Allow multiple separate fastq queries

[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.

superfocus -q file1.fastq -q file2.fastq -q file3.fastq -dir output

[metageni]

@linsalrob Cool bens! Could you please update the README? I'm happy to merge once it is done. thanks