will-rowe
Option to print "smash" to STDOUT?
I need to massage the output from "smash" to create a distance matrix in the same form as that from Mash so I can reuse downstream visualization code. Right now, I indicate a prefix for the output file, run "smash," then look for an expected file name, then read that and create a new file. If there were a "--stdout" type flag for "smash," then I could just capture the text directly and forego all that other stuff. Maybe a separate issue, but it would be nice if this default smash output were closer to the kind of matrix that Mash and other tools create (e.g., add the sample names along to the rows, allow for comma or tabs as separators).
Good suggestion. So as to not break HULK by changing the default smash matrix, I will look into adding a --mashFormat option or similar.
