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.
This isn't something that changed in this PR, but is there a significance to the output being referred to as a 'FASTA' while the input is described as a 'Fasta' (both here and in `input_file` and `output_file`)?