classes for specifying haplotype SNP values More...
Classes | |
class | VariantIndicator_Trivial |
trivial implementation: returns 0 More... | |
class | VariantIndicator_Composite |
encapsulates a list of VariantIndicators; returns first non-zero value for a given (haplotype id,locus) if one exists More... | |
class | VariantIndicator_IDRange |
returns variant values based on specified haplotype id ranges and loci More... | |
class | VariantIndicator_IDSet |
flexible implementation: user specifies per-locus value and id list More... | |
class | VariantIndicator_Random |
Assigns SNP values randomly to individuals in the initial populations, independently for each locus with specified allele frequencies, so that each SNP will be in Hardy-Weinberg equilibrium (in expectation). More... | |
class | VariantIndicator_File |
returns variant values based on an ms-format file More... | |
class | VariantIndicator_SingleLocusHardyWeinberg |
Assigns SNP value 1 to both haplotypes of the first Np^2 individuals, and to one haplotype of the next N*2pq individuals. More... | |
class | VariantIndicator_TwoLocusLD |
Assigns SNP values according to allele frequencies at two loci and specified linkage disequilibrium (D). Note: all individuals are homozygotes, i.e. their haplotypes are identical. More... | |