New functionalities added: Now outputs a concatenated Shortstack file called "concatenated_shortstacks.tsv" that contains all predicted sRNA loci from all samples. Small RNA loci corresponding to a MIR gene hairpin will have the hairpin sequence added. Finally, a unique cluster id (column "cluster_unique_id") is added so that all individual sRNA loci from every sample will have a unique identifier. That can be useful when several sRNA loci correspond have a common MIR gene homolog in miRBase for instance. Uses a "samples.tsv" file to list the sample names, their fastq file location and the genomic reference to use. Calculate the minimal folding energy for all predicted hairpins using Vienna RNA RNAfold program. This information can be used to fold the stem-loop structure of hairpins (using the RNAplot program from Vienna RNA package).