* samtools-0.1.5-12 (r415)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index c6fbafce979d93560d80265807833a8c9972dca0..2cadfcc6c73bd2f185616759d9ead6a75e543a14 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -297,7 +297,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                doff += c->l_qname;
        }
        { // flag, tid, pos, qual
-               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+               long flag;
+               char *s;
+               ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+               flag = strtol((char*)str->s, &s, 0);
+               c->flag = flag;
                ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
                if (c->tid < 0 && strcmp(str->s, "*")) {
                        if (header->n_targets == 0) {