Merge pull request #257 from holtgrewe/hotfix/store_swap

[FIX] Fixing swap() for FragmentStore.
Merge branch 'develop' of github.com:weese/seqan into develop
Merge pull request #266 from weese/hotfix/static-linkage

Enabled static linkage of libstdc++ and libgcc for apps (master, apply after develop)
Changed from pre-compilation to live compilation, added a portfile for
LEMON
Merge branch 'develop' of github.com:weese/seqan into develop
[DOC] Fixed and extended the docu around MatrixScore.
The world’s best formatted scoring tables!
typedefs
Rename “private” tags to by defining new typedefs. This is backward compatible. Adapted the documentation
Merge branch 'develop' of github.com:seqan/seqan into develop
Merge branch 'develop' of github.com:weese/seqan into develop
Changed .cpp to .txt. result is the same
[FEATURE] add samcat app for concatenation and conversion of SAM/BAM files
[FIX] replaced CharString by std::string
[FIX] registered samcat for KNIME and test system
[FIX] cosmetics
[FIX] Fixing mason2 on Windows

The fix looks quite esoteric and I think that the problem is also a bit esoteric.
I am not sure yet whether we did something wrong in SeqAn, or the MSVC optimizer
is a bit too harsh in is optimization.  In any case, it appears to be related to
using seqan::maxValue<int>() instead of seqan::MaxValue<int>::VALUE.  Note that
we do not have to replace all occurences but one is enough for each int and unsigned.
Merge pull request #286 from holtgrewe/hotfix/mason2_vs

[FIX] Fixing mason2 on Windows
[FIX] Fixing MSA with equal sequences.

Should fix #283 in upstream.
Merge pull request #287 from holtgrewe/hotfix/msa_equal_seqs

[FIX] Fixing MSA with equal sequences.