Merge pull request #17 from brainstorm/master

Several usability issues fixed, needs more human testing
conflict
Merge branch 'master' of github.com:SciLifeLab/facs
pulled the correct version from Roman
fix incorrect parameters for getopt in big_query.c
\r\n check for dos format text
dos and linux format extra line tolerant
elegant way of being extra line tolerant
Capital B for Bloom and threshold value instead of
classify help doc
Merge branch 'master' of https://github.com/SciLifeLab/facs
Added ecoli with chapmanb modifications
Merge