fixed a bug in realignment

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index dfc83e9407e3bf635be009af4d4be50240c13e61..5715f9aafca24abad9e0cc17e2ef1f567e9f3fc8 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -461,7 +461,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                for (i = 0; i < n_types; ++i) {
                        ka_param_t ap = ka_param_blast;
                        ap.band_width = 2 * types[n_types - 1] + 2;
-                       ap.gap_end = 0;
+                       ap.gap_end_ext = 0;
                        // write ref2
                        for (k = 0, j = left; j <= pos; ++j)
                                ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];