usage: java -jar ProbeSHIFTR.jar [-bf <arg>] [-blat <arg>] [-cw] [-d
       <arg>] [-D <arg>] [-f <arg>] [-g <arg>] [-h] [-irk] [-l <arg>]
       [-log] [-match <arg>] [-n <arg>] [-nm <arg>] [-o <arg>] [-p <arg>]
       [-pbl <arg>] [-r <arg>] [-rbl <arg>] [-rmf <arg>] [-rscript <arg>]
       [-s] [-score <arg>] [-t <arg>]
 -bf,--bases2filter <arg>               bases to filter for polybases in
                                        oligos (Default: ACGT)
 -blat,--blat-path <arg>                path to BLAT executable (Default:
                                        assumed to be in the environmental
                                        variable PATH)
 -cw,--check-within-target              check for homologies within target
                                        sequence (Default: false)
 -d,--database-fasta <arg>              database sequence file for BLAT
                                        searches (e.g. genome.fasta)
 -D,--database-dir <arg>                directory containing fasta files
                                        for BLAT searches
 -f,--fragment-size <arg>               if gaps between oligos are longer
                                        than the fragment size then oligos
                                        with too many off-targets are used
                                        to fill these gaps (Default: 200)
 -g,--gtf-files <arg>                   gtf/gff annotation files to
                                        consider protein-coding exonic
                                        off-target regions (separated by
                                        semicolon without spaces e.g.
                                        anno1.gtf;anno2.gtf)
 -h,--help                              print this message
 -irk,--include-repetitive-kmers        include repetitive kmers (Default:
                                        false)
 -l,--oligo-length <arg>                length of antisense oligos
 -log,--log-file                        write log file to evaluate
                                        sequence complexity filters
                                        (Default: false)
 -match,--min-match <arg>               minimal matches for BLAT searches
                                        (Default: 1)
 -n,--include-n <arg>                   include N in repeat filtering
                                        (Default: true)
 -nm,--n-repeats <arg>                  relative freuqnecies of N repeats
                                        in oligos (Default: 0.001)
 -o,--output-dir <arg>                  directory to store oligo designs
                                        and temporary files (e.g. BLAT
                                        results)
 -p,--processes <arg>                   number of parallel
                                        threads/processes to run BLAT
                                        comparisons
 -pbl,--polybase-length <arg>           relative length of polybases
                                        within oligo (Default: 0.8)
 -r,--max-repeats <arg>                 maximal percetage of repeats
                                        (Default: 0.07)
 -rbl,--repeat-length-polybases <arg>   length of polybase repreats within
                                        sequences (Default: 15)
 -rmf,--repeat-masking-format <arg>     repeats masked with upper or lower
                                        cases or no masking in data
                                        (lower, upper; Default: lower)
 -rscript,--rscript-path <arg>          path to Rscript executable
                                        (Default: assumed to be in the
                                        environmental variable PATH)
 -s,--get-sense                         create sense oligos (Default:
                                        false)
 -score,--min-score <arg>               mininmal score for BLAT searches
                                        (Default: 10)
 -t,--target-fasta <arg>                fasta containing target
                                        sequence(s)