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,TEST] Adding a new, updated realignment module including tests.
[DOC,NOP] Adding dox documentation, whitespace cleanup.
[FIX] updated seqan portfile (according to Macports recommendations), added archs to seqan-apps portfile
[FIX] license update
Merge pull request #272 from weese/feature/fix-macports

[FIX] adapted macports
[FIX] Thread: fixed thread start
[FIX] added const-ref constructor
Merge pull request #273 from esiragusa/fix/thread

Fixed class Thread
[INTERNAL] Refactorization of realign helper functions.
[DOX] Adding deprecation message to old reAlign() function.

Includes a fix such that links in @deprecated etc. are also translated.
[INTERNAL] Marking non-public functions and classes with underscores.
[FIX] ArgParse: fixed argument syntax
Merge pull request #274 from esiragusa/fix/dot

Fixed ArgParse version
[COMMENT] Adding a TODO comment in realignment.
Merge pull request #269 from holtgrewe/feature/realignment

[FEATURE,TEST] Adding a new, updated realignment module including tests.
[FIX] changed hash->std::hash, explicit cast
Merge pull request #276 from weese/feature/fix-bam-scanner

[FIX] removed compile errors of bam scanner
[DOC] Adding @headerfile for function reAlignment().