return cigar;
}
-/************************
- * Probabilistic glocal *
- ************************/
+/*****************************************
+ * Probabilistic banded glocal alignment *
+ *****************************************/
static float g_qual2prob[256];
// b[l_query-1..1]
for (i = l_query - 1; i >= 1; --i) {
int beg = 1, end = l_ref, x, _beg, _end;
- double *bi = b[i], *bi1 = b[i+1];
+ double *bi = b[i], *bi1 = b[i+1], y = (i > 1);
x = i - bw; beg = beg > x? beg : x;
x = i + bw; end = end < x? end : x;
for (k = end; k >= beg; --k) {
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];
// FIXME: I do not know why I need this (i>1) factor, but only with it the result makes sense.
- bi[u+2] = (e * m[6] * bi1[v11+0] + m[8] * bi[v01+2]) * (i > 1);
+ bi[u+2] = (e * m[6] * bi1[v11+0] + m[8] * bi[v01+2]) * y;
// fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG
}
// rescale
set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
- for (k = _beg; k <= _end; ++k) bi[k] /= s[i];
+ y = s[i];
+ for (k = _beg; k <= _end; ++k) bi[k] /= y;
}
{ // b[0]
int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
/*** MAP ***/
for (i = 1; i <= l_query; ++i) {
double sum = 0., *fi = f[i], *bi = b[i], max = 0.;
- int beg = 0, end = l_ref, x, max_k = -1;
+ int beg = 1, end = l_ref, x, max_k = -1;
x = i - bw; beg = beg > x? beg : x;
x = i + bw; end = end < x? end : x;
for (k = beg; k <= end; ++k) {
int u;
double z;
set_u(u, bw, i, k);
- z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = k<<2 | 0; sum += z;
- z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = k<<2 | 1; sum += z;
+ z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z;
+ z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z;
}
max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
if (state) state[i-1] = max_k;
- if (q) q[i-1] = -4.343 * log(1. - max);
+ if (q) k = -4.343 * log(1. - max), q[i-1] = k > 100? 99 : k;
#ifdef _MAIN
- fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%d)~%lg\n", pb, sum, i, max_k>>2, max_k&3, max); // DEBUG
+ fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%d)~%lg\n", pb, sum, i-1, max_k>>2, max_k&3, max); // DEBUG
#endif
}
/*** free ***/