you want. If you want to know how many unique k-mers overlapped,...

Hi, The first one means that by its estimate, the smaller sequence is almost entirely contained in the larger sequence. The second command-line says that 0.05% of the k-mers in...

Hi Ahmad, I'm happy to help, but I'm not quite sure exactly what you're looking for. Are you looking for multiset similarity, where multiple instances of the same k-mer are...

Hi! Thanks for making the issue. 1. For what you're trying to do, you want to use the `--cache-sketches/-W` option; this will cache a sketch adjacent to the input filename...

Hi Mihkel, Sorry for making you wait. You're correct, it is `--presketched`, not presketched-only. Presketched means that the files themselves contain one sketch per file. The `dist_by_seq` command is for...

Thank you! I was trying to address the cache-sketches issue, but modified the wrong variable. It should be fixed now in both master and dev.

Hi Mihkel, Thanks for the request! I think that's absolutely useful. I've pushed a patch to this branch (https://github.com/dnbaker/dashing/tree/dependency), which should emit the error message. However, the error is being...

https://github.com/dnbaker/dashing/commit/5210548e6ba96deb21963e7e2b3df735a1542e1a I merged that branch into master, sorry. Give that a shot? And yes, the cardinality will be garbage due to what the default (un-filled) value is. I think I...