Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/bwa-0.5.7-mh/main.c @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/main.c Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,58 @@ +#include <stdio.h> +#include <string.h> +#include "main.h" + +#ifndef PACKAGE_VERSION +#define PACKAGE_VERSION "0.5.7 (r1310)" +#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, "\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, " pac_rev generate reverse PAC\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; +} + +int main(int argc, char *argv[]) +{ + if (argc < 2) return usage(); + if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1); + else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1); + else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1); + else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1); + else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1); + else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1); + else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1); + else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1); + else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1); + else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1); + else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1); + else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1); + else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1); + else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1); + else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1); + else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1); + else { + fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); + return 1; + } + return 0; +}