dnbaker / dashing2

Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.
MIT License
62 stars 7 forks source link

Breaking changes: default output mode #28

Closed dnbaker closed 3 years ago

dnbaker commented 3 years ago

For dashing2 sketch --cmpout <path> or dashing2 cmp, the default distance mode was PHYLIP upper-triangular. This didn't match Dashing and could be confusing. Now, the default output mode matches Dashing (upper-triangular, with dashes to represent the diagonal and the lower triangular.

To get the PHYLIP output, use --phylip.

Besides this, there's additional error-handling, and automatic batch-size selection based on the sketch sizes and estimated (largest) cache size.