return cigar;
}
+
+#define get_k(b, i, kk) ((i) < (b)? (kk)/3 : (kk)/3+(i)-(b))
+#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }
+
+ka_probpar_t ka_probpar_def = { 0.0001, 0.1, 10 };
+
+int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float *_qual,
+ const ka_probpar_t *c, int *state, uint8_t *q)
+{
+ double **f, **b, m[9], f_sink, sI, sM, pf, pb;
+ float *qual;
+ uint8_t *ref, *query;
+ int bw, bw2, i, k;
+ /*** initialization ***/
+ ref = _ref - 1;
+ query = _query - 1;
+ qual = _qual - 1;
+ bw = c->bw;
+ bw2 = c->bw * 2 + 1;
+ f = calloc(l_query+1, sizeof(void*));
+ b = calloc(l_query+1, sizeof(void*));
+ for (i = 0; i <= l_query; ++i) {
+ f[i] = calloc(bw2 * 3 + 6, sizeof(double));
+ b[i] = calloc(bw2 * 3 + 6, sizeof(double));
+ }
+ // initialize m
+ sM = sI = 1. / (2 * l_query + 1);
+ m[0*3+0] = (1 - c->d - c->d) * (1 - sM);
+ m[0*3+1] = m[0*3+2] = c->d * (1 - sM);
+ m[1*3+0] = (1 - c->e) * (1 - sI);
+ m[1*3+1] = c->e * (1 - sI);
+ m[1*3+2] = 0.;
+ m[2*3+0] = 1 - c->e;
+ m[2*3+1] = 0.;
+ m[2*3+2] = c->e;
+ /*** forward ***/
+ // f[0]
+ set_u(k, bw, 0, 0);
+ f[0][k] = 1.;
+ // f[1..l_query]; core loop
+ for (i = 1; i <= l_query; ++i) {
+ double *fi = f[i], *fi1 = f[i-1];
+ int beg = 0, end = l_ref, x;
+ x = i - bw; beg = beg > x? beg : x;
+ x = i + bw; end = end < x? end : x;
+ for (k = beg; k <= end; ++k) {
+ int u, v11, v01, v10;
+ double e;
+ e = (ref[k] == 4 || query[i] == 4)? 1. : ref[k] == query[i]? 1. - qual[i] : qual[i]; // FIXME: can be better
+ set_u(u, bw, i, k);
+ set_u(v11, bw, i-1, k-1);
+ set_u(v10, bw, i-1, k);
+ set_u(v01, bw, i, k-1);
+ fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
+ fi[u+1] = .25 * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
+ fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
+ fprintf(stderr, "{%d,%d}@%d %.10lg,%.10lg,%.10lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]);
+ }
+ }
+ // sink
+ for (k = 0, f_sink = 0.; k <= l_ref; ++k) {
+ int u;
+ set_u(u, bw, l_query, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ f_sink += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
+ }
+ pf = f_sink;
+ /*** backward ***/
+ // sink
+ for (k = 0; k <= l_ref; ++k) {
+ int u;
+ double *bi = b[l_query];
+ set_u(u, bw, l_query, k);
+ if (u < 3 || u >= bw2*3+3) continue;
+ bi[u+0] = sM; bi[u+1] = sI;
+ fprintf(stderr, "[%d,%d]@%d %.10lg,%.10lg,%.10lg\n", l_query, k, u, bi[u], bi[u+1], bi[u+2]);
+ }
+ // b[l_query..1]; core loop
+ for (i = l_query - 1; i > 0; --i) {
+ int beg = 0, end = l_ref, x;
+ double *bi = b[i], *bi1 = b[i+1];
+ x = i - bw; beg = beg > x? beg : x;
+ x = i + bw; end = end < x? end : x;
+ for (k = end; k >= beg; --k) {
+ int u, v11, v01, v10;
+ double e;
+ e = k >= l_ref? 0 : (ref[k+1] == 4 || query[i+1] == 4)? 1. : ref[k+1] == query[i+1]? 1. - qual[i+1] : qual[i+1];
+ set_u(u, bw, i, k);
+ set_u(v11, bw, i+1, k+1);
+ set_u(v10, bw, i+1, k);
+ set_u(v01, bw, i, k+1);
+ bi[u+0] = e * m[0] * bi1[v11+0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2];
+ bi[u+1] = e * m[3] * bi1[v11+0] + .25 * m[4] * bi1[v10+1];
+ bi[u+2] = e * m[6] * bi1[v11+0] + m[8] * bi[v01+2];
+ fprintf(stderr, "[%d,%d]@%d %.10lg,%.10lg,%.10lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]);
+ }
+ }
+ {
+ int beg = 0, end = l_ref, x;
+ double *bi = b[0], *bi1 = b[1];
+ x = i - bw; beg = beg > x? beg : x;
+ x = i + bw; end = end < x? end : x;
+ for (k = end; k >= beg; --k) {
+ int u, v11, v01, v10;
+ double e;
+ e = k >= l_ref? 0 : (ref[k+1] == 4 || query[1] == 4)? 1. : ref[k+1] == query[1]? 1. - qual[1] : qual[1];
+ set_u(u, bw, 0, k);
+ set_u(v11, bw, 1, k+1);
+ set_u(v10, bw, 1, k);
+ set_u(v01, bw, 0, k+1);
+ bi[u+0] = e * m[0] * bi1[v11+0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2];
+ fprintf(stderr, "[%d,%d]@%d %.10lg,%.10lg,%.10lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]);
+ }
+ }
+ set_u(k, bw, 0, 0);
+ pb = b[0][k];
+ fprintf(stderr, "(%.10lg,%.10lg):(%.10lg,%.10lg)\n", pf, pb, pb-pf, pb/pf-1);
+ /*** MAP ***/
+ return 0;
+}
+
+#ifdef _MAIN
+int main()
+{
+ int l_ref = 5, l_query = 4;
+ uint8_t *ref = (uint8_t*)"\0\1\3\3\1";
+ uint8_t *query = (uint8_t*)"\0\1\3\1";
+// uint8_t *query = "\1\3\3\1";
+ static float qual[4] = {.2, .01, .01, .01};
+ ka_prob_extend(ref, l_ref, query, l_query, qual, &ka_probpar_def, 0, 0);
+ return 0;
+}
+#endif
projects / samtools.git / blobdiff