X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=3ca730993cbc01065eb2c76bd66df1640808e032;hb=020baf39a16a31e33a736d347714e2551f6273df;hp=ead2346e4ec21f75b8ceb88a4b78690d2a3d3b39;hpb=030a404097c6f8b094eca03a8380b35ff81e6c70;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index ead2346..3ca7309 100644
--- 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;
@@ -130,8 +132,11 @@ int bam_fillmd(int argc, char *argv[])
 				free(ref);
 				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 				tid = b->core.tid;
+				if (ref == 0)
+					fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+							fp->header->target_name[tid]);
 			}
-			bam_fillmd1(b, ref, is_equal);
+			if (ref) bam_fillmd1(b, ref, is_equal);
 		}
 		samwrite(fpout, b);
 	}