diagonal values with dashing dist

[sinamajidian]

Hi Daniel!

I copied a genome in FASTA format into two separate genome files and ran Dashing on them with the following parameters:

$ dashing dist  -O out.txt -o size.txt --use-full-khash-sets a.fa  b.fa 
Dashing version: v1.0.2-4-g0635
$ cat out.txt 
##Names	a.fa	b.fa
a.fa	-	1
b.fa	-	-

which is fine. Based on the output of dashing dist -h I assume dashing dist by default report similarity (i.e. Jaccard similarity Index).

===Distance Emission Types===
Default: Jaccard Index
Alternatives:
-M, --mash-dist    	Emit Mash distance
..

But when I use --full-tsv it shows zero for diagonal values:

$ dashing dist  -O out.txt -o size.txt --use-full-khash-sets --full-tsv a.fa b.fa 
Dashing version: v1.0.2-4-g0635

$ cat out.txt 
#Names a.fa	b.fa
a.fa	0	1
b.fa	1	0

I would have expected the diagonal values to be 1 as well. Probably they were initiated as zero for the distance, the dissimilarity mode.

Best, Sina