- `antitarget`: Choose an appropriate default minimum bin size based on the user-provided average bin size.
- `breaks`: Added an option `--min-probes`, which applies to both sides of the detected breakpoint within a gene.
- `export`: Fixed the `nexus-basic` format to work with Biodiscovery Nexus Copy Number again.
- `target`, `refFlat2bed.py`: Handle overlapping gene annotations a little better.
- Made the dependency on SciPy "soft", only triggered when using the segmentation algorithm `haar`.