paoloczi
commented
4 years ago Getting close! I you just remove those using I will merge it, then I will add an explanation in the description of --MarkerGraph.minCoverage in the help message and the documentation, and expand the error message. This is a nice piece of work that simplifies using Shasta, particularly at low coverage.
This adds a method for dynamically selecting a Marker.minCoverage cutoff, using the distribution of coverages from the marker disjoint set object during runtime.
So far it passes all test cases I could generate, but I am going to spend a bit more time evaluating the no-peak cases, so it shouldn't be merged until then.