Merge branch 'hotfix/apps/masai'
Merge pull request #440 from esiragusa/apps/masai/master

Removing app masai from master
Merge pull request #447 from holtgrewe/hotfix/fiona_updates

[FEATURE] Updates to Fiona and compute_gain.
[FEATURE] Adding support for "supplementary" flag for BAM I/O.

Includes tests and documentation.
Merge pull request #466 from holtgrewe/hotfix/bam_supplementary_flag

[FEATURE] Adding support for "supplementary" flag for BAM I/O (master).
Merge branch 'master' into develop