[FIX] Normalizing line endings when comparing text files.
Merge pull request #422 from holtgrewe/hotfix/compare_text_file_line_endings

[FIX] Normalizing line endings when comparing text files (master).
[Fix] Converted double align scores to int scores to avoid different 32bit 64bit behaviour.
Merge pull request #428 from skrakau/master

Bisar: converted alignment scores to integers
[FIX] Fixing default parameters for quality values in Mason 2.
Merge pull request #430 from holtgrewe/master

[FIX] Fixing default parameters for quality values in Mason 2.
[FIX] Adjusting tests to updated quality parameters.
Merge pull request #432 from holtgrewe/fix/mason2_tests

[FIX] Adjusting tests to updated quality parameters.
[DOC] Masai: Updated README
[DOC] Masai: Updated INFO
[NOP] Masai: added deprecation warning
Merge branch 'hotfix/masai-0.7.2'
[CLI, TEST] Masai: removed the whole app
Merge branch 'hotfix/apps/masai'
Merge pull request #440 from esiragusa/apps/masai/master

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

[FEATURE] Updates to Fiona and compute_gain.
[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.