[FEATURE] Added a very simple app determines for each read in a reference file if it has an entry in the provided sam files.
[INTERNAL] Moved from extras to core.
[DOC, INTERNAL] Added a read and made some minor description changes.
[FIX] Changed the CMake files such that all files are found and some additional info.
[FIX] removed VS12 ambigous bug
Merge pull request #308 from weese/hotfix/fix-vs12

[FIX] removed VS12 ambigous bug
[FIX] simplified some math and conversions
Merge pull request #310 from weese/hotfix/snp-store

[FIX] simplified some math and conversions
[FIX] Disabling Mason2 in Visual Studio <10

Somehow copy constructors are not properly called with 64 bit binaries.  32 bit binaries are fine.
Merge pull request #314 from holtgrewe/hotfix/disable_mason2_old_vs

[FIX] Disabling Mason2 in Visual Studio <10
[FIX] fixed broken CMakeLists.txt
[FIX] fixed numerical instability
Merge pull request #316 from weese/hotfix/snp-store

[FIX] fixed numerical instability
[FIX] MSC version check
Merge pull request #320 from weese/hotfix/snp-store

[FIX] MSC version check
[TEST] added test documenting the issue
[FIX] added missing gkn-ignore tag to file arguments
[DOC] Changed some docu of sam2matrix.
[DOC] Added some documentation.
[TEST] Adapted the test to new command line usage.