[FIX] Fixed access on profileChar.count
[FIX] defined lots of default values
[API,FEATURE] added additional input and output type prefix to arg_parse.

Added two new ArgumentTypes, INPUTPREFIX and OUTPUTPREFIX. The user can now declare prefix
options/arguments which will be returned by the parser like a string option/argument but
indicate that more then one file with this shared prefix will be generated by the tool.
The user is responsible to make sure that all files he creates really share the prefix.
Note that no restriction checking is carried out while parsing. The supported format is
only an indicator for workflow engines like knime.
[NOP]
[FIX] cleaned up tool and file names, simplified build file, fixed bugs
Merge pull request #368 from weese/hotfix/knime-snpstore

[FIX] defined default values for snp-store
[FIX] added missing files
Merge branch 'master' of https://github.com/skrakau/seqan into skrakau-master
[FIX] add dependent libraries to tests
Merge pull request #371 from weese/singerj-hotfix-knime-flexbar

[FIX] Prepared seqan::flexbar for KNIME (master)
[FIX] removed OpenMP bug
[FIX] fixed clang warning
Merge branch 'hotfix/bs-tools' of github.com:weese/seqan into skrakau-master
Merge pull request #373 from weese/hotfix/bs-tools

[FIX] fixed bs_tools compiler bugs
[FIX] Fixed a cake problem when Boost is not available.
[FIX] Fixed a cake problem when Boost is not available.
Merge pull request #375 from singerj/hotfix-bs_tools

[FIX] Fixed a cake problem when Boost is not available.
[FIX] fixed unused typedef warnings
Merge branch 'master' into hotfix/bs-tools
[FIX] removed unused typedefs