[FEATURE] Updates to Fiona and compute_gain.

* fiona uses different default values now
* compute_gain accepts BAM format for the gold standard file now
Merge branch 'hotfix/fiona_updates' into hotfix/fiona_updates_dev

Conflicts:
	core/apps/fiona/compute_gain.cpp
Merge pull request #448 from holtgrewe/hotfix/fiona_updates_dev

Hotfix/fiona updates dev