* samtools-0.1.5-27 (r443)

[samtools.git] / bam.c

diff --git a/bam.c b/bam.c
index 52d97a6959dfad2076afdb3c64f37fd76b87fb40..619b46a6718a773aa073e7ecede13ef5cd10dee8 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -271,10 +271,12 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
        else if (c->mtid == c->tid) kputs("=\t", &str);
        else ksprintf(&str, "%s\t", header->target_name[c->mtid]);
        ksprintf(&str, "%d\t%d\t", c->mpos + 1, c->isize);
-       for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
-       kputc('\t', &str);
-       if (t[0] == 0xff) kputc('*', &str);
-       else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+       if (c->l_qseq) {
+               for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
+               kputc('\t', &str);
+               if (t[0] == 0xff) kputc('*', &str);
+               else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+       } else ksprintf(&str, "*\t*");
        s = bam1_aux(b);
        while (s < b->data + b->data_len) {
                uint8_t type, key[2];