new fitness method added to genetic algorithm
removed unnecessary require
implemented new fitness score fully, distribution plots can be made for this (and hyp, ht and hm snps), tests updated
distribution plots for correct permutation are now also made
removed Gencorrect_lists from generation count in restart
made examples_close... plots for dataset using new_fitness method
new quit condition added to algorithm: are
files for unit testing
started testing reform ratio, total_pos method may not be correct
removed -1 from so_far in total_pos method
removed adding 1 to snp position in vcf_array method, because snps generated in R and so will never have a position 0
removed adding 1 to snp position in vcf_array method, because snps generated in R and so will never have a position 0
snps_right? showing that the snps in the correct permutation are not same as input to R SNPs (saved as txts) when creating the model genome. why???
changed het_hom method to better choose the correct types of SNP from VCF
modified to use correct permutation as comparable ratio, reading off the VCF is accurate according to tests, so there may have been some discrepancy between the SNPs being generated by R, and the ones that ended up in the VCF in create_model_genome
added parameter of area under curve
added parameter of area under curve
new big dataset, ready for cluster runs
quit condition
quit condition