support inserting RG lines

format.c

@@ -6,6 +6,8 @@
 #include "kalloc.h"
 #include "mmpriv.h"
 
+static char *mm_rg_line, mm_rg_id[256];
+
 static inline void str_enlarge(kstring_t *s, int l)
 {
 	if (s->l + l + 1 > s->m) {
@@ -56,6 +58,60 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
 	s->s[s->l] = 0;
 }
 
+static inline char *mm_escape(char *s)
+{
+	char *p, *q;
+	for (p = q = s; *p; ++p) {
+		if (*p == '\\') {
+			++p;
+			if (*p == 't') *q++ = '\t';
+			else if (*p == 'n') *q++ = '\n';
+			else if (*p == 'r') *q++ = '\r';
+			else if (*p == '\\') *q++ = '\\';
+		} else *q++ = *p;
+	}
+	*q = '\0';
+	return s;
+}
+
+void mm_set_rg(const char *s)
+{
+	char *p, *q, *r, *rg_line = 0;
+	memset(mm_rg_id, 0, 256);
+	if (mm_rg_line) {
+		free(mm_rg_line);
+		mm_rg_line = 0;
+	}
+	if (s == 0) return;
+	if (strstr(s, "@RG") != s) {
+		if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
+		goto err_set_rg;
+	}
+	if (strstr(s, "\t") != NULL) {
+		if (mm_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\n", __func__);
+		goto err_set_rg;
+	}
+	rg_line = strdup(s);
+	mm_escape(rg_line);
+	if ((p = strstr(rg_line, "\tID:")) == 0) {
+		if (mm_verbose >= 1) fprintf(stderr, "[E::%s] no ID within the read group line\n", __func__);
+		goto err_set_rg;
+	}
+	p += 4;
+	for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
+	if (q - p + 1 > 256) {
+		if (mm_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);
+		goto err_set_rg;
+	}
+	for (q = p, r = mm_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
+		*r++ = *q;
+	mm_rg_line = rg_line;
+	return;
+
+err_set_rg:
+	free(rg_line);
+}
+
 static void write_cs(void *km, kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
 {
 	extern unsigned char seq_nt4_table[256];
@@ -158,6 +214,14 @@ static char comp_tab[] = {
 	'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
 };
 
+void sam_write_sam_header(const mm_idx_t *idx)
+{
+	uint32_t i;
+	for (i = 0; i < idx->n_seq; ++i)
+		printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
+	if (mm_rg_line) puts(mm_rg_line);
+}
+
 static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
 {
 	if (rev) {
@@ -214,6 +278,8 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
 			else mm_sprintf_lite(s, "*");
 		}
 		write_tags(s, r);
+		if (mm_rg_line && mm_rg_id[0])
+			mm_sprintf_lite(s, "\tRG:Z:%s", mm_rg_id);
 		if (r->parent == r->id && r->p && n_regs > 1 && regs && r >= regs && r - regs < n_regs) { // supplementary aln may exist
 			int i, n_sa = 0; // n_sa: number of SA fields
 			for (i = 0; i < n_regs; ++i)

main.c

@@ -68,7 +68,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:", long_options, &long_idx)) >= 0) {
+	while ((c = getopt_long(argc, argv, "aSw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:", long_options, &long_idx)) >= 0) {
 		if (c == 'w') w = atoi(optarg), idx_par_set = 1;
 		else if (c == 'k') k = atoi(optarg), idx_par_set = 1;
 		else if (c == 'H') is_hpc = 1, idx_par_set = 1;
@@ -96,6 +96,7 @@ int main(int argc, char *argv[])
 		else if (c == 's') opt.min_dp_max = atoi(optarg);
 		else if (c == 'I') batch_size = mm_parse_num(optarg);
 		else if (c == 'K') minibatch_size = (int)mm_parse_num(optarg);
+		else if (c == 'R') mm_set_rg(optarg); // WARNING: this modifies global variables in format.c
 		else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits
 		else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
 		else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
@@ -194,14 +195,15 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -s INT       minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(stderr, "    -u CHAR      how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
 		fprintf(stderr, "  Input/Output:\n");
-		fprintf(stderr, "    -Q           ignore base quality in the input\n");
 		fprintf(stderr, "    -a           output in the SAM format (PAF by default)\n");
+		fprintf(stderr, "    -Q           don't output base quality in SAM\n");
+		fprintf(stderr, "    -R STR       SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
 		fprintf(stderr, "    -c           output CIGAR in PAF\n");
-		fprintf(stderr, "    -S           output the cs tag in PAF\n");
+		fprintf(stderr, "    -S           output the cs tag in PAF (cs encodes both query and ref sequences)\n");
 		fprintf(stderr, "    -t INT       number of threads [%d]\n", n_threads);
 		fprintf(stderr, "    -K NUM       minibatch size [200M]\n");
 //		fprintf(stderr, "    -v INT       verbose level [%d]\n", mm_verbose);
-		fprintf(stderr, "    -V           show version number\n");
+		fprintf(stderr, "    --version    show version number\n");
 		fprintf(stderr, "  Preset:\n");
 		fprintf(stderr, "    -x STR       preset (recommended to be applied before other options) []\n");
 		fprintf(stderr, "                 map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");

map.c

@@ -386,11 +386,7 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
 	if (pl.fp == 0) return -1;
 	pl.opt = opt, pl.mi = idx;
 	pl.n_threads = n_threads, pl.mini_batch_size = mini_batch_size;
-	if (opt->flag & MM_F_OUT_SAM) {
+	if (opt->flag & MM_F_OUT_SAM) sam_write_sam_header(idx);
-		uint32_t i;
-		for (i = 0; i < idx->n_seq; ++i)
-			printf("@SQ\tSN:%s\tLN:%d\n", idx->seq[i].name, idx->seq[i].len);
-	}
 	kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
 	free(pl.str.s);
 	mm_bseq_close(pl.fp);

minimap2.1

@@ -219,13 +219,18 @@ no attempt to match GT-AG [n]
 Cost of non-canonical splicing sites [0].
 .SS Input/output options
 .TP 10
-.B -Q
-Ignore base quality in the input file.
-.TP
 .B -a
 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
 by default.
 .TP
+.B -Q
+Ignore base quality in the input file.
+.TP
+.BI -R \ STR
+SAM read group line in a format like
+.B @RG\\\\tID:foo\\\\tSM:bar
+[].
+.TP
 .B -c
 Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
 .TP

mmpriv.h

@@ -40,6 +40,8 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
 void radix_sort_64(uint64_t *beg, uint64_t *end);
 uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
 
+void mm_set_rg(const char *s);
+void sam_write_sam_header(const mm_idx_t *idx);
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int intron_thres);
 void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, int n_regs, const mm_reg1_t *regs, int intron_thres);
 int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int64_t n, mm128_t *a, uint64_t **_u, void *km);