Remove duplicate sequences from fasta file

See https://jira.gsc.wustl.edu/browse/AT-497. 

In the epitope prediction pipeline, downstream steps will fail if the fasta file contains duplicate entries (specifically if the header is the same). This change removes entries that are identical, i.e. the header and the sequence are the same. It will fail if the id is the same but the sequence is different.
I unified the usage to have it be FASTA.