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r419: print the @PG line

This commit is contained in:
Heng Li 2013-11-19 11:08:45 -05:00
parent deb19593aa
commit ff6faf811a
2 changed files with 11 additions and 1 deletions
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2
bwa.c
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@ -277,9 +277,11 @@ void bwa_idx_destroy(bwaidx_t *idx)
void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line) void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
{ {
int i; int i;
extern char *bwa_pg;
for (i = 0; i < bns->n_seqs; ++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); 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); if (rg_line) err_printf("%s\n", rg_line);
err_printf("%s\n", bwa_pg);
} }
static char *bwa_escape(char *s) static char *bwa_escape(char *s)

10
main.c
View File

@ -1,9 +1,10 @@
#include <stdio.h> #include <stdio.h>
#include <string.h> #include <string.h>
#include "kstring.h"
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.5a-r418" #define PACKAGE_VERSION "0.7.5a-r419"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); 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[]); int main_pemerge(int argc, char *argv[]);
char *bwa_pg;
static int usage() static int usage()
{ {
fprintf(stderr, "\n"); fprintf(stderr, "\n");
@ -63,7 +66,11 @@ int main(int argc, char *argv[])
{ {
int i, ret; int i, ret;
double t_real; double t_real;
kstring_t pg = {0,0,0};
t_real = realtime(); 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 (argc < 2) return usage();
if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1); 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); 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, " %s", argv[i]);
fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime()); fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
} }
free(bwa_pg);
return ret; return ret;
} }