From ff6faf811a543ca2acebd81ecd0de727a6779a32 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 19 Nov 2013 11:08:45 -0500
Subject: [PATCH] r419: print the @PG line

---
 bwa.c  |  2 ++
 main.c | 10 +++++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/bwa.c b/bwa.c
index f8949f7d..33edd7f2 100644
--- a/bwa.c
+++ b/bwa.c
@@ -277,9 +277,11 @@ void bwa_idx_destroy(bwaidx_t *idx)
 void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
 {
 	int i;
+	extern char *bwa_pg;
 	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);
+	err_printf("%s\n", bwa_pg);
 }
 
 static char *bwa_escape(char *s)
diff --git a/main.c b/main.c
index 8f767060..a7839240 100644
--- a/main.c
+++ b/main.c
@@ -1,9 +1,10 @@
 #include <stdio.h>
 #include <string.h>
+#include "kstring.h"
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.5a-r418"
+#define PACKAGE_VERSION "0.7.5a-r419"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);
@@ -24,6 +25,8 @@ int main_mem(int argc, char *argv[]);
 
 int main_pemerge(int argc, char *argv[]);
 
+char *bwa_pg;
+
 static int usage()
 {
 	fprintf(stderr, "\n");
@@ -63,7 +66,11 @@ int main(int argc, char *argv[])
 {
 	int i, ret;
 	double t_real;
+	kstring_t pg = {0,0,0};
 	t_real = realtime();
+	ksprintf(&pg, "@PG\tID:bwa\tPN:bwa\tVN:%s\tCL:%s", PACKAGE_VERSION, argv[0]);
+	for (i = 1; i < argc; ++i) ksprintf(&pg, " %s", argv[i]);
+	bwa_pg = pg.s;
 	if (argc < 2) return usage();
 	if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
 	else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
@@ -93,5 +100,6 @@ int main(int argc, char *argv[])
 			fprintf(stderr, " %s", argv[i]);
 		fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
 	}
+	free(bwa_pg);
 	return ret;
 }