@brainstorm 
(py2.7)-bash-4.1$ ./facs query

Usage: ./facs query [options]
Options:
        -r reference Bloom filter to query against
        -q FASTA/FASTQ file containing the query
        -l input list containing all Bloom filters, one per line
        -t threshold value
        -s sampling rate, default is 1 so it reads the whole query file

(py2.7)-bash-4.1$ ./facs query -h

Usage: ./facs query [options]
Options:
        -r reference Bloom filter to query against
        -q FASTA/FASTQ file containing the query
        -l input list containing all Bloom filters, one per line
        -t threshold value
        -s sampling rate, default is 1 so it reads the whole query file