Fixes bug at chromosome boundaries, refactors the code, changed het_ratio calculation

[biomonika]

• fixes the bug discovered by Emily Xu; when at the chromosome boundaries, sometimes the clustering of variants would go across, creating large regions that include the coordinates from the two original chromosomes
• het_ratio is now the average across all second and first alleles (sum_second/(sum_first+sum_second))

[mrvollger]

Thanks for the PR! But @glogsdon1 contributed this code to NucFreq so I'd like/need her input on these changes before accepting a PR.