popgen

type Afs struct {
	Sites []*SegSite
}

type Group struct {
	Name    string
	Members []string
}

type LikelihoodFunction byte

type McmcSettings struct {
	Iterations              int
	MuStep                  float64
	MuZero                  float64
	SigmaStep               float64
	SigmaZero               float64
	RandSeed                bool  //pseudorandom number generation control: set the seed as current unix time
	SetSeed                 int64 //pseudorandom number generation control: set the seed to a user-specified int64.
	UnPolarized             bool
	DivergenceAscertainment bool
	FixedSigma              bool
	D                       int //D is the size of the ascertainment subset.
	IntegralError           float64
	Verbose                 int
	SigmaPriorAlpha         float64 //defines the alpha parameter for the prior distribution for the Theta hyperparameter sigma.
	SigmaPriorBeta          float64 //defines the beta parameter for the prior distribution for the Theta hyperparameter sigma.
	MuPriorMean             float64 //defines the mean of the prior distribution for the Theta hyperparameter mu.
	MuPriorSigma            float64 //defines the standard deviation of the prior distribution for the Theta hyperparameter mu.
	IncludeRef              bool    //If true, includes the reference genome allele state as a datapoint in the allele frequency spectrum.
}

type MleSettings struct {
	Left                    float64 //left bound of MLE search space
	Right                   float64 //right bound of MLE search space
	Error                   float64 //desired accuracy in output maximum likelihood estimate
	UnPolarized             bool    //disable the need for ancestor annotation in the vcf file. Assumes the reference allele is in the ancestral state. Use with caution.
	DivergenceAscertainment bool    //if true, use the divergence-based ascertainment bias-corrected likelihood function for selection.
	D                       int     //for DivergenceAscertainment, set the size of the ascertainment subset.
	IntegralError           float64 //set the acceptable error in the internal integral calculations in the likelihood function.
	Verbose                 int     //default 0. When set to 1, debug prints appear in standard output.
	IncludeRef              bool    //Includes the reference genome allele state in the derived allele frequency spectrum.
}

type SegSite struct {
	I int                //individuals with the allele
	N int                //total number of individuals
	L LikelihoodFunction //specifies with likelihood function to use. 1 for ancestral, 0 for uncorrected, 2 for derived.
}

type Theta struct {
	// contains filtered or unexported fields
}

type WrightFisherPopData struct {
	Fasta     []fasta.Fasta
	Vcf       vcf.Vcf
	Meta      []string
	Freq      [][][]float64
	Ancestral []string //Ancestral states of each allele on each site (aka replicates)
	Settings  WrightFisherSettings
}

type WrightFisherSettings struct {
	PopSize         int
	MutRate         float64
	NumGen          int
	GenomeSize      int
	RFitness        float64
	GcContent       float64
	InitFreq        string
	FitnessString   string
	SetSeed         int64
	Verbose         bool
	Fasta           bool
	Vcf             bool
	AncestralAllele string
}