popsim/init.c at master · julienfumey/popsim · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
/**
 * AstyanaxPopSim
 *
 * \file init.c
 * \author Julien Fumey <julien.fumey@legs.cnrs-gif.fr>, LEGS - CNRS UPR 9034
 * \brief Initialization of population
 * \version 2.0
 * \copyright (C) 2014
 *
*/

#include "init.h"

/**
 * \fn Locus* initializeSimulation(Param* P)
 * \brief Create the linked list of locus to initialize simulation
 *
 * \Param P Simulation parameters
 * \returns pointer to the first element of the linked list of locus
*/
Locus* initializeSimulation(Param* P, gsl_rng* r){
	double* tableFrequence = freqTable(P);

	Locus* pop;

	if(P->generatePopInit == 1){
		if(P->mutaRate == 0 && P->nbLocus == 0){
			fprintf(stderr, "Error : You have to specify number of locus to generate or mutation rate\n");
			exit(0);
		}
		if(P->nbLocus == 0){
			P->nbLocus = nbLocusInit(P->mutaRate, P->texas_popsize);
		}
		printf("%ld\n", P->nbLocus);
		pop	= initPop(P, tableFrequence, P->nbLocus, r);
	}else{
		pop = calloc(1, sizeof(Locus));
		if(pop == NULL){
			fprintf(stderr, "ERROR : Cannot create initial population\n");
			exit(0);
		}
	}

	free(tableFrequence);

	return(pop);
}

/**
 * \fn int nbLocusInit(int mutaRate, int popsize)int nbLocusInit(int mutaRate, int popsize)
 * \brief calculate number of locus to generate at equilibrium
*/
int nbLocusInit(float mutaRate, int popsize){
	return (int) 4 * popsize * mutaRate * watterson(popsize);
}

/**
 * \fn Locus* initPop(Param* P, float* freq, long nbLocus)
 * \brief Initialize population
 *
 * \param P parameters
 * \param freq
 * \param nbLocus Number of locus to create
 * \returns Pointer to the first element of the linked list of locus
*/
Locus* initPop(Param* P, double* freq, long nbLocus, gsl_rng* r){
	Locus* locus = calloc(1, sizeof(Locus));
	if(locus == NULL){
		fprintf(stderr, "Cannot allocate initial population\n");
		exit(0);
	}

	float freqLocus = freqInit(freq, P->texas_popsize, r);

	locus->cf = (P->elabra_gen == 0)?freqLocus:0;
	locus->sf = freqLocus;
	locus->texas = freqLocus;
	locus->gene = 0;

	if(nbLocus > 1){
		locus->next = initPop(P, freq, --nbLocus, r);
	}

	return locus;
}

/**
 * \fn inline float freqInit(float* table, long popSize)
 * \brief Give a initial frequency for a locus
 *
 * \param table distribution of DAF
 * \param popSize Size of population
 * \return Initial frequency of the locus
*/
inline double freqInit(double* table, long popSize, gsl_rng* r){
	//printf("%.38f\n", (float)random()/RAND_MAX);
	//float f = (float)random()/RAND_MAX;
	double f = gsl_rng_uniform(r);
	int i;
	for(i = 1; i < 2*popSize; i++){
		if(f <= table[i]){
			return((double)i/(2*popSize));
		}
	}
	return 0;
}

/**
 * \fn float* freqTable(Param* P)
 * \brief Calculate the frequency of the 2N-1 allele
 *
 * \param P simulation parameters
 * \returns distribution of DAF
*/
double* freqTable(Param* P){
	double* table = calloc((2*P->texas_popsize),sizeof(double));
	if(table == NULL){
		fprintf(stderr, "Error at line %d of file %s\n", __LINE__, __FILE__);
		exit(0);
	}

	table[0] = 0.;

	double nbWatterson = watterson(P->texas_popsize);

	long i;
	for(i = 1; i < 2*P->texas_popsize; i++){
		double freqSite = (double) 1/(i*nbWatterson);
		table[i] = table[(i-1)] + freqSite;
	}

	return table;
}

/**
 * \fn float watterson(long popSize)
 * \brief Calculate Watterson coefficient
 *
 * \param popSize Size of population
 * \returns Watterson coefficient
*/
double watterson(long popSize){
	double nb = 0;
	int i;

	for(i = 1; i < 2*popSize; i++){
		nb += (double) 1/i;

	}

	return nb;
}