From e32b6f09cc615932e7371ebf479b09ad3fb34e1e Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 28 Sep 2010 03:05:12 +0000 Subject: [PATCH] * fixed that weird issue. * the banded version is NOT working --- kaln.c | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/kaln.c b/kaln.c index ec8c6df..072375f 100644 --- a/kaln.c +++ b/kaln.c @@ -428,6 +428,16 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float // f[0] set_u(k, bw, 0, 0); f[0][k] = 1.; + { + int beg = 1, 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, 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]; @@ -442,7 +452,7 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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 +// fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG } } // sink @@ -463,7 +473,7 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float bi[u+0] = sM; bi[u+1] = sI; } // b[l_query-1..1]; core loop - for (i = l_query - 1; i > 0; --i) { + 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; @@ -476,16 +486,9 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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 +// 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] > 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]; pD = (pf + pb) / 2.; -- 2.39.5