* Minor code changes. No real effect.

 * change quality to 30 in toy.sam

diff --git a/examples/toy.sam b/examples/toy.sam
index eae1e2d93d113d9b19b17236fb5386161e373fcd..c6d0570277cdaf3877c0388a37f88c58baa1659b 100644 (file)
--- a/examples/toy.sam
+++ b/examples/toy.sam
@@ -6,9 +6,9 @@ r003    0       ref     9       30      5H6M    *       0       0       AGCTAA  *
 r004   0       ref     16      30      6M14N1I5M       *       0       0       ATAGCTCTCAGC    *
 r003   16      ref     29      30      6H5M    *       0       0       TAGGC   *
 r001   83      ref     37      30      9M      =       7       -39     CAGCGCCAT       *
-x1     0       ref2    1       30      20M     *       0       0       aggttttataaaacaaataa    ::::::::::::::::::::
-x2     0       ref2    2       30      21M     *       0       0       ggttttataaaacaaataatt   :::::::::::::::::::::
-x3     0       ref2    6       30      9M4I13M *       0       0       ttataaaacAAATaattaagtctaca      ::::::::::::::::::::::::::
-x4     0       ref2    10      30      25M     *       0       0       CaaaTaattaagtctacagagcaac       :::::::::::::::::::::::::
-x5     0       ref2    12      30      24M     *       0       0       aaTaattaagtctacagagcaact        ::::::::::::::::::::::::
-x6     0       ref2    14      30      23M     *       0       0       Taattaagtctacagagcaacta :::::::::::::::::::::::
+x1     0       ref2    1       30      20M     *       0       0       aggttttataaaacaaataa    ????????????????????
+x2     0       ref2    2       30      21M     *       0       0       ggttttataaaacaaataatt   ?????????????????????
+x3     0       ref2    6       30      9M4I13M *       0       0       ttataaaacAAATaattaagtctaca      ??????????????????????????
+x4     0       ref2    10      30      25M     *       0       0       CaaaTaattaagtctacagagcaac       ?????????????????????????
+x5     0       ref2    12      30      24M     *       0       0       aaTaattaagtctacagagcaact        ????????????????????????
+x6     0       ref2    14      30      23M     *       0       0       Taattaagtctacagagcaacta ???????????????????????

diff --git a/kaln.c b/kaln.c
index 331fbb0aba6b803f4163e6d1acec46a31f6ec99d..680779113ce7c2220434727cf578845d1e840d40 100644 (file)
--- a/kaln.c
+++ b/kaln.c
@@ -377,6 +377,8 @@ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const
 
 static float g_qual2prob[256];
 
+#define EI .25
+#define EM .3333333333333
 #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 = { 0.001, 0.1, 10 };
@@ -450,9 +452,9 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
                for (k = beg, sum = 0.; k <= end; ++k) {
                        int u;
-                       double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
+                       double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
                        set_u(u, bw, 1, k);
-                       fi[u+0] = e * bM; fi[u+1] = .25 * bI;
+                       fi[u+0] = e * bM; fi[u+1] = EI * bI;
                        sum += fi[u] + fi[u+1];
                }
                // rescale
@@ -470,10 +472,10 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                for (k = beg, sum = 0.; k <= end; ++k) {
                        int u, v11, v01, v10;
                        double e;
-                       e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli / 3.;
+                       e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli * EM;
                        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+1] = EI * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
                        fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
                        sum += fi[u] + fi[u+1] + fi[u+2];
 //                     fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG
@@ -513,9 +515,9 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                        int u, v11, v01, v10;
                        double e;
                        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);
-                       e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 / 3.) * bi1[v11];
-                       bi[u+0] = e * m[0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
-                       bi[u+1] = e * m[3] + .25 * m[4] * bi1[v10+1];
+                       e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 * EM) * bi1[v11];
+                       bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
+                       bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1];
                        bi[u+2] = (e * m[6] + 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
                }
@@ -528,10 +530,10 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                double sum = 0.;
                for (k = end; k >= beg; --k) {
                        int u;
-                       double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
+                       double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
                        set_u(u, bw, 1, k);
                        if (u < 3 || u >= bw2*3+3) continue;
-                   sum += e * b[1][u+0] * bM + .25 * b[1][u+1] * bI;
+                   sum += e * b[1][u+0] * bM + EI * b[1][u+1] * bI;
                }
                set_u(k, bw, 0, 0);
                pb = b[0][k] = sum / s[0]; // if everything works as is expected, pb == 1.0