From 1027e43a3e1724521df87fba3b29fdd9c8d07ce5 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 28 Sep 2010 03:17:16 +0000 Subject: [PATCH] fixed a bug in banded DP --- kaln.c | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/kaln.c b/kaln.c index 072375f..07fd42b 100644 --- a/kaln.c +++ b/kaln.c @@ -377,7 +377,7 @@ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const #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 }; +ka_probpar_t ka_probpar_def = { 0.0001, 0.1, 1 }; /* The profile HMM is: @@ -430,8 +430,8 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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; + 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); @@ -510,7 +510,7 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float 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 + 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 ***/ @@ -524,7 +524,7 @@ int ka_prob_extend(uint8_t *_ref, int l_ref, uint8_t *_query, int l_query, float #ifdef _MAIN int main() { - int l_ref = 5, l_query = 4; + 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!!! -- 2.39.5