[FEATURE] moved fiona from sandbox_weese to github
[FIX] switched to mismatches-only mode
[FIX] re-enabled old behavior, indel correction, only mismatches in overlap, consensus, max overlapsum
[FIX] unused-variable-warning removed
[FIX] fixed concurrency bug
[FIX] restored ISMB behavior with defines, added define sections for
ISMB and indels
[FIX] removed overlapSumCutoff hack
increased allowed overlap errors to at least 2
Merge branch 'master' of github.com:seqan/seqan into feature/fiona
[DOC] Readme updated
[FIX] fixed warnings
[FIX] fixed includes
[FIX] master version fix and include fix
[FIX] version.h include
[FIX] no longer add line breaks in output file
[FIX] disabled line breaking
[TEST] added app test
[FIX] Fixed access on profileChar.count
[FEATURE] Adjusted flexbar to KNIME (splitted flexbar into smaller sub-programs)
[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.