fixed a bug in realignment

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index 63c25e961d704b0c555eaea115fe69f38275e17b..a4f4e01ce2672556746c399af379a325b61273af 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -142,6 +142,7 @@ int bam_realn(bam1_t *b, const char *ref)
        cigar = ka_global_core(s_ref, l_ref, s_read, c->l_qseq, &par, &score, &n_cigar);
        if (score <= 0) { // realignment failed
                free(cigar); free(s_ref); free(s_read);
+               return -1;
        }
        // copy over the alignment
        if (4 * (n_cigar - (int)c->n_cigar) + b->data_len > b->m_data) { // enlarge b->data