Add -C param for sampe/samse, to copy fastq comments into sam output

bwa.1

@@ -513,6 +513,12 @@ written. [3]
 .TP
 .BI -r \ STR
 Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
+.TP
+.BI -C
+Append FASTA/Q comment to SAM output. This option can be used to
+transfer read meta information (e.g. barcode) to the SAM output. Note that the
+FASTA/Q comment (the string after a space in the header line) must conform the SAM
+spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
 .RE
 
 .TP
@@ -553,6 +559,12 @@ XA tag will not be written. [10]
 .TP
 .BI -r \ STR
 Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
+.TP
+.BI -C
+Append FASTA/Q comment to SAM output. This option can be used to
+transfer read meta information (e.g. barcode) to the SAM output. Note that the
+FASTA/Q comment (the string after a space in the header line) must conform the SAM
+spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
 .RE
 
 .TP

bwape.c

@@ -735,9 +735,10 @@ int bwa_sai2sam_pe(int argc, char *argv[])
 	int c;
 	pe_opt_t *popt;
 	char *prefix, *rg_line = 0;
+	extern int copy_comment;
 
 	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:C")) >= 0) {
 		switch (c) {
 		case 'r':
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
@@ -751,6 +752,7 @@ 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 'C': copy_comment = 1; break;
 		default: return 1;
 		}
 	}
@@ -768,6 +770,7 @@ 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, "         -C       append FASTA/FASTQ comment to SAM output\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");

bwase.c

@@ -477,6 +477,8 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 				}
 			}
 		}
+		if (p->comment)
+			err_printf("\t%s", p->comment);
 		err_putchar('\n');
 	} else { // this read has no match
 		//ubyte_t *s = p->strand? p->rseq : p->seq;
@@ -494,6 +496,8 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
 		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
 		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
+		if (p->comment)
+			err_printf("\t%s", p->comment);
 		err_putchar('\n');
 	}
 }
@@ -580,20 +584,22 @@ int bwa_sai2sam_se(int argc, char *argv[])
 {
 	int c, n_occ = 3;
 	char *prefix, *rg_line = 0;
-	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
+	extern int copy_comment;
+	while ((c = getopt(argc, argv, "hn:f:r:C")) >= 0) {
 		switch (c) {
 		case 'h': break;
 		case 'r':
 			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
 			break;
 		case 'n': n_occ = atoi(optarg); break;
 		case 'f': xreopen(optarg, "w", stdout); break;
+		case 'C': copy_comment = 1; break;
 		default: return 1;
 		}
 	}
 
 	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] [-f out.sam] [-r RG_line] [-C] <prefix> <in.sai> <in.fq>\n");
 		return 1;
 	}
 	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {

bwaseqio.c

@@ -13,6 +13,7 @@ KSEQ_DECLARE(gzFile)
 
 extern unsigned char nst_nt4_table[256];
 static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+int copy_comment = 0;
 
 struct __bwa_seqio_t {
 	// for BAM input
@@ -199,6 +200,8 @@ bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int tri
 			p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
 			if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
 		}
+		if (copy_comment && seq->comment.l)
+			p->comment = strdup(seq->comment.s);
 		p->rseq = (ubyte_t*)calloc(p->full_len, 1);
 		memcpy(p->rseq, p->seq, p->len);
 		seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
@@ -228,6 +231,8 @@ void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
 		for (j = 0; j < p->n_multi; ++j)
 			if (p->multi[j].cigar) free(p->multi[j].cigar);
 		free(p->name);
+		if (p->comment)
+			free(p->comment);
 		free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
 		free(p->cigar);
 	}

bwtaln.h

@@ -64,7 +64,7 @@ typedef struct {
 } bwt_multi1_t;
 
 typedef struct {
-	char *name;
+	char *name, *comment;
 	ubyte_t *seq, *rseq, *qual;
 	uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
 	uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;