First commit

The mutation count program at its first version
Style fixes

Fixed some double empty lines and lacking parentheses, etc.
Multi-line sequence support and mutCount added

Can now support multi-line sequence fasta files. Also added feature to only
count unique mutations that appear N or greater times.
Fixed bug with the multi-line parser

No longer repeats clones after germlines
Fixed error with empty list in fasta formatting

Seems to be due to double newline "\n\n" or more, cannot find them so removing
them all.
Fixed bug with taking out duplicate newlines

Was taking out single newlines as well.
Fixed newline bug once and for all

Was an error in the entry fasta files (no sequence under a few headers) so fixed
that by removing those with no sequences. Also kept in the repeated newline
remover.
Removed debugging writefile line
codon2aa unifies gap symbols
Can now remove N or n
Removed bug where N's were removed from headers
Ready for pushing
Merge https://github.com/GregorySchwartz/count-mutations

Conflicts:
	README.md