[TEST] Yara: updated reference files
[FIX] Yara: removed a debug warning
[FIX] Yara: oveloaded StringSetLimits<> to use 32 bit sizes for contig seqs and names
[TEST] Yara: updated reference files
[NOP] Yara: cleaned up includes
Merge pull request #446 from esiragusa/fix/apps/yara

Fix Yara tests
[FIX] Lambda Find: fixed const reference problem reported by gcc 4.7
Merge branch 'fix/apps/yara' into develop

* fix/apps/yara:
  [FIX] Lambda Find: fixed const reference problem reported by gcc 4.7
[FIX] Started to adapt the demos to the new stream module.
[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.