support read group in bwa-mem

bwa.c

@@ -1,10 +1,13 @@
+#include <string.h>
 #include <stdio.h>
 #include <zlib.h>
 #include "bntseq.h"
 #include "bwa.h"
 #include "ksw.h"
+#include "utils.h"
 
 int bwa_verbose = 3;
+char bwa_rg_id[256];
 
 /************************
  * Batch FASTA/Q reader *
@@ -132,8 +135,7 @@ bwt_t *bwa_idx_load_bwt(const char *hint)
 	bwt_t *bwt;
 	prefix = bwa_idx_infer_prefix(hint);
 	if (prefix == 0) {
-		if (bwa_verbose >= 1)
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
-			fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
 		return 0;
 	}
 	tmp = calloc(strlen(prefix) + 5, 1);
@@ -150,7 +152,10 @@ bwaidx_t *bwa_idx_load(const char *hint, int which)
 	bwaidx_t *idx;
 	char *prefix;
 	prefix = bwa_idx_infer_prefix(hint);
-	if (prefix == 0) return 0;
+	if (prefix == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
+		return 0;
+	}
 	idx = calloc(1, sizeof(bwaidx_t));
 	if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
 	if (which & BWA_IDX_BNS) {
@@ -174,3 +179,58 @@ void bwa_idx_destroy(bwaidx_t *idx)
 	if (idx->pac) free(idx->pac);
 	free(idx);
 }
+
+/***********************
+ * SAM header routines *
+ ***********************/
+
+void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
+{
+	int i;
+	for (i = 0; i < bns->n_seqs; ++i)
+		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
+	if (rg_line) err_printf("%s\n", rg_line);
+}
+
+static char *bwa_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;
+}
+
+char *bwa_set_rg(const char *s)
+{
+	char *p, *q, *r, *rg_line = 0;
+	memset(bwa_rg_id, 0, 256);
+	if (strstr(s, "@RG") != s) return 0;
+	rg_line = strdup(s);
+	bwa_escape(rg_line);
+	if ((p = strstr(rg_line, "\tID:")) == 0) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID in the @RG line\n", __func__);
+		goto err_set_rg;
+	}
+	p += 4;
+	for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
+	if (q - p + 1 > 256) {
+		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] RG:ID is longer than 255 characters\n", __func__);
+		goto err_set_rg;
+	}
+	for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
+		*r++ = *q;
+	return rg_line;
+
+err_set_rg:
+	free(rg_line);
+	return 0;
+}
+

bwa.h

@@ -22,6 +22,7 @@ typedef struct {
 } bseq1_t;
 
 extern int bwa_verbose;
+extern char bwa_rg_id[256];
 
 #ifdef __cplusplus
 extern "C" {
@@ -36,6 +37,9 @@ extern "C" {
 	bwaidx_t *bwa_idx_load(const char *hint, int which);
 	void bwa_idx_destroy(bwaidx_t *idx);
 
+	void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line);
+	char *bwa_set_rg(const char *s);
+
 #ifdef __cplusplus
 }
 #endif

bwamem.c

@@ -571,6 +571,7 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
 	}
 	if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
 	if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
+	if (bwa_rg_id) { kputsn("\tRG:i:", 6, str); kputs(bwa_rg_id, str); }
 	kputc('\n', str);
 	free(cigar);
 #undef is_mapped

bwape.c

@@ -611,7 +611,7 @@ 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)
+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)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
 	int i, j, n_seqs, tot_seqs = 0;
@@ -654,7 +654,7 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 	}
 
 	// core loop
-	bwa_print_sam_SQ(bns);
+	bwa_print_sam_hdr(bns, rg_line);
 	bwa_print_sam_PG();
 	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
 		int cnt_chg;
@@ -715,20 +715,15 @@ void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const f
 
 int bwa_sai2sam_pe(int argc, char *argv[])
 {
-	extern char *bwa_rg_line, *bwa_rg_id;
-	extern int bwa_set_rg(const char *s);
 	int c;
 	pe_opt_t *popt;
-	char *prefix;
+	char *prefix, *rg_line = 0;
 
 	popt = bwa_init_pe_opt();
 	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
 		switch (c) {
 		case 'r':
-			if (bwa_set_rg(optarg) < 0) {
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
-				fprintf(stderr, "[%s] malformated @RG line\n", __func__);
-				return 1;
-			}
 			break;
 		case 'a': popt->max_isize = atoi(optarg); break;
 		case 'o': popt->max_occ = atoi(optarg); break;
@@ -764,11 +759,9 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
-		free(bwa_rg_line); free(bwa_rg_id);
 		return 0;
 	}
-	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt);
+	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
-	free(bwa_rg_line); free(bwa_rg_id); free(prefix);
+	free(prefix); free(popt);
-	free(popt);
 	return 0;
 }

bwase.c

@@ -13,7 +13,6 @@
 #include "bwa.h"
 
 int g_log_n[256];
-char *bwa_rg_line, *bwa_rg_id;
 
 void bwa_print_sam_PG();
 
@@ -490,56 +489,13 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 	}
 }
 
-void bwa_print_sam_SQ(const bntseq_t *bns)
-{
-	int i;
-	for (i = 0; i < bns->n_seqs; ++i)
-		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
-	if (bwa_rg_line) err_printf("%s\n", bwa_rg_line);
-}
-
 void bwase_initialize() 
 {
 	int i;
 	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
 }
 
-char *bwa_escape(char *s)
+void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
-{
-	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;
-}
-
-int bwa_set_rg(const char *s)
-{
-	char *p, *q, *r;
-	if (strstr(s, "@RG") != s) return -1;
-	if (bwa_rg_line) free(bwa_rg_line);
-	if (bwa_rg_id) free(bwa_rg_id);
-	bwa_rg_line = strdup(s);
-	bwa_rg_id = 0;
-	bwa_escape(bwa_rg_line);
-	p = strstr(bwa_rg_line, "\tID:");
-	if (p == 0) return -1;
-	p += 4;
-	for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
-	bwa_rg_id = calloc(q - p + 1, 1);
-	for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
-		*r++ = *q;
-	return 0;
-}
-
-void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ)
 {
 	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
 	int i, n_seqs, tot_seqs = 0, m_aln;
@@ -559,7 +515,7 @@ void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_f
 
 	m_aln = 0;
 	fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
-	bwa_print_sam_SQ(bns);
+	bwa_print_sam_hdr(bns, rg_line);
 	//bwa_print_sam_PG();
 	// set ks
 	ks = bwa_open_reads(opt.mode, fn_fa);
@@ -608,15 +564,12 @@ 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;
-	char *prefix;
+	char *prefix, *rg_line = 0;
 	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
 		switch (c) {
 		case 'h': break;
 		case 'r':
-			if (bwa_set_rg(optarg) < 0) {
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
-				fprintf(stderr, "[%s] malformated @RG line\n", __func__);
-				return 1;
-			}
 			break;
 		case 'n': n_occ = atoi(optarg); break;
 		case 'f': xreopen(optarg, "w", stdout); break;
@@ -630,10 +583,8 @@ int bwa_sai2sam_se(int argc, char *argv[])
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
 		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
-		free(bwa_rg_line); free(bwa_rg_id);
 		return 0;
 	}
-	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ);
+	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
-	free(bwa_rg_line); free(bwa_rg_id);
 	return 0;
 }

fastmap.c

@@ -14,14 +14,15 @@ extern unsigned char nst_nt4_table[256];
 int main_mem(int argc, char *argv[])
 {
 	mem_opt_t *opt;
-	int c, n, l;
+	int c, n;
 	gzFile fp, fp2 = 0;
 	kseq_t *ks, *ks2 = 0;
 	bseq1_t *seqs;
 	bwaidx_t *idx;
+	char *rg_line = 0;
 
 	opt = mem_opt_init();
-	while ((c = getopt(argc, argv, "PHk:c:v:s:r:t:")) >= 0) {
+	while ((c = getopt(argc, argv, "PHk:c:v:s:r:t:R:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg);
 		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
 		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
@@ -29,7 +30,9 @@ int main_mem(int argc, char *argv[])
 		else if (c == 'c') opt->max_occ = atoi(optarg);
 		else if (c == 'v') mem_verbose = atoi(optarg);
 		else if (c == 'r') opt->split_factor = atof(optarg);
-		else if (c == 's') opt->split_width = atoi(optarg);
+		else if (c == 'R') {
+			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
+		} else if (c == 's') opt->split_width = atoi(optarg);
 	}
 	if (optind + 1 >= argc) {
 		fprintf(stderr, "\n");
@@ -39,15 +42,15 @@ int main_mem(int argc, char *argv[])
 		fprintf(stderr, "         -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
 		fprintf(stderr, "         -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
 		fprintf(stderr, "         -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
+		fprintf(stderr, "         -R STR     read group header line such as '@RG\tID:foo\tSM:bar' [null]\n");
 		fprintf(stderr, "         -v INT     verbose level [%d]\n", mem_verbose);
 		fprintf(stderr, "\n");
 		free(opt);
 		return 1;
 	}
 	mem_fill_scmat(opt->a, opt->b, opt->mat);
-	idx = bwa_idx_load(argv[optind], BWA_IDX_ALL);
+	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
-	for (l = 0; l < idx->bns->n_seqs; ++l)
+	bwa_print_sam_hdr(idx->bns, rg_line);
-		printf("@SQ\tSN:%s\tLN:%d\n", idx->bns->anns[l].name, idx->bns->anns[l].len);
 
 	fp = strcmp(argv[optind + 1], "-")? gzopen(argv[optind + 1], "r") : gzdopen(fileno(stdin), "r");
 	ks = kseq_init(fp);