Allowing either one or multiple fasta/q files

[linsalrob]

This PR overloads the --query option to allow any of

• a single fasta/q file
• multiple fasta/q files
• a directory of fasta/q files

You can now specify multiple fasta/q files independently rather than providing a directory with them.

e.g.

focus -q file1.fastq -q file2.fastq -q file3.fastq --ouput_directory output