feat: add an option to output MD in the XA tag

bwape.c

@@ -621,7 +621,7 @@ ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs,
 	return pacseq;
 }
 
-void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line)
+void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line, int with_md)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
 	int i, j, n_seqs;
@@ -692,7 +692,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 		fprintf(stderr, "[bwa_sai2sam_pe_core] refine gapped alignments... ");
 		for (j = 0; j < 2; ++j)
-			bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq);
+			bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq, with_md);
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 		if (pac == 0) free(pacseq);
 
@@ -732,12 +732,12 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 int bwa_sai2sam_pe(int argc, char *argv[])
 {
-	int c;
+	int c, with_md = 0;
 	pe_opt_t *popt;
 	char *prefix, *rg_line = 0;
 
 	popt = bwa_init_pe_opt();
-	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
+	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:d")) >= 0) {
 		switch (c) {
 		case 'r':
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
@@ -751,6 +751,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		case 'c': popt->ap_prior = atof(optarg); break;
 		case 'f': xreopen(optarg, "w", stdout); break;
 		case 'A': popt->force_isize = 1; break;
+		case 'd': with_md = 1; break;
 		default: return 1;
 		}
 	}
@@ -768,6 +769,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		fprintf(stderr, "         -P       preload index into memory (for base-space reads only)\n");
 		fprintf(stderr, "         -s       disable Smith-Waterman for the unmapped mate\n");
 		fprintf(stderr, "         -A       disable insert size estimate (force -s)\n\n");
+		fprintf(stderr, "         -d       output the MD to each alignment in the XA tag, otherwise use \".\"\n\n");
 		fprintf(stderr, "Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
 		fprintf(stderr, "       2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
 		fprintf(stderr, "          to get a sensible speed at the cost of pairing accuracy.\n");
@@ -778,7 +780,7 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		return 1;
 	}
-	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
+	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line, with_md);
 	free(prefix); free(popt);
 	return 0;
 }

bwase.c

@@ -284,11 +284,11 @@ 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, 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);
@@ -305,15 +305,25 @@ 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) {
@@ -504,7 +514,7 @@ void bwase_initialize()
 	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
 }
 
-void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
+void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line, int with_md)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
 	int i, n_seqs, m_aln;
@@ -557,7 +567,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 		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_gapped(bns, n_seqs, seqs, 0, with_md);
 		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
 
 		fprintf(stderr, "[bwa_aln_core] print alignments... ");
@@ -578,11 +588,12 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 
 int bwa_sai2sam_se(int argc, char *argv[])
 {
-	int c, n_occ = 3;
+	int c, n_occ = 3, with_md = 0;
 	char *prefix, *rg_line = 0;
-	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
+	while ((c = getopt(argc, argv, "hdn:f:r:")) >= 0) {
 		switch (c) {
 		case 'h': break;
+		case 'd': with_md = 1; break;
 		case 'r':
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
 			break;
@@ -593,14 +604,14 @@ int bwa_sai2sam_se(int argc, char *argv[])
 	}
 
 	if (optind + 3 > argc) {
-		fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
+		fprintf(stderr, "Usage: bwa samse [-n max_occ] [-d] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
 		return 1;
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
 		return 1;
 	}
-	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
+	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line, with_md);
 	free(prefix);
 	return 0;
 }

bwase.h

@@ -14,7 +14,7 @@ extern "C" {
 	// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
 	void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
 	// Refine the approximate position of the sequence to an actual placement for the sequence.
-	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, int with_md);
 	// Backfill certain alignment properties mainly centering around number of matches.
 	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
 	// Calculate the end position of a read given a certain sequence.

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 {