* vcfutils.pl: fixed a typo in help message

[samtools.git] / kaln.c

diff --git a/kaln.c b/kaln.c
index 3cf8f71cdd1f4096cdb852104c38fa0ad98eb3a8..331fbb0aba6b803f4163e6d1acec46a31f6ec99d 100644 (file)
--- a/kaln.c
+++ b/kaln.c
@@ -392,9 +392,19 @@ ka_probpar_t ka_probpar_def = { 0.001, 0.1, 10 };
                 \      \/        \/      \/      /
                  \     /\        /\      /\     /
                        -> D[k-1] -> D[k] ->
-                          \/        \/
 
    M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1].
+
+   On input, _ref is the reference sequence and _query is the query
+   sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an
+   ambiguous residue. iqual is the base quality. c sets the gap open
+   probability, gap extension probability and band width.
+
+   On output, state and q are arrays of length l_query. The higher 30
+   bits give the reference position the query base is matched to and the
+   lower two bits can be 0 (an alignment match) or 1 (an
+   insertion). q[i] gives the phred scaled posterior probability of
+   state[i] being wrong.
  */
 int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
                                   const ka_probpar_t *c, int *state, uint8_t *q)
@@ -471,7 +481,7 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                // rescale
                s[i] = sum;
                set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
-               for (k = _beg; k <= _end; ++k) fi[k] /= sum;
+               for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
        }
        { // f[l_query+1]
                double sum;
@@ -502,16 +512,16 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                for (k = end; k >= beg; --k) {
                        int u, v11, v01, v10;
                        double e;
-                       e = k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 / 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]) * y;
+                       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];
+                       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
                }
                // rescale
                set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
-               for (k = _beg; k <= _end; ++k) bi[k] /= s[i];
+               for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
        }
        { // b[0]
                int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
@@ -542,7 +552,7 @@ int ka_prob_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_
                }
                max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
                if (state) state[i-1] = max_k;
-               if (q) k = -4.343 * log(1. - max), q[i-1] = k > 100? 99 : k;
+               if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k;
 #ifdef _MAIN
                fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%d)~%lg\n", pb, sum, i-1, max_k>>2, max_k&3, max); // DEBUG
 #endif