--bamfiles            Only process BAM files
 --bedtools_path       path to BEDTools executable (leave blank if in path)
 --bins                Width of bins to use for mapping reads
                         [Current value: 75]
 --bowtie              Perform bowtie2 alignment [1/0]
                         [Current value: 1]
 --bowtie2_add_flags   Additional flags to use for bowtie2 alignment
 --bowtie2_genome_dir  Directory and basename for bowtie2 .bt2 indices
 --bowtie2_path        path to bowtie2 executable (leave blank if in path)
 --dam                 Specify file to use as Dam control
 --extend_reads        Perform read extension [1/0]
                         [Current value: 1]
 --extension_method    Read extension method to use; options are:
                         full: Method used by version 1.3 and earlier.  Extends all reads to the value set with --len.
                         gatc: Default for version 1.4 and above. Extends reads to --len or to the next GATC site, whichever is shorter.  Using this option increases peak resolution.
                         [Current value: gatc]
 --full_data_files     Output full binned ratio files (not only GATC array)
 --gatc_frag_file      GFF file containing all instances of the sequence GATC
 --just_align          Just align the FASTQ files, generate BAM files, and exit
 --kde_plot            create an Rplot of the kernel density fit for normalisation (requires R)
 --keep_original_bams  Keep unextended BAM files if using single-end reads
 --len                 Length to extend reads to
                         [Current value: 300]
 --load_defaults       Load this saved set of defaults
                         (use 'list' to list current saved options)
 --max_norm_value      Maximum log2 value to limit normalisation search at (default = +5)
                         [Current value: 5]
 --method_subtract     Output values are (Dam_fusion - Dam) instead of log2(Dam_fusion/Dam) (not recommended)
 --min_norm_value      Minimum log2 value to limit normalisation search at (default = -5)
                         [Current value: -5]
 --no_file_filters     Do not trim filenames for output
                         [Current value: 1]
 --norm_method         Normalisation method to use; options are:
                         kde: use kernel density estimation of log2 GATC fragment ratio (default)
                         rpm: use readcounts per million reads (not recommended for most use cases)
                         rawbins: new experimental method, may be more accurate
                         [Current value: kde]
 --norm_override       Normalise by this amount instead
 --norm_steps          Number of points in normalisation routine (default = 300)
                         [Current value: 300]
 --out_name            Use this as the fusion-protein name when saving the final ratio
 --output_format       Output tracks in this format [gff/bedgraph]
                         [Current value: bedgraph]
 --paired              Process paired-end reads (experimental, use with caution)
 --ps_debug            Print extra debugging info on pseudocount calculations in log file
 --ps_factor           Value of c in c*(reads/bins) formula for calculating pseudocounts (default = 10)
                         [Current value: 10]
 --pseudocounts        Add this value of psuedocounts instead (default: optimal number of pseudocounts determined algorithmically)
 --q                   Cutoff average Q score for aligned reads
                         [Current value: 30]
 --qscore1max          max decile for normalising from Dam array
                         [Current value: 1]
 --qscore1min          min decile for normalising from Dam array
                         [Current value: 0.4]
 --qscore2max          max decile for normalising from fusion-protein array
                         [Current value: 0.9]
 --reset_defaults      Delete user-defined parameters
 --samtools_path       path to samtools executable (leave blank if in path)
 --save_defaults       Save runtime parameters as default
                         (provide a name to differentiate different genomes -- these can be loaded with 'load_defaults')
 --threads             threads for bowtie2 to use
                         [Current value: 7]
 --write_raw           Write TSV file with raw counts for each Dam, sample pair