[FIX] Error rate in Stellar has to be > 0.

git-svn-id: http://svn.seqan.de/seqan/trunk@13269 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Checking exact alignment columns for overlaps in Stellar.

git-svn-id: http://svn.seqan.de/seqan/trunk@13270 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing gapped extension for very high gap penalties.

git-svn-id: http://svn.seqan.de/seqan/trunk@13271 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] find_backtracking: old ifdef updated

git-svn-id: http://svn.seqan.de/seqan/trunk@13272 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] index_fm.h from extras renamed to index_extras.h

git-svn-id: http://svn.seqan.de/seqan/trunk@13273 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] masai: index_fm.h changed to index_extras.h

git-svn-id: http://svn.seqan.de/seqan/trunk@13274 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] index_fm.h from extras renamed to index_extras.h

git-svn-id: http://svn.seqan.de/seqan/trunk@13275 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] fix wait() and disabled mmap file pages for now

git-svn-id: http://svn.seqan.de/seqan/trunk@13276 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Removed a deprecated header file.

git-svn-id: http://svn.seqan.de/seqan/trunk@13277 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Updating musceteer headers.

git-svn-id: http://svn.seqan.de/seqan/trunk@13278 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing synopsis module to not depend on config.h

git-svn-id: http://svn.seqan.de/seqan/trunk@13279 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Corrected the documentation for countOccurrences of wavelet trees.

git-svn-id: http://svn.seqan.de/seqan/trunk@13280 e6417c60-b987-48fd-844e-b20f0fcc1017
[FEATURE] Rewrite of the SeqAn build system.

 * Enables per-app build system creation which makes creating packages easier.
 * Automatically recursively adds all demos which makes it less probable to forget to add a CMakeLists.txt when adding a subdirectory in demos.
 * All binaries go to `bin/` now.
 * Release is the default build mode.
 * Separate SeqAn build system and finding the SeqAn library.  The FindSeqan.cmake module can be used to find the SeqAn library independently of the SeqAn build system now.
 * Applications can now enable ceratin SeqAn features in their own directory without affecting all other binaries.
 * Adjustment of all core and extras apps.
 * Adding backward compatibility such that developers are not force to upgrade their sandbox right now.




git-svn-id: http://svn.seqan.de/seqan/trunk@13281 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] find_backtracking_bfs

git-svn-id: http://svn.seqan.de/seqan/trunk@13282 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] index_sa_stree: using the right index size type

git-svn-id: http://svn.seqan.de/seqan/trunk@13283 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] find_backtracking: using _min() instead of std::min()

git-svn-id: http://svn.seqan.de/seqan/trunk@13284 e6417c60-b987-48fd-844e-b20f0fcc1017
[INTERNAL] masai: genome size/limits metafunction overloaded

git-svn-id: http://svn.seqan.de/seqan/trunk@13285 e6417c60-b987-48fd-844e-b20f0fcc1017
masai: find_backtracking_bfs added to app CMakeLists.txt

git-svn-id: http://svn.seqan.de/seqan/trunk@13286 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] masai_sorter: debug message removed

git-svn-id: http://svn.seqan.de/seqan/trunk@13287 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] file_page: warning removed

git-svn-id: http://svn.seqan.de/seqan/trunk@13288 e6417c60-b987-48fd-844e-b20f0fcc1017