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felsenstein_test.c
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felsenstein_test.c
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#include <stdint.h>
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include "felsenstein_lin.h"
int main() {
int i = 0;
int j = 1;
int N = 4;
int L = 5;
uint8_t* msa = (uint8_t*) malloc(sizeof(u_int8_t)*N*L);
for(int i = 0; i < L; i++) {
msa[0*L + i] = 1;
msa[1*L + i] = 1;
msa[2*L + i] = 2;
msa[3*L + i] = 2;
}
c_float_t t1 = 0.2;
c_float_t phi1 = exp(-t1);
c_float_t t2 = 0.2;
c_float_t phi2 = exp(-t2);
c_float_t* aa_freqs = (c_float_t*) calloc(A, sizeof(c_float_t));
c_float_t aa_counts[A] = {1e-9};
for(int a = 0; a < N*L; a++) {
aa_counts[msa[a]] += 1;
}
c_float_t norm = 0;
for(int a = 0; a < A; a++) {
norm += aa_counts[a];
}
for(int a = 0; a < A; a++) {
aa_freqs[a] = aa_counts[a] / norm;
}
c_float_t* x = (c_float_t*) malloc(sizeof(c_float_t)*(N_COL*A + A*A));
for(int idx = 0; idx < N_COL*A + A*A; idx++) {
x[idx] = (c_float_t)rand() / (c_float_t)RAND_MAX;
x[idx] = 0;
}
c_float_t* grad = (c_float_t*) malloc(sizeof(c_float_t)*(N_COL*A + A*A));
Node ll_node;
ll_node.seq_id = 0;
ll_node.left = NULL;
ll_node.right = NULL;
Node lr_node;
lr_node.seq_id = 1;
lr_node.left = NULL;
lr_node.right = NULL;
Node rl_node;
rl_node.seq_id = 2;
rl_node.left = NULL;
rl_node.right = NULL;
Node rr_node;
rr_node.seq_id = 3;
rr_node.left = NULL;
rr_node.right = NULL;
Node left_node;
left_node.left = &ll_node;
left_node.right = &lr_node;
left_node.phi_left = phi1;
left_node.phi_right = phi2;
left_node.seq_id = -2;
Node right_node;
right_node.left = &rl_node;
right_node.right = &rr_node;
right_node.phi_left = phi1;
right_node.phi_right = phi2;
right_node.seq_id = -3;
Node* root = malloc(sizeof(Node));
root->phi_left = phi1;
root->phi_right = phi2;
root->left = &left_node;
root->right = &right_node;
root->seq_id = -1;
Constants* consts = malloc(sizeof(Constants));
consts->phylo_tree = root;
consts->msa = msa;
consts->L = L;
consts->i = i;
consts->j = j;
initialize_constants(consts);
Buffer* buffer = malloc(sizeof(Buffer));
buffer->left = malloc(sizeof(NodeBuffer));
initialize_buffer(buffer->left, consts);
buffer->right = malloc(sizeof(NodeBuffer));
initialize_buffer(buffer->right, consts);
c_float_t fx = calculate_fx_grad(x, grad, consts, buffer);
printf("log fx= %e\n", log(fx));
c_float_t epsilon = 1e-9;
int pos = 0;
for(int l = 0; l < N_COL; l++) {
for(int c = 0; c < A; c++) {
calculate_fx_grad(x, grad, consts, buffer);
c_float_t target_grad = grad[pos];
x[pos] += epsilon;
c_float_t fx_fwd = calculate_fx_grad(x, grad, consts, buffer);
x[pos] -= 2*epsilon;
c_float_t fx_rev = calculate_fx_grad(x, grad, consts, buffer);
x[pos] += epsilon;
printf("v|i=%d|c=%d %e / %e\n", l, c, target_grad, (fx_fwd - fx_rev) / (2*epsilon));
pos++;
}
}
for(int c = 0; c < A; c++) {
for(int d = 0; d < A; d++) {
calculate_fx_grad(x, grad, consts, buffer);
c_float_t target_grad = grad[pos];
x[pos] += epsilon;
c_float_t fx_fwd = calculate_fx_grad(x, grad, consts, buffer);
x[pos] -= 2*epsilon;
c_float_t fx_rev = calculate_fx_grad(x, grad, consts, buffer);
x[pos] += epsilon;
printf("w|c=%d|d=%d %e / %e\n", c, d, target_grad, (fx_fwd - fx_rev) / (2*epsilon));
pos++;
}
}
// cleanup
free(x);
free(grad);
deinitialize_buffer(buffer->left);
deinitialize_buffer(buffer->right);
free(buffer->left);
free(buffer->right);
free(buffer);
deinitialize_constants(consts);
free(consts->msa);
free(consts->phylo_tree);
free(consts);
}