4 KSORT_INIT_GENERIC(uint16_t)
6 typedef struct __errmod_coef_t {
7 double *fk, *beta, *lhet;
11 double fsum[16], bsum[16];
15 static errmod_coef_t *cal_coef(double depcorr, double eta)
18 long double sum, sum1;
22 ec = calloc(1, sizeof(errmod_coef_t));
24 ec->fk = (double*)calloc(256, sizeof(double));
26 for (n = 1; n != 256; ++n)
27 ec->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta;
29 ec->beta = (double*)calloc(256 * 256 * 64, sizeof(double));
30 lC = (double*)calloc(256 * 256, sizeof(double));
31 for (n = 1; n != 256; ++n) {
32 double lgn = lgamma(n+1);
33 for (k = 1; k <= n; ++k)
34 lC[n<<8|k] = lgn - lgamma(k+1) - lgamma(n-k+1);
36 for (q = 1; q != 64; ++q) {
37 double e = pow(10.0, -q/10.0);
39 double le1 = log(1.0 - e);
40 for (n = 1; n <= 255; ++n) {
41 double *beta = ec->beta + (q<<16|n<<8);
43 for (k = n; k >= 0; --k, sum1 = sum) {
44 sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
45 beta[k] = -10. / M_LN10 * logl(sum1 / sum);
50 ec->lhet = (double*)calloc(256 * 256, sizeof(double));
51 for (n = 0; n < 256; ++n)
52 for (k = 0; k < 256; ++k)
53 ec->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n;
58 errmod_t *errmod_init(float depcorr)
61 em = (errmod_t*)calloc(1, sizeof(errmod_t));
62 em->depcorr = depcorr;
63 em->coef = cal_coef(depcorr, 0.03);
67 void errmod_destroy(errmod_t *em)
70 free(em->coef->lhet); free(em->coef->fk); free(em->coef->beta);
71 free(em->coef); free(em);
73 // qual:6, strand:1, base:4
74 int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q)
80 memset(q, 0, m * m * sizeof(float));
82 // calculate aux.esum and aux.fsum
83 if (n > 255) { // then sample 255 bases
84 ks_shuffle(uint16_t, n, bases);
87 ks_introsort(uint16_t, n, bases);
88 memset(w, 0, 32 * sizeof(int));
89 memset(&aux, 0, sizeof(call_aux_t));
90 for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
91 uint16_t b = bases[j];
92 int q = b>>5 < 4? 4 : b>>5;
95 aux.fsum[k&0xf] += em->coef->fk[w[k]];
96 aux.bsum[k&0xf] += em->coef->fk[w[k]] * em->coef->beta[q<<16|n<<8|aux.c[k&0xf]];
100 // generate likelihood
101 for (j = 0; j != m; ++j) {
105 for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != m; ++k) {
106 if (k == j) continue;
107 tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k];
110 bar_e = (int)(tmp1 / tmp3 + 0.499);
111 if (bar_e > 63) bar_e = 63;
115 for (k = j + 1; k < m; ++k) {
116 int cjk = aux.c[j] + aux.c[k];
117 for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) {
118 if (i == j || i == k) continue;
119 tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i];
122 bar_e = (int)(tmp1 / tmp3 + 0.499);
123 if (bar_e > 63) bar_e = 63;
124 q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]] + tmp1;
125 } else q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]]; // all the bases are either j or k
127 for (k = 0; k != m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0;