From 8587a0ee0b25743a072ec67ede7076e5e24e4573 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 28 Sep 2010 02:57:05 +0000 Subject: [PATCH] More comments. This version seems working, but something is a little weird... --- kaln.c | 76 +++++++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 62 insertions(+), 14 deletions(-) diff --git a/kaln.c b/kaln.c index f5c9d89..ec8c6df 100644 --- a/kaln.c +++ b/kaln.c @@ -371,18 +371,42 @@ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const return cigar; } -#define get_k(b, i, kk) ((i) < (b)? (kk)/3 : (kk)/3+(i)-(b)) +/*************************** + * 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, 10 }; +/* + 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; + double **f, **b, m[9], f_sink, sI, sM, pf, pb, pD; float *qual; uint8_t *ref, *query; - int bw, bw2, i, k; + int bw, bw2, i, k, is_diff = 0; /*** initialization ***/ ref = _ref - 1; query = _query - 1; @@ -396,7 +420,7 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float b[i] = calloc(bw2 * 3 + 6, sizeof(double)); } // initialize m - sM = sI = 1. / (2 * l_query + 1); + sM = sI = 1. / (2 * l_query + 2); 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; @@ -413,11 +437,12 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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 + 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 @@ -446,27 +471,50 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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]; + 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 } } { // the "zero" coordinate (i==k==0) double *bi = b[0], *bi1 = b[1]; int u, v11, v01, v10; - double e = (ref[1] == 4 || query[1] == 4)? 1. : ref[1] == query[1]? 1. - qual[1] : qual[1]; + double e = (ref[1] > 3 || query[1] > 3)? 1. : ref[1] == query[1]? 1. - qual[1] : qual[1] / 3.; set_u(u, bw, 0, 0); set_u(v11, bw, 1, 1); set_u(v10, bw, 1, 0); set_u(v01, bw, 0, 1); bi[u+0] = e * m[0] * bi1[v11+0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; } set_u(k, bw, 0, 0); pb = b[0][k]; - { // pf should equal pb as they are both the likelihood of data but calculated in different ways - double z = fabs(pb/pf - 1.); - if (z > 1e-7) fprintf(stderr, "[%s] %lg!=%lg\n", __func__, pf, pb); - } + 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],%d,%lg,%d:%d,%lg\n", is_diff, i, sum, max_k>>2, max_k&3, max); // DEBUG +#endif + } + /*** free ***/ + for (i = 0; i <= l_query; ++i) { + free(f[i]); free(b[i]); + } + free(f); free(b); return 0; } @@ -475,9 +523,9 @@ 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}; +// 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; } -- 2.39.5