yeastsim

1. Make chrV vcf and fasta (in helperfiles)
2. Read in vcf
3. initially two types of mutations m1 are the markers of each haploid genome, m3 are SNPs - at this stage there are 17 alleles - and about 8K SNPs
4. pick a subset of m3 SNPs to make causative (NSNPs), these become flavor m2 mutations
5. give these mutations causative effects - with effects scaled by 1/ (minorAlleleCount)^scaling_constant - the scaling constant allows one to make rarer alleles have bigger effects
6. now mix these 17 founders to create the population with counts given by K0 - known mixing proportions * K0 pop size
7. random mate for 12 generations
8. grow to size K1 before starting actual evolution experiment