97 lines
4.1 KiB
C
97 lines
4.1 KiB
C
#include <stdio.h>
|
|
#include <string.h>
|
|
#include "utils.h"
|
|
|
|
#ifndef PACKAGE_VERSION
|
|
#define PACKAGE_VERSION "0.7.4-r396-beta"
|
|
#endif
|
|
|
|
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_pemerge(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 <lh3@sanger.ac.uk>\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, " 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");
|
|
fprintf(stderr, "Note: To use BWA, you need to first index the genome with `bwa index'. There are\n");
|
|
fprintf(stderr, " three alignment algorithms in BWA: `mem', `bwasw' and `aln/samse/sampe'. If\n");
|
|
fprintf(stderr, " you are not sure which to use, try `bwa mem' first. Please `man ./bwa.1' for\n");
|
|
fprintf(stderr, " for the manual.\n\n");
|
|
return 1;
|
|
}
|
|
|
|
void bwa_print_sam_PG()
|
|
{
|
|
err_printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
|
|
}
|
|
|
|
int main(int argc, char *argv[])
|
|
{
|
|
int i, ret;
|
|
double t_real;
|
|
t_real = realtime();
|
|
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], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
|
|
else {
|
|
fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
|
|
return 1;
|
|
}
|
|
err_fflush(stdout);
|
|
err_fclose(stdout);
|
|
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;
|
|
}
|