Thomas Sicheritz-Pontén

Thank you! I noticed that the binary option does only work for symmetric "all vs all" runs, but not for -F and -Q asymmetric distance calculations. As the resulting distance...

It seems the new version has troubles with the -T flag Instead of an expected tsv file, one get binary output instead of a text file ``` ./dashing_s512 cmp -p...

Thank you, that worked! Although only for smaller runs where I have 10,000 genomes. The current run where I have 400,000 genomes works nicely with "-T" writing the csv files...

unfortunately it did not work ... When only using "-k 15" in the second Dashing2 call, I get sensible values - but I can see that it created new sketches...

I assume that one could access them with `network.storePositions()` as mentioned [here](https://stackoverflow.com/questions/40489700/visjs-save-manipulated-data-to-json) But I have no idea if that should be added before or after ` network = new vis.Network(container,...

In line with the original paper, we solved it by adding following line at the end of the `_count_codon` method: ``` self.codon_count = {c:n if n else 0.5 for c,n...

My current solution is a bit clumsy, but it works for me to get the positions after I moved the nodes around. After displaying the html file and turning off...

Thank you for looking into this. Unfortunately, using the toy example "-k 15 -S 65536" still returns inf values. ``` #Dashing2 Panel (Query/Refernce) Output #Dashing2Options: Dashing2Options;k:15;parsebyfile;trimchr;sketchsize:65536;sketchtype:onepermsetsketch;Fastx;canon #Sources genomeA.fasta genomeB.fasta genomeA.fasta...

@ericmjl Did you find the solution to this? We encounter the same inotify problem when implementing cachier in our prediction server.

> @tsp-kucbd I tried using a while loop, as you can see in the PR #25 referenced above. Please try it out and see if it works for you --...