This is a fork of longshot for use in the smrest mutation caller. It was modified to expose additional data structures, and to use the kprobaln model from HTSlib. End users should not need to use this repository directly. All credit for this code goes to the authors of Longshot, with thanks for providing it under the MIT license for extension and use here.

If you use Longshot, please cite the publication:

Edge, P. and Bansal, V., 2019. Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Nature communications, 10(1), pp.1-10.