Imported Upstream version 0.1.9

[samtools.git] / errmod.c

diff --git a/errmod.c b/errmod.c
new file mode 100644 (file)
index 0000000..fba9a8d
--- /dev/null
+++ b/errmod.c
@@ -0,0 +1,130 @@
+#include <math.h>
+#include "errmod.h"
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint16_t)
+
+typedef struct __errmod_coef_t {
+       double *fk, *beta, *lhet;
+} errmod_coef_t;
+
+typedef struct {
+       double fsum[16], bsum[16];
+       uint32_t c[16];
+} call_aux_t;
+
+static errmod_coef_t *cal_coef(double depcorr, double eta)
+{
+       int k, n, q;
+       long double sum, sum1;
+       double *lC;
+       errmod_coef_t *ec;
+
+       ec = calloc(1, sizeof(errmod_coef_t));
+       // initialize ->fk
+       ec->fk = (double*)calloc(256, sizeof(double));
+       ec->fk[0] = 1.0;
+       for (n = 1; n != 256; ++n)
+               ec->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta;
+       // initialize ->coef
+       ec->beta = (double*)calloc(256 * 256 * 64, sizeof(double));
+       lC = (double*)calloc(256 * 256, sizeof(double));
+       for (n = 1; n != 256; ++n) {
+               double lgn = lgamma(n+1);
+               for (k = 1; k <= n; ++k)
+                       lC[n<<8|k] = lgn - lgamma(k+1) - lgamma(n-k+1);
+       }
+       for (q = 1; q != 64; ++q) {
+               double e = pow(10.0, -q/10.0);
+               double le = log(e);
+               double le1 = log(1.0 - e);
+               for (n = 1; n <= 255; ++n) {
+                       double *beta = ec->beta + (q<<16|n<<8);
+                       sum1 = sum = 0.0;
+                       for (k = n; k >= 0; --k, sum1 = sum) {
+                               sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
+                               beta[k] = -10. / M_LN10 * logl(sum1 / sum);
+                       }
+               }
+       }
+       // initialize ->lhet
+       ec->lhet = (double*)calloc(256 * 256, sizeof(double));
+       for (n = 0; n < 256; ++n)
+               for (k = 0; k < 256; ++k)
+                       ec->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n;
+       free(lC);
+       return ec;
+}
+
+errmod_t *errmod_init(float depcorr)
+{
+       errmod_t *em;
+       em = (errmod_t*)calloc(1, sizeof(errmod_t));
+       em->depcorr = depcorr;
+       em->coef = cal_coef(depcorr, 0.03);
+       return em;
+}
+
+void errmod_destroy(errmod_t *em)
+{
+       if (em == 0) return;
+       free(em->coef->lhet); free(em->coef->fk); free(em->coef->beta);
+       free(em->coef); free(em);
+}
+// qual:6, strand:1, base:4
+int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q)
+{
+       call_aux_t aux;
+       int i, j, k, w[32];
+
+       if (m > m) return -1;
+       memset(q, 0, m * m * sizeof(float));
+       if (n == 0) return 0;
+       // calculate aux.esum and aux.fsum
+       if (n > 255) { // then sample 255 bases
+               ks_shuffle(uint16_t, n, bases);
+               n = 255;
+       }
+       ks_introsort(uint16_t, n, bases);
+       memset(w, 0, 32 * sizeof(int));
+       memset(&aux, 0, sizeof(call_aux_t));
+       for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
+               uint16_t b = bases[j];
+               int q = b>>5 < 4? 4 : b>>5;
+               if (q > 63) q = 63;
+               k = b&0x1f;
+               aux.fsum[k&0xf] += em->coef->fk[w[k]];
+               aux.bsum[k&0xf] += em->coef->fk[w[k]] * em->coef->beta[q<<16|n<<8|aux.c[k&0xf]];
+               ++aux.c[k&0xf];
+               ++w[k];
+       }
+       // generate likelihood
+       for (j = 0; j != m; ++j) {
+               float tmp1, tmp3;
+               int tmp2, bar_e;
+               // homozygous
+               for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != m; ++k) {
+                       if (k == j) continue;
+                       tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k];
+               }
+               if (tmp2) {
+                       bar_e = (int)(tmp1 / tmp3 + 0.499);
+                       if (bar_e > 63) bar_e = 63;
+                       q[j*m+j] = tmp1;
+               }
+               // heterozygous
+               for (k = j + 1; k < m; ++k) {
+                       int cjk = aux.c[j] + aux.c[k];
+                       for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) {
+                               if (i == j || i == k) continue;
+                               tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i];
+                       }
+                       if (tmp2) {
+                               bar_e = (int)(tmp1 / tmp3 + 0.499);
+                               if (bar_e > 63) bar_e = 63;
+                               q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]] + tmp1;
+                       } 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
+               }
+               for (k = 0; k != m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0;
+       }
+       return 0;
+}