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main.c
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main.c
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/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 Genome Research Ltd. (GRL)
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include <stdio.h>
#include <string.h>
#include "kstring.h"
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.18-r1243-dirty-julian"
#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_alnse(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 <[email protected]>\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, " alnse gapped/ungapped alignment for SE reads\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 (DEPRECATED)\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");
fprintf(stderr,
"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], "alnse") == 0) ret = bwa_alnse(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;
}
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());
}
free(bwa_pg);
return ret;
}