Added numeric CSV output
Added - options for stdin and stdout
Added GAPMM (AVERAGED and gap vs a character is like an N versus a character) resolution mode
Shortest Path Added (pass 1)
Shortest Path Added (pass 1)
Real valued vectors and better scaling functions
Added two output options (FASTA and JSON)
Added the option to set the source sequence
Using double-quotes in JSON ouput
Added the penalty argument; fixed the bug that would connect sequences with insufficient overlap; added distance output to FASTA files
Now reporting mean distances; also reduced the # of critical blocks
Merge branch 'master' of github.com:veg/TN93
Added sequence randomization for pairwise comparisons
Fixed segfault crash with 6 CLI arguments
not sure what this was for
Merge branch 'master' of github.com:veg/TN93

Conflicts:
	src/TN93.cpp
Factored out common code; started working on read_reducer; updated CMakeLists.txt
Read reducer kind of working now
read_reducer working
Initial Commit