* samtools-0.1.7-r607

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 51f56a9e5c4a0f58e06b81e0500ff1aaf12a4aad..9a25380f36b77411ecc34336b5a92fe2d2f734d4 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -446,6 +446,7 @@ 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;
                        // write ref2
                        for (k = 0, j = left; j <= pos; ++j)
                                ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
@@ -490,10 +491,10 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                                                if (ref2[x+k] != rs[y+k] && ref2[x+k] < 4) ps += bam1_qual(p->b)[y+k];
                                                        x += len; y += len;
                                                } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
-                                                       if (op == BAM_CINS) ps += mi->q_indel * len;
+                                                       if (op == BAM_CINS && l > 0 && l < n_acigar - 1) ps += mi->q_indel * len;
                                                        y += len;
                                                } else if (op == BAM_CDEL) {
-                                                       ps += mi->q_indel * len;
+                                                       if (l > 0 && l < n_acigar - 1) ps += mi->q_indel * len;
                                                        x += len;
                                                }
                                        }