* samtools-0.1.3-24 (r296)

[samtools.git] / bam_maqcns.c

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 230f891c9020c2b744d32f33050993baae2908be..c6c9af7dee454ed91cd75363470473405d7c97ea 100644 (file)
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -408,7 +408,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
                                if (types[i] != 0) { // then try the other way to calculate the score
                                        for (ps = s = 0, l = seg.qbeg; c->pos + l + types[i] < right && l < seg.qend; ++l) {
                                                int cq = bam1_seqi(bam1_seq(p->b), l), ct;
-                                               ct = c->pos + l + types[i] >= left? ref2[c->pos + l + types[i] - left] : 15;
+                                               ct = c->pos + l - seg.qbeg + types[i] >= left? ref2[c->pos + l - seg.qbeg + types[i] - left] : 15;
                                                if (cq < 15 && ct < 15) {
                                                        s += cq == ct? 1 : -mi->mm_penalty;
                                                        if (cq != ct) ps += bam1_qual(p->b)[l];