Merge pull request #257 from holtgrewe/hotfix/store_swap

[FIX] Fixing swap() for FragmentStore.
Merge pull request #266 from weese/hotfix/static-linkage

Enabled static linkage of libstdc++ and libgcc for apps (master, apply after develop)
[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.
Merge branch 'master' into develop
Merge pull request #285 from weese/feature/app-samcat

[FEATURE] added a new app for SAM/BAM concatenation and conversion (develop)
[FIX] replaced C++11 dependency by boost::math for isnan, warnings removed
Merge pull request #289 from weese/hotfix/snp-store

[FIX] fixed snp_store under Windows (develop)
[TEST] Masai: updated fm-index test files
[FIX] String: fixed save()
[FIX] String: typo
Merge pull request #294 from esiragusa/fix/masai

Fix Masai FM-index test
[FIX] ConcatDirect StringSet: fixed types of Infix<>, Suffix<>, Prefix<> and GetValue<>
[FIX] ConcatDirect StringSet: fixed types for thrust overloads