Mercurial > repos > ashvark > qiime_1_8_0
diff bwa-0.6.2/main.c @ 0:dd1186b11b3b draft
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:14 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-0.6.2/main.c Fri Jul 18 07:55:14 2014 -0400 @@ -0,0 +1,76 @@ +#include <stdio.h> +#include <string.h> +#include "main.h" +#include "utils.h" + +#ifndef PACKAGE_VERSION +#define PACKAGE_VERSION "0.6.2-r126" +#endif + +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, " 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, " fastmap identify super-maximal exact matches\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, " pac2cspac convert PAC to color-space PAC\n"); + fprintf(stderr, " stdsw standard SW/NW alignment\n"); + fprintf(stderr, "\n"); + return 1; +} + +void bwa_print_sam_PG() +{ + 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], "sw") == 0) ret = bwa_stdsw(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], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1); + else if (strcmp(argv[1], "stdsw") == 0) ret = bwa_stdsw(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 { + 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 0; +}