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] 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
[API/FIX] add FreeBSD support to build system

Tested on FreeBSD 10.0. Both gcc49 and system compiler (clang with libc++) tested.
[NOP] cosmetic correction
[BUILD] reverse e80c156c18699fe3b82c6d9302fe54c1462eca89
[BUILD] reverse 920d338ac1ef9d294a34249de33b02fafeed57e7 partially
[BUILD] moved platform to top and exit with warning if unknown platform is detected
Merge pull request #453 from h-2/feature/freebsd-support

Feature/freebsd support
[FIX,BUILD] cmake file lacked target_link_libraries thus missing out on -lexecinfo
[FIX,BUILD] explicitly link against pthread for FreeBSD+Clang
[DOC] fix description and add Remark
Merge pull request #458 from h-2/fix/build_issues_freebsd

Fix/build issues freebsd
[DOC] typos, grammar
Merge pull request #459 from h-2/dox/align_extend

[DOC] fix description and add Remark
[FIX] Gustaf: adapting bp positions from rev strand matches in reference adjacency