Better fasta/q functionality

[gstarrett]

Current code is seemingly functional only for SRR data. If the user inputs a fasta/q file, when it comes to using the magicblast sam file, it attempts to use a directory with the same name as the fastq file. Software also attempts to sort the sam file using pysam and errors out due to NotImplementedError: pileup of samfiles not implemented yet.

Lastly if fasta/q are going to be thoroughly supported, VirusFriends should also be able to accept gzipped versions of fasta/q files.