Initial commit of Remove Germlines

Not yet tested but in full theoretical working order.
Totally revamped functionality.

Now filters CLIP fasta files to do what is requested. Not yet tested but
theoretically fully working.
Can now remove N or n
Added codon mut feature

Can now remove codons (replace with "---") with more than a certain number of
mutations from the germline.
Removed bug where remove stops is ignored
Removed bug where N's were removed from headers
Added custom filter feature

Users can now add their own filter to find in the header and remove all
sequences that do not meet such a criteria. Can also specify which field (split
by "|") the term should be in.
Added several features

Can now filter by germline, can filter normal fasta files, can remove by the
custom filter, and maybe more.
Various bug fixes
Added a basic README, added missing parentheses
Merge https://github.com/GregorySchwartz/modify-fasta