#include <stdlib.h>
#include <string.h>
#include <stdio.h>
+#include <errno.h>
#include "prob1.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
#define MC_AVG_ERR 0.007
#define MC_MAX_EM_ITER 16
#define MC_EM_EPS 1e-4
+//#define _BCF_QUAD
+
unsigned char seq_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
};
struct __bcf_p1aux_t {
- int n, M;
+ int n, M, n1;
double *q2p, *pdg; // pdg -> P(D|g)
double *phi;
double *z, *zswap; // aux for afs
+ double *z1, *z2; // only calculated when n1 is set
+ double t, t1, t2;
double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
+ double *k1k2;
const uint8_t *PL; // point to PL
int PL_len;
};
}
}
-bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
+int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
+{
+ gzFile fp;
+ kstring_t s;
+ kstream_t *ks;
+ long double sum;
+ int dret, k;
+ memset(&s, 0, sizeof(kstring_t));
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
+ if (strstr(s.s, "[afs] ") == s.s) {
+ char *p = s.s + 6;
+ for (k = 0; k <= ma->M; ++k) {
+ int x;
+ double y;
+ x = strtol(p, &p, 10);
+ if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
+ ++p;
+ y = strtod(p, &p);
+ if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
+ ma->phi[ma->M - k] += y;
+ }
+ }
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(s.s);
+ for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
+ fprintf(stderr, "[prior]");
+ for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
+ for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
+ fputc('\n', stderr);
+ for (sum = 0., k = 1; k <= ma->M; ++k) sum += k * ma->phi[ma->M - k];
+ fprintf(stderr, "[heterozygosity] %lf\n", (double)sum / ma->M);
+ return 0;
+}
+
+bcf_p1aux_t *bcf_p1_init(int n)
{
bcf_p1aux_t *ma;
int i;
ma = calloc(1, sizeof(bcf_p1aux_t));
+ ma->n1 = -1;
ma->n = n; ma->M = 2 * n;
ma->q2p = calloc(256, sizeof(double));
ma->pdg = calloc(3 * ma->n, sizeof(double));
ma->phi = calloc(ma->M + 1, sizeof(double));
ma->z = calloc(2 * ma->n + 1, sizeof(double));
ma->zswap = calloc(2 * ma->n + 1, sizeof(double));
+ ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
+ ma->z2 = calloc(ma->M + 1, sizeof(double));
ma->afs = calloc(2 * ma->n + 1, sizeof(double));
ma->afs1 = calloc(2 * ma->n + 1, sizeof(double));
for (i = 0; i < 256; ++i)
return ma;
}
+#ifdef _BCF_QUAD
+static double lbinom(int n, int k)
+{
+ return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+#endif
+
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+ if (n1 == 0 || n1 >= b->n) return -1;
+ b->n1 = n1;
+#ifdef _BCF_QUAD
+ {
+ int k1, k2, n2 = b->n - b->n1;
+ b->k1k2 = calloc((2*n1+1) * (2*n2+1), sizeof(double));
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ b->k1k2[k1*(2*n2+1)+k2] = exp(lbinom(2*n1,k1) + lbinom(2*n2,k2) - lbinom(b->M,k1+k2));
+ }
+#endif
+ return 0;
+}
+
void bcf_p1_destroy(bcf_p1aux_t *ma)
{
if (ma) {
free(ma->q2p); free(ma->pdg);
free(ma->phi);
- free(ma->z); free(ma->zswap);
+ free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
free(ma->afs); free(ma->afs1);
+ free(ma->k1k2);
free(ma);
}
}
}
max = 1. - max;
if (max < 1e-308) max = 1e-308;
- q = (int)(-3.434 * log(max) + .499);
+ q = (int)(-4.343 * log(max) + .499);
if (q > 99) q = 99;
return q<<2|max_i;
}
#define TINY 1e-20
-static void mc_cal_y(bcf_p1aux_t *ma)
+static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
{
- double *z[2], *tmp, *pdg, last_min, last_max;
- int k, j;
+ double *z[2], *tmp, *pdg;
+ int _j, last_min, last_max;
z[0] = ma->z;
z[1] = ma->zswap;
pdg = ma->pdg;
- z[0][0] = 1.; z[0][1] = z[0][2] = 0.;
+ memset(z[0], 0, sizeof(double) * (ma->M + 1));
+ memset(z[1], 0, sizeof(double) * (ma->M + 1));
+ z[0][0] = 1.;
last_min = last_max = 0;
- for (j = 0; j < ma->n; ++j) {
- int _min = last_min, _max = last_max;
+ ma->t = 0.;
+ for (_j = beg; _j < ma->n; ++_j) {
+ int k, j = _j - beg, _min = last_min, _max = last_max;
double p[3], sum;
- pdg = ma->pdg + j * 3;
+ pdg = ma->pdg + _j * 3;
p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
-// for (; _min < _max && z[0][_min] < TINY; ++_min) z[1][_min] = 0.;
-// for (; _max > _min && z[0][_max] < TINY; --_max) z[1][_max] = 0.;
+ for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
+ for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
_max += 2;
if (_min == 0)
k = 0, 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]
+ k*(k-1)* p[2] * z[0][k-2];
for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
+ ma->t += log(sum / ((2. * j + 2) * (2. * j + 1)));
for (k = _min; k <= _max; ++k) z[1][k] /= sum;
+ if (_min >= 1) z[1][_min-1] = 0.;
+ if (_min >= 2) z[1][_min-2] = 0.;
if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
+ if (_j == ma->n1 - 1) { // set pop1
+ ma->t1 = ma->t;
+ memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
+ }
tmp = z[0]; z[0] = z[1]; z[1] = tmp;
last_min = _min; last_max = _max;
}
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
}
+static void mc_cal_y(bcf_p1aux_t *ma)
+{
+ if (ma->n1 > 0 && ma->n1 < ma->n) {
+ int k;
+ long double x;
+ memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
+ memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+ ma->t1 = ma->t2 = 0.;
+ mc_cal_y_core(ma, ma->n1);
+ ma->t2 = ma->t;
+ memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
+ mc_cal_y_core(ma, 0);
+ // rescale z
+ x = expl(ma->t - (ma->t1 + ma->t2));
+ for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
+ } else mc_cal_y_core(ma, 0);
+#ifdef _BCF_QUAD
+/*
+ if (ma->n1 > 0 && ma->n1 < ma->n) { // DEBUG: consistency check; z[i] should equal y[i]
+ int i, k1, k2, n1 = ma->n1, n2 = ma->n - n1;
+ double *y;
+ printf("*** ");
+ y = calloc(ma->M + 1, sizeof(double));
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2)
+ y[k1+k2] += ma->k1k2[k1*(2*n2+1)+k2] * ma->z1[k1] * ma->z2[k2];
+ for (i = 0; i <= ma->M; ++i) printf("(%lf,%lf) ", ma->z[i], y[i]);
+ printf("\n");
+ free(y);
+ }
+*/
+#endif
+}
+
+static void contrast(bcf_p1aux_t *ma, double pc[4]) // mc_cal_y() must be called before hand
+{
+ int k, n1 = ma->n1, n2 = ma->n - ma->n1;
+ long double sum = -1., x, sum_alt;
+ double y;
+ pc[0] = pc[1] = pc[2] = pc[3] = -1.;
+ if (n1 <= 0 || n2 <= 0) return;
+#ifdef _BCF_QUAD
+ { // FIXME: can be improved by skipping zero cells
+ int k1, k2;
+ long double z[3];
+ z[0] = z[1] = z[2] = 0.;
+ for (k1 = 0; k1 <= 2*n1; ++k1)
+ for (k2 = 0; k2 <= 2*n2; ++k2) {
+ double zz = ma->phi[k1+k2] * ma->z1[k1] * ma->z2[k2] * ma->k1k2[k1*(2*n2+1)+k2];
+ if ((double)k1/n1 < (double)k2/n2) z[0] += zz;
+ else if ((double)k1/n1 > (double)k2/n2) z[1] += zz;
+ else z[2] += zz;
+ }
+ sum = z[0] + z[1] + z[2];
+ pc[2] = z[0] / sum; pc[3] = z[1] / sum;
+ }
+#else
+ pc[2] = pc[3] = 0.;
+#endif
+ for (k = 0, sum_alt = 0.; k <= ma->M; ++k)
+ sum_alt += (long double)ma->phi[k] * ma->z[k];
+// printf("* %lg, %lg *\n", (double)sum, (double)sum_alt); // DEBUG: sum should equal sum_alt
+ sum = sum_alt;
+ // the variant is specific to group2
+// printf("%lg %lg %lg %lg\n", ma->z[2*(n1+n2)]/exp(ma->t - (ma->t1 + ma->t2)), ma->z1[2*n1], ma->z2[2*n2], (double)sum);
+ y = lgamma(2*n2 + 1) - lgamma(ma->M + 1);
+ for (k = 0, x = 0.; k < 2 * n2; ++k)
+ x += ma->phi[2*n1+k] * ma->z2[k] * expl(lgamma(2*n1 + k + 1) - lgamma(k + 1) + y);
+ pc[1] = ma->z1[2*n1] * x / sum;
+ for (k = 1, x = 0.; k <= 2 * n2; ++k)
+ x += ma->phi[k] * ma->z2[k] * expl(lgamma(ma->M - k + 1) - lgamma(2*n2 - k + 1) + y);
+ pc[1] += ma->z1[0] * x / sum;
+ // the variant is specific to group1
+ y = lgamma(2*n1 + 1) - lgamma(ma->M + 1);
+ for (k = 0, x = 0.; k < 2 * n1; ++k)
+ x += ma->phi[2*n2+k] * ma->z1[k] * expl(lgamma(2*n2 + k + 1) - lgamma(k + 1) + y);
+ pc[0] = ma->z2[2*n2] * x / sum;
+ for (k = 1, x = 0.; k <= 2 * n1; ++k)
+ x += ma->phi[k] * ma->z1[k] * expl(lgamma(ma->M - k + 1) - lgamma(2*n1 - k + 1) + y);
+ pc[0] += ma->z2[0] * x / sum;
+ // rescale
+ for (k = 2; k < 4; ++k) {
+ y = 1. - pc[k];
+ if (y <= 0.) y = 1e-100;
+ pc[k] = (int)(-4.343 * log(y) + .499);
+ if (pc[k] > 99.) pc[k] = 99.;
+ }
+}
+
static double mc_cal_afs(bcf_p1aux_t *ma)
{
int k;
return sum / ma->M;
}
-static long double p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
+long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3])
{
long double pd = 0., g2[3];
int i, k;
flast = rst->f_em;
}
}
- p1_cal_g3(ma, rst->g);
+ rst->g[0] = rst->g[1] = rst->g[2] = -1.;
+ contrast(ma, rst->pc);
+// bcf_p1_cal_g3(ma, rst->g);
return 0;
}
projects / samtools.git / blobdiff