Logo Search packages:      
Sourcecode: samtools version File versions  Download package

errmod.c

#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;
}

Generated by  Doxygen 1.6.0   Back to index