6 #define MC_MAX_SUMQ 3000
7 #define MC_MAX_SUMQP 1e-300
13 double *q2p, *pdg; // pdg -> P(D|g)
18 void mc_init_prior(mc_aux_t *ma, double theta)
23 for (i = 0, sum = 0.; i < 2 * ma->n; ++i)
24 sum += (ma->alpha[i] = ma->theta / (2 * ma->n - i));
25 ma->alpha[2 * ma->n] = 1. - sum;
28 mc_aux_t *mc_init(int n) // FIXME: assuming diploid
32 ma = calloc(1, sizeof(mc_aux_t));
33 ma->n = n; ma->N = 2 * n;
34 ma->q2p = calloc(MC_MAX_SUMQ + 1, sizeof(double));
35 ma->qsum = calloc(4 * ma->n, sizeof(int));
36 ma->bcnt = calloc(4 * ma->n, sizeof(int));
37 ma->pdg = calloc(3 * ma->n, sizeof(double));
38 ma->alpha = calloc(2 * ma->n + 1, sizeof(double));
39 ma->beta = calloc((2 * ma->n + 1) * 3, sizeof(double));
40 for (i = 0; i <= MC_MAX_SUMQ; ++i)
41 ma->q2p[i] = pow(10., -i / 10.);
42 for (i = 0; i <= 2 * ma->n; ++i) { // beta[k][g]=P(g|k/M)
43 double *bi = ma->beta + 3 * i;
44 double f = (double)i / (2 * ma->n);
45 bi[0] = (1. - f) * (1. - f);
46 bi[1] = 2 * f * (1. - f);
49 mc_init_prior(ma, 1e-3); // the simplest prior
53 void mc_destroy(mc_aux_t *ma)
56 free(ma->qsum); free(ma->bcnt);
57 free(ma->q2p); free(ma->pdg);
58 free(ma->alpha); free(ma->beta);
63 static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
66 memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
67 memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
68 for (j = 0; j < ma->n; ++j) {
69 int tmp, *qsum = ma->qsum + j * 4;
70 int *bcnt = ma->bcnt + j * 4;
71 for (i = tmp = 0; i < n[j]; ++i) {
72 const bam_pileup1_t *p = plp[j] + i;
74 if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
75 q = bam1_qual(p->b)[p->qpos];
76 if (p->b->core.qual < q) q = p->b->core.qual;
77 if (q < MC_MIN_QUAL) continue; // small qual
78 b = bam_nt16_nt4_table[(int)bam1_seqi(bam1_seq(p->b), p->qpos)];
79 if (b > 3) continue; // N
87 static void set_allele(int ref, mc_aux_t *ma)
89 int i, j, sum[4], tmp;
90 sum[0] = sum[1] = sum[2] = sum[3] = 0;
91 for (i = 0; i < ma->n; ++i)
92 for (j = 0; j < 4; ++j)
93 sum[j] += ma->qsum[i * 4 + j];
94 for (j = 0; j < 4; ++j) sum[j] = sum[j]<<2 | j;
95 for (i = 1; i < 4; ++i) // insertion sort
96 for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
97 tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
98 ma->ref = sum[3]&3; ma->alt = sum[2]&3;
99 if (ref == ma->alt) tmp = ma->ref, ma->ref = ma->alt, ma->alt = tmp;
100 // note that ma->ref might not be ref in case of triallele
103 static void cal_pdg(mc_aux_t *ma)
106 for (j = 0; j < ma->n; ++j) {
107 int pi[3], *qsum, *bcnt;
108 double *pdg = ma->pdg + j * 3;
109 qsum = ma->qsum + j * 4;
110 bcnt = ma->bcnt + j * 4;
111 pi[1] = 3 * (bcnt[ma->ref] + bcnt[ma->alt]);
112 pi[0] = qsum[ma->ref];
113 pi[2] = qsum[ma->alt];
114 for (i = 0; i < 3; ++i)
115 pdg[i] = pi[i] > MC_MAX_SUMQ? MC_MAX_SUMQP : ma->q2p[pi[i]];
118 // return the reference allele frequency
119 double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt)
126 *_ref = ma->ref; *alt = ma->alt;
127 for (i = cnt = 0, f = 0.; i < ma->n; ++i) {
128 int *bcnt = ma->bcnt + i * 4;
129 int x = bcnt[ma->ref] + bcnt[ma->alt];
132 f += (double)bcnt[ma->ref] / x;
137 // f0 is the reference allele frequency
138 double mc_freq_iter(double f0, mc_aux_t *ma)
142 f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
143 for (i = 0, f = 0.; i < ma->n; ++i) {
145 pdg = ma->pdg + i * 3;
146 for (j = 1, up = 0.; j < 3; ++j)
147 up += j * pdg[j] * f3[j];
148 for (j = 0, dn = 0.; j < 3; ++j)
149 dn += pdg[j] * f3[j];
156 double mc_freq_post(mc_aux_t *ma)
160 for (i = 0; i < ma->n; ++i) {
161 double *pdg = ma->pdg + i * 3;
162 long double y = 0., z = 0.;
163 for (k = 0; k <= ma->n * 2; ++k) {
164 double *bk = ma->beta + k * 3;
167 double yk = 0., zk = 0.;
168 for (g = 0; g < 3; ++g) {
169 yk += g * pdg[g] * bk[g];
170 zk += pdg[g] * bk[g];
172 y += yk * ma->alpha[k];
173 z += zk * ma->alpha[k];
175 y += (pdg[1] * bk[1] + 2. * pdg[2] * bk[2]) * ma->alpha[k];
176 z += (pdg[0] * bk[0] + pdg[1] * bk[1] + pdg[2] * bk[2]) * ma->alpha[k];
180 return f / ma->n / 2;
183 double mc_ref_prob(mc_aux_t *ma)
186 long double PD = 0., Pref = 0.;
187 for (k = 0; k <= ma->n * 2; ++k) {
189 double *bk = ma->beta + k * 3;
190 for (i = 0; i < ma->n; ++i) {
191 double *pdg = ma->pdg + i * 3;
192 // int g; double y=0.; for (g = 0; g < 3; ++g) y += pdg[g] * bk[g];
193 x *= pdg[0] * bk[0] + pdg[1] * bk[1] + pdg[2] * bk[2];
195 PD += x * ma->alpha[k];
197 for (k = 0; k <= ma->n * 2; ++k) {
199 for (i = 0; i < ma->n; ++i)
200 x *= ma->pdg[i * 3 + 2] * ma->beta[k * 3 + 2];
201 Pref += x * ma->alpha[k];
206 int mc_call_gt(const mc_aux_t *ma, double f0, int k)
209 double max, f3[3], *pdg = ma->pdg + k * 3;
211 f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
212 for (i = 0, sum = 0.; i < 3; ++i)
213 sum += (g[i] = pdg[i] * f3[i]);
214 for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
216 if (g[i] > max) max = g[i], max_i = i;
218 // printf("***%lg,%lg,%lg,%lg,%lg,%lg\n", g[0], g[1], g[2], pdg[0], pdg[1], pdg[2]);
220 if (max < 1e-308) max = 1e-308;
221 q = (int)(-3.434 * log(max) + .499);