Usage

Command line usage:

sparcs -h

Parameter	Description
--vcf	Absolute path to the VCF file
--gtf	Absolute path to the GTF/GFF file
--ref	Absolute path to the reference genome in FASTA format
--out-dir	Absolute path to the output directory
--chunks	Number of chunks to split the VCF file into for parallel processing
--cores	Number of cores to use for parallel processing
--structure-pred-tool	Structure prediction tool to use (RNAfold or RNAstructure, Default: RNAfold)
--ribosnitch-tool	RiboSNitch prediction tool to use (SNPfold or Riprap, Default: SNPfold)
--ribosnitch-flank	Flanking length for RiboSNitch prediction (Default: 40)
--ribosnitch_prediction_tool	Tool to use for riboSNitch prediction. Options are SNPfold and RipRap
--temperature	Temperature for structural prediction (Default: 37.0)
--minwindow	Minimum window size for RipRap