A bug fix, "samtools view" is now working again.

[samtools.git] / bam_md.c

diff --git a/bam_md.c b/bam_md.c
index ead2346e4ec21f75b8ceb88a4b78690d2a3d3b39..8d074870d336677cee2e606ab05ee81a2b4a6f1e 100644 (file)
--- a/bam_md.c
+++ b/bam_md.c
@@ -16,10 +16,6 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
        uint8_t *old_md, *old_nm;
        int32_t old_nm_i = -1, nm = 0;
 
-       old_md = bam_aux_get(b, "MD");
-       old_nm = bam_aux_get(b, "NM");
-       if (c->flag & BAM_FUNMAP) return;
-       if (old_nm) old_nm_i = bam_aux2i(old_nm);
        str = (kstring_t*)calloc(1, sizeof(kstring_t));
        for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
                int j, l = cigar[i]>>4, op = cigar[i]&0xf;
@@ -57,12 +53,18 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
                }
        }
        ksprintf(str, "%d", u);
+       // update NM
+       old_nm = bam_aux_get(b, "NM");
+       if (c->flag & BAM_FUNMAP) return;
+       if (old_nm) old_nm_i = bam_aux2i(old_nm);
        if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        else if (nm != old_nm_i) {
                fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
                bam_aux_del(b, old_nm);
                bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
        }
+       // update MD
+       old_md = bam_aux_get(b, "MD");
        if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
        else {
                int is_diff = 0;