* This revision is SERIOUSLY BUGGY. Please NOT use it.

[samtools.git] / kaln.c

diff --git a/kaln.c b/kaln.c
index 65f6c497298e3ee5983307e4a011b18add99a54c..9fa40d0be3999e66b885486d7a03e50994bfbfdd 100644 (file)
--- a/kaln.c
+++ b/kaln.c
@@ -182,17 +182,6 @@ typedef struct {
        int M, I, D;
 } dpscore_t;
 
-/* build score profile for accelerating alignment, in theory */
-static void aln_init_score_array(uint8_t *seq, int len, int row, int *score_matrix, int **s_array)
-{
-       int *tmp, *tmp2, i, k;
-       for (i = 0; i != row; ++i) {
-               tmp = score_matrix + i * row;
-               tmp2 = s_array[i];
-               for (k = 0; k != len; ++k)
-                       tmp2[k] = tmp[seq[k]];
-       }
-}
 /***************************
  * banded global alignment *
  ***************************/
@@ -216,7 +205,8 @@ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const
        b = ap->band_width;
        score_matrix = ap->matrix;
        N_MATRIX_ROW = ap->row;
-       
+
+       *n_cigar = 0;
        if (len1 == 0 || len2 == 0) return 0;
 
        /* calculate b1 and b2 */