our $bin_size = 1000; #number of bases pairs to comprise one region in the arrays below
our $localization_window_size = 10000; #number of regions to sum together. Each entry in the arrays below is the sum of this many regions
our $expected_mutation_density = 0.0000005;
our $collapse_regions = 1;
our $outlier_deviation = 2;
our $translocation_cut_off_count = 8;
#Hallmark Weightings
our $genome_localization_weight = 0.1145;
our $chromosome_localization_weight = 0.1697;
our $cnv_weight = 0.2724;
our $translocation_weight = 0.2724;
our $insertion_breakpoint_weight = 0.0657;
our $loh_weight = 0.0648;
our $tp53_mutated_weight = 0.0406;