[FIX] Adapted the parse_lm module to the new stream module.
Merge branch 'feature/stream/stellar_parser' into feature/stream/fix-demos
[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
[FIX] Fixed a compile issue.
[FIX] Adapted the sam tool to the new stream module.
Merge pull request #448 from holtgrewe/hotfix/fiona_updates_dev

Hotfix/fiona updates dev
Merge pull request #447 from holtgrewe/hotfix/fiona_updates

[FEATURE] Updates to Fiona and compute_gain.
[FIX] Started to adjust the roi_io to the new stream module.
[FIX] Fixing file extensions in compute_gain's arg parser.
[TEST] App tests for fiona.
[FIX] Adapted the roi_io module to the new stream module.
[FEATURE] Some adjustments for Gustaf.

Updating versions etc.
Merge pull request #449 from holtgrewe/feature/gustaf_1_0_0

[FEATURE] Some adjustments for Gustaf.
[FIX] Thread: initialized pointers inside constructor
Merge pull request #450 from esiragusa/fix/thread

Fixed Thread class
added enum and function with run-time parameter
Updated translation module to contain an enum for Spec-selection -> more user-friendly
[FEATURE/FIX/API] cleanup translation module; c++11-ify; changed parameters; seqan Parallalism instead of macros
[DOC] fix documentation for GeneticCodeSpec