Output the MD tag for each XA record with -D.

bwase.c

@@ -291,11 +291,17 @@ void bwa_correct_trimmed(bwa_seq_t *s)
 	s->len = s->full_len;
 }
 
-void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq)
+
+void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq) 
+{
+	bwa_refine_gapped2(bns, n_seqs, seqs, _pacseq, 0);
+}
+
+void bwa_refine_gapped2(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, int with_md)
 {
 	ubyte_t *pacseq;
 	int i, j, k;
-	kstring_t *str;
+	kstring_t *str = (kstring_t*)calloc(1, sizeof(kstring_t));
 
 	if (!_pacseq) {
 		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
@@ -312,15 +318,25 @@ void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t
 				q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, q->ref_shift, &q->pos, &n_cigar);
 				q->n_cigar = n_cigar;
 				if (q->cigar) s->multi[k++] = *q;
-			} else s->multi[k++] = *q;
+			} else {
+				s->multi[k++] = *q;
+				if (with_md) { // create the cigar, needed for bwa_cal_md1 below
+					q->n_cigar = 1;
+					q->cigar = calloc(q->n_cigar, sizeof(uint32_t));
+					q->cigar[0] = __cigar_create(FROM_M, s->len);
+				}
+			}
+			if (with_md) {
+				int nm;
+				q->md = bwa_cal_md1(q->n_cigar, q->cigar, s->len, q->pos, q->strand? s->rseq : s->seq, bns->l_pac, pacseq, str, &nm);
+			}
 		}
 		s->n_multi = k; // this squeezes out gapped alignments which failed the CIGAR generation
 		if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
 		s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, s->ref_shift, &s->pos, &s->n_cigar);
 		if (s->cigar == 0) s->type = BWA_TYPE_NO_MATCH;
 	}
 	// generate MD tag
-	str = (kstring_t*)calloc(1, sizeof(kstring_t));
 	for (i = 0; i != n_seqs; ++i) {
 		bwa_seq_t *s = seqs + i;
 		if (s->type != BWA_TYPE_NO_MATCH) {
@@ -480,7 +496,8 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 						for (k = 0; k < q->n_cigar; ++k)
 							err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
 					} else err_printf("%dM", p->len);
-					err_printf(",%d;", q->gap + q->mm);
+					if (q->md) err_printf(",%d,%s;", q->gap + q->mm, q->md);
+					else err_printf(",%d,.;", q->gap + q->mm);
 				}
 			}
 		}

bwase.h

@@ -26,6 +26,7 @@ extern "C" {
 	void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr);
 	void bwa_cal_pac_pos_with_bwt(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr, bwt_t *bwt);
 	void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq);
+	void bwa_refine_gapped2(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, int with_md);
 	void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
 
 #ifdef __cplusplus

bwtaln.c

@@ -37,10 +37,11 @@ gap_opt_t *gap_init_opt()
 	o->n_threads = 1;
 	o->max_top2 = 30;
 	o->trim_qual = 0;
+	o->n_occ = 3;
 	o->sam = 0;
-	o->interactive_mode = 0;
 	o->rg_line = NULL;
-	o->n_occ = 3;
+	o->interactive_mode = 0;
+	o->with_md = 0;
 	return o;
 }
 
@@ -247,7 +248,7 @@ void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
 			fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 
 			fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
-			bwa_refine_gapped(bns, n_seqs, seqs, 0);
+			bwa_refine_gapped2(bns, n_seqs, seqs, 0, opt->with_md);
 			fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 
 			fprintf(stderr, "[bwa_aln_core] print alignments... ");
@@ -283,7 +284,7 @@ int bwa_aln(int argc, char *argv[])
 	char *prefix;
 
 	opt = gap_init_opt();
-	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:LR:m:t:NM:O:E:q:f:b012IYB:Sr:X:Z")) >= 0) {
+	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:LR:m:t:NM:O:E:q:f:b012IYB:Sr:X:ZD")) >= 0) {
 		switch (c) {
 		case 'n':
 			if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
@@ -318,6 +319,7 @@ int bwa_aln(int argc, char *argv[])
 			break;
 		case 'X': opt->n_occ = atoi(optarg); break;
 		case 'Z': opt->interactive_mode = 1; break;
+		case 'D': opt->with_md = 1; break;
 		default: return 1;
 		}
 	}
@@ -359,6 +361,7 @@ int bwa_aln(int argc, char *argv[])
 		fprintf(stderr, "         -r STR    read group line for SAM output\n");
 		fprintf(stderr, "         -X INT    maximum # of hits to report (SAM output only, equivalent to -n in samse)\n");
 		fprintf(stderr, "         -Z        interactive mode (no input buffer and empty lines between records force processing)\n");
+		fprintf(stderr, "         -D        output the MD to each alignment in the XA tag, otherwise use \".\"\n");
 		fprintf(stderr, "\n");
 		return 1;
 	}

bwtaln.h

@@ -61,6 +61,7 @@ typedef struct {
 	int ref_shift;
 	bwtint_t pos;
 	bwa_cigar_t *cigar;
+	char *md;
 } bwt_multi1_t;
 
 typedef struct {
@@ -117,6 +118,7 @@ typedef struct {
         char *rg_line;
         int n_occ;
         int interactive_mode;
+        int with_md;
 } gap_opt_t;
 
 #define BWA_PET_STD   1