[FIX] a more secure way of _toBamTagValue that replaces memcpy by unions
[FEATURE] added alignment functors and refactored getCigarString and getMDString
[FIX] fixed too short MD tag format
Merge branch 'develop' into feature/new-fragstore-sam-output
[NOP] debug infos
Merge branch 'feature/new-fragstore-sam-output' of github.com:weese/seqan into feature/new-fragstore-sam-output
[FIX] added missing test files for test_store
[FIX] changed permissions
[FIX] fixed error paired-end SAM import
Merge branch 'feature/new-fragstore-sam-output' of github.com:weese/seqan into feature/new-fragstore-sam-output
[FIX] removed debug output
[FIX] added 2-way merge for aligned reads
[FIX] added and fixed test for merging sam files
[FIX] adapted tests to fixed MD strings
[FIX] adapted mason's gold standard to new MD strings
[FIX] fixed razers3 and its test for new MD strings
[FIX] fix masai to new fragment store SAM I/O
[FIX] fixed consensus test to new SAMtools like format of printAlignment()
[FIX] replaced old SAM writer completely
[FIX] fixed fillRecord for single-end reads
[FIX] fixed const bug