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#include <stdio.h>
#include <string.h>
#include "kstring.h"
#include "utils.h"
#define PACKAGE_VERSION "0.7.16a-r1185-dirty"
int bwa_fa2pac(int argc, char *argv[]);
int bwa_pac2bwt(int argc, char *argv[]);
int bwa_bwtupdate(int argc, char *argv[]);
int bwa_bwt2sa(int argc, char *argv[]);
int bwa_index(int argc, char *argv[]);
int bwt_bwtgen_main(int argc, char *argv[]);
int bwa_aln(int argc, char *argv[]);
int bwa_sai2sam_se(int argc, char *argv[]);
int bwa_sai2sam_pe(int argc, char *argv[]);
int bwa_bwtsw2(int argc, char *argv[]);
int main_fastmap(int argc, char *argv[]);
int main_mem(int argc, char *argv[]);
int main_shm(int argc, char *argv[]);
int main_pemerge(int argc, char *argv[]);
int main_maxk(int argc, char *argv[]);
static int usage()
fprintf(stderr, "\n");
fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <>\n\n");
fprintf(stderr, "Usage: bwa <command> [options]\n\n");
fprintf(stderr, "Command: index index sequences in the FASTA format\n");
fprintf(stderr, " mem BWA-MEM algorithm\n");
fprintf(stderr, " fastmap identify super-maximal exact matches\n");
fprintf(stderr, " pemerge merge overlapping paired ends (EXPERIMENTAL)\n");
fprintf(stderr, " aln gapped/ungapped alignment\n");
fprintf(stderr, " samse generate alignment (single ended)\n");
fprintf(stderr, " sampe generate alignment (paired ended)\n");
fprintf(stderr, " bwasw BWA-SW for long queries\n");
fprintf(stderr, "\n");
fprintf(stderr, " shm manage indices in shared memory\n");
fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
fprintf(stderr, " pac2bwt generate BWT from PAC\n");
fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n");
fprintf(stderr, " bwtupdate update .bwt to the new format\n");
fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
fprintf(stderr, "\n");
"Note: To use BWA, you need to first index the genome with `bwa index'.\n"
" There are three alignment algorithms in BWA: `mem', `bwasw', and\n"
" `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'\n"
" first. Please `man ./bwa.1' for the manual.\n\n");
return 1;
int main(int argc, char *argv[])
extern char *bwa_pg;
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);
else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
else if (strcmp(argv[1], "shm") == 0) ret = main_shm(argc-1, argv+1);
else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
else if (strcmp(argv[1], "maxk") == 0) ret = main_maxk(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
if (ret == 0) {
fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
fprintf(stderr, "[%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
return ret;