9 KSTREAM_INIT(gzFile, gzread, 16384)
11 #define MC_AVG_ERR 0.007
12 #define MC_MAX_EM_ITER 16
13 #define MC_EM_EPS 1e-4
15 unsigned char seq_nt4_table[256] = {
16 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
17 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
18 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4,
19 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
20 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
21 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
22 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
23 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
24 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
25 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
26 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
27 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
28 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
29 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
30 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
31 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
34 struct __bcf_p1aux_t {
36 double *q2p, *pdg; // pdg -> P(D|g)
38 double *z, *zswap; // aux for afs
39 double *z1, *z2; // only calculated when n1 is set
41 double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
42 const uint8_t *PL; // point to PL
46 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
49 if (type == MC_PTYPE_COND2) {
50 for (i = 0; i <= ma->M; ++i)
51 ma->phi[i] = 2. * (i + 1) / (ma->M + 1) / (ma->M + 2);
52 } else if (type == MC_PTYPE_FLAT) {
53 for (i = 0; i <= ma->M; ++i)
54 ma->phi[i] = 1. / (ma->M + 1);
57 for (i = 0, sum = 0.; i < ma->M; ++i)
58 sum += (ma->phi[i] = theta / (ma->M - i));
59 ma->phi[ma->M] = 1. - sum;
63 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
70 memset(&s, 0, sizeof(kstring_t));
71 fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
73 memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
74 while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
75 if (strstr(s.s, "[afs] ") == s.s) {
77 for (k = 0; k <= ma->M; ++k) {
80 x = strtol(p, &p, 10);
81 if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
84 if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
85 ma->phi[ma->M - k] += y;
92 for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
93 fprintf(stderr, "[prior]");
94 for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
95 for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
100 bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
104 ma = calloc(1, sizeof(bcf_p1aux_t));
106 ma->n = n; ma->M = 2 * n;
107 ma->q2p = calloc(256, sizeof(double));
108 ma->pdg = calloc(3 * ma->n, sizeof(double));
109 ma->phi = calloc(ma->M + 1, sizeof(double));
110 ma->z = calloc(2 * ma->n + 1, sizeof(double));
111 ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
112 ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
113 ma->z2 = calloc(ma->M + 1, sizeof(double));
114 ma->afs = calloc(2 * ma->n + 1, sizeof(double));
115 ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
116 for (i = 0; i < 256; ++i)
117 ma->q2p[i] = pow(10., -i / 10.);
118 bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
122 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
124 if (n1 == 0 || n1 >= b->n) return -1;
129 void bcf_p1_destroy(bcf_p1aux_t *ma)
132 free(ma->q2p); free(ma->pdg);
134 free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
135 free(ma->afs); free(ma->afs1);
140 #define char2int(s) (((int)s[0])<<8|s[1])
142 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
146 p = alloca(b->n_alleles * sizeof(long));
147 memset(p, 0, sizeof(long) * b->n_alleles);
148 for (j = 0; j < ma->n; ++j) {
149 const uint8_t *pi = ma->PL + j * ma->PL_len;
150 double *pdg = ma->pdg + j * 3;
151 pdg[0] = ma->q2p[pi[b->n_alleles]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
152 for (i = k = 0; i < b->n_alleles; ++i) {
154 k += b->n_alleles - i;
157 for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
158 for (i = 1; i < b->n_alleles; ++i) // insertion sort
159 for (j = i; j > 0 && p[j] < p[j-1]; --j)
160 tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
161 for (i = b->n_alleles - 1; i >= 0; --i)
162 if ((p[i]&0xf) == 0) break;
165 // f0 is the reference allele frequency
166 static double mc_freq_iter(double f0, const bcf_p1aux_t *ma)
170 f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
171 for (i = 0, f = 0.; i < ma->n; ++i) {
173 pdg = ma->pdg + i * 3;
174 f += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
175 / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
181 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
184 double max, f3[3], *pdg = ma->pdg + k * 3;
186 f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
187 for (i = 0, sum = 0.; i < 3; ++i)
188 sum += (g[i] = pdg[i] * f3[i]);
189 for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
191 if (g[i] > max) max = g[i], max_i = i;
194 if (max < 1e-308) max = 1e-308;
195 q = (int)(-3.434 * log(max) + .499);
202 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
204 double *z[2], *tmp, *pdg;
205 int _j, last_min, last_max;
209 memset(z[0], 0, sizeof(double) * (ma->M + 1));
210 memset(z[1], 0, sizeof(double) * (ma->M + 1));
212 last_min = last_max = 0;
214 for (_j = beg; _j < ma->n; ++_j) {
215 int k, j = _j - beg, _min = last_min, _max = last_max;
217 pdg = ma->pdg + _j * 3;
218 p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
219 for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
220 for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
223 k = 0, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k];
225 k = 1, z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k] + k*(2*j+2-k) * p[1] * z[0][k-1];
226 for (k = _min < 2? 2 : _min; k <= _max; ++k)
227 z[1][k] = (2*j+2-k)*(2*j-k+1) * p[0] * z[0][k]
228 + k*(2*j+2-k) * p[1] * z[0][k-1]
229 + k*(k-1)* p[2] * z[0][k-2];
230 for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
231 ma->t += log(sum / ((2. * j + 2) * (2. * j + 1)));
232 for (k = _min; k <= _max; ++k) z[1][k] /= sum;
233 if (_min >= 1) z[1][_min-1] = 0.;
234 if (_min >= 2) z[1][_min-2] = 0.;
235 if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
236 if (_j == ma->n1 - 1) { // set pop1
238 memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
240 tmp = z[0]; z[0] = z[1]; z[1] = tmp;
241 last_min = _min; last_max = _max;
243 if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
246 static void mc_cal_y(bcf_p1aux_t *ma)
248 if (ma->n1 > 0 && ma->n1 < ma->n) {
251 memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
252 memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
253 ma->t1 = ma->t2 = 0.;
254 mc_cal_y_core(ma, ma->n1);
256 memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
257 mc_cal_y_core(ma, 0);
259 x = exp(ma->t - (ma->t1 + ma->t2));
260 for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
261 } else mc_cal_y_core(ma, 0);
263 if (ma->n1 > 0 && ma->n1 < ma->n) {
267 for (i = 0; i <= 2; ++i)
268 printf("(%lf,%lf) ", ma->z1[i], ma->z2[i]);
270 y[0] = ma->z1[0] * ma->z2[0];
271 y[1] = 1./2. * (ma->z1[0] * ma->z2[1] + ma->z1[1] * ma->z2[0]);
272 y[2] = 1./6. * (ma->z1[0] * ma->z2[2] + ma->z1[2] * ma->z2[0]) + 4./6. * ma->z1[1] * ma->z2[1];
273 y[3] = 1./2. * (ma->z1[1] * ma->z2[2] + ma->z1[2] * ma->z2[1]);
274 y[4] = ma->z1[2] * ma->z2[2];
275 for (i = 0; i <= 4; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
281 static double mc_cal_afs(bcf_p1aux_t *ma)
284 long double sum = 0.;
285 memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
287 for (k = 0, sum = 0.; k <= ma->M; ++k)
288 sum += (long double)ma->phi[k] * ma->z[k];
289 for (k = 0; k <= ma->M; ++k) {
290 ma->afs1[k] = ma->phi[k] * ma->z[k] / sum;
291 if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
293 for (k = 0, sum = 0.; k <= ma->M; ++k) {
294 ma->afs[k] += ma->afs1[k];
295 sum += k * ma->afs1[k];
300 long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
302 long double pd = 0., g2[3];
304 memset(g2, 0, sizeof(long double) * 3);
305 for (k = 0; k < p1a->M; ++k) {
306 double f = (double)k / p1a->M, f3[3], g1[3];
308 g1[0] = g1[1] = g1[2] = 0.;
309 f3[0] = (1. - f) * (1. - f); f3[1] = 2. * f * (1. - f); f3[2] = f * f;
310 for (i = 0; i < p1a->n; ++i) {
311 double *pdg = p1a->pdg + i * 3;
312 double x = pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
314 g1[0] += pdg[0] * f3[0] / x;
315 g1[1] += pdg[1] * f3[1] / x;
316 g1[2] += pdg[2] * f3[2] / x;
318 pd += p1a->phi[k] * z;
319 for (i = 0; i < 3; ++i)
320 g2[i] += p1a->phi[k] * z * g1[i];
322 for (i = 0; i < 3; ++i) g[i] = g2[i] / pd;
326 int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
329 long double sum = 0.;
331 for (i = 0; i < b->n_gi; ++i) {
332 if (b->gi[i].fmt == char2int("PL")) {
333 ma->PL = (uint8_t*)b->gi[i].data;
334 ma->PL_len = b->gi[i].len;
338 if (b->n_alleles < 2) return -1; // FIXME: find a better solution
340 rst->rank0 = cal_pdg(b, ma);
341 rst->f_exp = mc_cal_afs(ma);
342 rst->p_ref = ma->afs1[ma->M];
343 // calculate f_flat and f_em
344 for (k = 0, sum = 0.; k <= ma->M; ++k)
345 sum += (long double)ma->z[k];
347 for (k = 0; k <= ma->M; ++k) {
348 double p = ma->z[k] / sum;
349 rst->f_flat += k * p;
351 rst->f_flat /= ma->M;
353 double flast = rst->f_flat;
354 for (i = 0; i < MC_MAX_EM_ITER; ++i) {
355 rst->f_em = mc_freq_iter(flast, ma);
356 if (fabs(rst->f_em - flast) < MC_EM_EPS) break;
360 rst->g[0] = rst->g[1] = rst->g[2] = -1.;
361 // bcf_p1_cal_g3(ma, rst->g);
365 void bcf_p1_dump_afs(bcf_p1aux_t *ma)
368 fprintf(stderr, "[afs]");
369 for (k = 0; k <= ma->M; ++k)
370 fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
371 fprintf(stderr, "\n");
372 memset(ma->afs, 0, sizeof(double) * (ma->M + 1));