Imported Upstream version 0.1.9

[samtools.git] / bcftools / ld.c

diff --git a/bcftools/ld.c b/bcftools/ld.c
new file mode 100644 (file)
index 0000000..aa7ec07
--- /dev/null
+++ b/bcftools/ld.c
@@ -0,0 +1,100 @@
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include "bcf.h"
+
+static double g_q2p[256];
+
+#define LD_ITER_MAX 50
+#define LD_ITER_EPS 1e-4
+
+#define _G1(h, k) ((h>>1&1) + (k>>1&1))
+#define _G2(h, k) ((h&1) + (k&1))
+
+// 0: the previous site; 1: the current site
+static int freq_iter(int n, double *pdg[2], double f[4])
+{
+       double ff[4];
+       int i, k, h;
+       memset(ff, 0, 4 * sizeof(double));
+       for (i = 0; i < n; ++i) {
+               double *p[2], sum, tmp;
+               p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
+               for (k = 0, sum = 0.; k < 4; ++k)
+                       for (h = 0; h < 4; ++h)
+                               sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
+               for (k = 0; k < 4; ++k) {
+                       tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+                               + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+                               + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+                               + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
+                       ff[k] += f[k] * tmp / sum;
+               }
+       }
+       for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
+       return 0;
+}
+
+double bcf_ld_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
+{
+       const bcf1_t *b[2];
+       uint8_t *PL[2];
+       int i, j, PL_len[2], n_smpl;
+       double *pdg[2], flast[4], r;
+       // initialize g_q2p if necessary
+       if (g_q2p[0] == 0.)
+               for (i = 0; i < 256; ++i)
+                       g_q2p[i] = pow(10., -i / 10.);
+       // initialize others
+       if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
+       n_smpl = b0->n_smpl;
+       b[0] = b0; b[1] = b1;
+       f[0] = f[1] = f[2] = f[3] = -1.;
+       if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
+       // set PL and PL_len
+       for (j = 0; j < 2; ++j) {
+               const bcf1_t *bj = b[j];
+               for (i = 0; i < bj->n_gi; ++i) {
+                       if (bj->gi[i].fmt == bcf_str2int("PL", 2)) {
+                               PL[j] = (uint8_t*)bj->gi[i].data;
+                               PL_len[j] = bj->gi[i].len;
+                               break;
+                       }
+               }
+               if (i == bj->n_gi) return -1; // no PL
+       }
+       // fill pdg[2]
+       pdg[0] = malloc(3 * n_smpl * sizeof(double));
+       pdg[1] = malloc(3 * n_smpl * sizeof(double));
+       for (j = 0; j < 2; ++j) {
+               for (i = 0; i < n_smpl; ++i) {
+                       const uint8_t *pi = PL[j] + i * PL_len[j];
+                       double *p = pdg[j] + i * 3;
+                       p[0] = g_q2p[pi[b[j]->n_alleles]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
+               }
+       }
+       // iteration
+       f[0] = f[1] = f[2] = f[3] = 0.25; // this is a really bad guess...
+       for (j = 0; j < LD_ITER_MAX; ++j) {
+               double eps = 0;
+               memcpy(flast, f, 4 * sizeof(double));
+               freq_iter(n_smpl, pdg, f);
+               for (i = 0; i < 4; ++i) {
+                       double x = fabs(f[0] - flast[0]);
+                       if (x > eps) eps = x;
+               }
+               if (eps < LD_ITER_EPS) break;
+       }
+       // free
+       free(pdg[0]); free(pdg[1]);
+       { // calculate r^2
+               double p[2], q[2], D;
+               p[0] = f[0] + f[1]; q[0] = 1 - p[0];
+               p[1] = f[0] + f[2]; q[1] = 1 - p[1];
+               D = f[0] * f[3] - f[1] * f[2];
+               r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
+               // fprintf(stderr, "R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r2);
+               if (isnan(r)) r = -1.;
+       }
+       return r;
+}