Updates includes:
- bug fixes
- addition of haplotype-constraint groups and automatic pipeline for inferring them form long reads
- adjacency output in bedpe other new formats
- karyotype stats utility
- adjacency stats utility
- improved error handling and correction for main and utility RCK inputs
- improved performance via new ability to presolve on a per-chromosome level and use the results as an (incomplete) starting vector for the main ILP.
- additional input/output formats for both Adjacencies and Segments (in general and CNA specifically)