[FEATURE] Added a very simple app determines for each read in a reference file if it has an entry in the provided sam files.
[INTERNAL] Moved from extras to core.
[DOC, INTERNAL] Added a read and made some minor description changes.
[FIX] Changed the CMake files such that all files are found and some additional info.
[TEST] added test documenting the issue
[FIX] added missing gkn-ignore tag to file arguments
[DOC] Changed some docu of sam2matrix.
[DOC] Added some documentation.
[TEST] Adapted the test to new command line usage.
[DOC] Changed one format to be tsv instead of csv
[INTERNAL] Changed the file handling if no reference files are specified.
Merge pull request #299 from singerj/sam2matrix

sam2matrix - This program outputs for each read the ids of references it. (master)
[TEST] Search/Join: truncated dna datasets
[TEST] Search/Join: updated dna results
[TEST] Search/Join: truncated geo datasets
[TEST] Search/Join: updated geo results
[TEST] Search/Join: lowered the number of parameters tested
Merge branch 'hotfix/test/searchjoin'
Merge pull request #325 from aiche/fix/arg-parse-argument-missing-gkn-ignore-tag

[FIX] arg parse argument missing gkn ignore tag
[DOC] Segment: fixed dox typos