[FIX] Fixing file extensions in compute_gain's arg parser.
[TEST] App tests for fiona.
[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).
[FIX] Fixing dox tests to run with Python nosetests.

Also, integrating into travis builds.
[FIX] Requiring python-jinja2 for master as well (dox tests).
Merge pull request #468 from holtgrewe/hotfix/dox_nosetests

[FIX] Fixing dox tests to run with Python nosetests.
Merge pull request #463 from holtgrewe/hotfix/fiona_tests

Changes to fiona and app tests