handle empty edge arrays
Fixed merge graph issues

- fixed bug not correctly saving and loading pickle information in merge
  step
- fixed replacement of sub-matrices in merge graphs step that did not
  correctly handle the replacement in scipy syntax
Bugfix in merge duplicate exons

- fixed bug that used wrong index when merging duplicate exons that
  caused exons to be deleted
- fixed deep copy issue of gene list
adapted max edge validation threshold to number of samples
fixed typo