X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kaln.c;h=4cba98d3ae4bcc9d9e3ab9a30d537412dbd0f2ed;hb=168ad095c3483f195ae3e404b3cd1fe949681909;hp=bfb011dbcb0b5c73d2094e1aaa02809d214fc62a;hpb=3f2413d3c5f459cd934239f27f34137d7bb7e3af;p=samtools.git diff --git a/kaln.c b/kaln.c index bfb011d..4cba98d 100644 --- a/kaln.c +++ b/kaln.c @@ -370,171 +370,3 @@ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const return cigar; } - -/*************************** - * Probabilistic extension * - ***************************/ - -#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, 1 }; - -/* - The profile HMM is: - - /\ /\ /\ /\ /\ - I[0] I[1] I[k-1] I[k] I[L] - ^ \ ^ \ \ ^ \ ^ \ \ ^ - | \ | \ \ | \ | \ \ | - M[0] -> M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1] - \ \/ \/ \/ \/ / - \ /\ /\ /\ /\ / - D[1] -> -> D[k-1] -> D[k] -> - \/ \/ \/ - - Every {M,I}[k], k=0..L connects M[L+1] at the same probability, while - no D[k], k=1..L-1 connects M[L+1]. This means an alignment can end up - with M or I but not D. - - Deletions are dumb states which do not emit residues. Frankly, I am - not sure if they are handled properly in the following - implementation. This is a potential concern to be resolved in future. - */ -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, pD; - float *qual; - uint8_t *ref, *query; - int bw, bw2, i, k, is_diff = 0; - - // FIXME: floating point underflow - - /*** initialization ***/ - ref = _ref - 1; // change to 1-based coordinate - query = _query - 1; - qual = _qual - 1; - bw = c->bw; - bw2 = c->bw * 2 + 1; - // allocate forward and backward matrices f[][] and b[][] - 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)); // FIXME: this is over-allocated for very short seqs - b[i] = calloc(bw2 * 3 + 6, sizeof(double)); - } - // initialize transition probability - sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof - 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.; - { // write D cells - int beg = 1, end = l_ref, x; - x = 0 - bw; beg = beg > x? beg : x; - x = 0 + bw; end = end < x? end : x; - for (k = beg; k <= end; ++k) { - int u, v01; - set_u(u, bw, 0, k); set_u(v01, bw, 0, k-1); - f[0][u+2] = m[2] * f[0][v01+0] + m[8] * f[0][v01+2]; - } - } - // 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; // band start - x = i + bw; end = end < x? end : x; // band end - for (k = beg; k <= end; ++k) { - int u, v11, v01, v10; - double e; - // FIXME: the following line can be optimized without branching! - e = (ref[k] > 3 || query[i] > 3)? 1. : ref[k] == query[i]? 1. - qual[i] : qual[i] / 3.; - 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, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG - } - } - // 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; // this P(x) calculated by the forward algorithm - /*** 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; - } - // b[l_query-1..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] > 3 || query[i+1] > 3)? 1. : ref[k+1] == query[i+1]? 1. - qual[i+1] : qual[i+1] / 3.; - 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, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG - } - } - set_u(k, bw, 0, 0); - pb = b[0][k]; - pD = (pf + pb) / 2.; - is_diff = fabs(pb/pf - 1.) > 1e-7? 1 : 0; - /*** 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; - 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; - } - max /= sum; sum /= pD; // 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); -#ifdef _MAIN - fprintf(stderr, "[%d,%.10lg,%.10lg],%d,%lg,%d:%d,%lg\n", is_diff, pf, pb, i, sum, max_k>>2, max_k&3, max); -#endif - } - /*** free ***/ - for (i = 0; i <= l_query; ++i) { - free(f[i]); free(b[i]); - } - free(f); free(b); - return 0; -} - -#ifdef _MAIN -int main() -{ - int l_ref = 5, l_query = 3; - uint8_t *ref = (uint8_t*)"\0\1\3\3\1"; -// uint8_t *query = (uint8_t*)"\0\3\3\1"; - uint8_t *query = (uint8_t*)"\1\3\3\1"; // FIXME: the output is not so right given this input!!! - static float qual[4] = {.01, .01, .01, .01}; - ka_prob_extend(ref, l_ref, query, l_query, qual, &ka_probpar_def, 0, 0); - return 0; -} -#endif