Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/main.c @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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1:a9636dc1e99a | 2:a294fbfcb1db |
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1 #include <stdio.h> | |
2 #include <string.h> | |
3 #include "main.h" | |
4 #include "utils.h" | |
5 | |
6 #ifndef PACKAGE_VERSION | |
7 #define PACKAGE_VERSION "0.6.2-r126" | |
8 #endif | |
9 | |
10 static int usage() | |
11 { | |
12 fprintf(stderr, "\n"); | |
13 fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n"); | |
14 fprintf(stderr, "Version: %s\n", PACKAGE_VERSION); | |
15 fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n"); | |
16 fprintf(stderr, "Usage: bwa <command> [options]\n\n"); | |
17 fprintf(stderr, "Command: index index sequences in the FASTA format\n"); | |
18 fprintf(stderr, " aln gapped/ungapped alignment\n"); | |
19 fprintf(stderr, " samse generate alignment (single ended)\n"); | |
20 fprintf(stderr, " sampe generate alignment (paired ended)\n"); | |
21 fprintf(stderr, " bwasw BWA-SW for long queries\n"); | |
22 fprintf(stderr, " fastmap identify super-maximal exact matches\n"); | |
23 fprintf(stderr, "\n"); | |
24 fprintf(stderr, " fa2pac convert FASTA to PAC format\n"); | |
25 fprintf(stderr, " pac2bwt generate BWT from PAC\n"); | |
26 fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n"); | |
27 fprintf(stderr, " bwtupdate update .bwt to the new format\n"); | |
28 fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n"); | |
29 fprintf(stderr, " pac2cspac convert PAC to color-space PAC\n"); | |
30 fprintf(stderr, " stdsw standard SW/NW alignment\n"); | |
31 fprintf(stderr, "\n"); | |
32 return 1; | |
33 } | |
34 | |
35 void bwa_print_sam_PG() | |
36 { | |
37 printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION); | |
38 } | |
39 | |
40 int main(int argc, char *argv[]) | |
41 { | |
42 int i, ret; | |
43 double t_real; | |
44 t_real = realtime(); | |
45 if (argc < 2) return usage(); | |
46 if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1); | |
47 else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1); | |
48 else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1); | |
49 else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1); | |
50 else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1); | |
51 else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1); | |
52 else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1); | |
53 else if (strcmp(argv[1], "sw") == 0) ret = bwa_stdsw(argc-1, argv+1); | |
54 else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1); | |
55 else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1); | |
56 else if (strcmp(argv[1], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1); | |
57 else if (strcmp(argv[1], "stdsw") == 0) ret = bwa_stdsw(argc-1, argv+1); | |
58 else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1); | |
59 else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1); | |
60 else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1); | |
61 else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1); | |
62 else { | |
63 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); | |
64 return 1; | |
65 } | |
66 err_fflush(stdout); | |
67 err_fclose(stdout); | |
68 if (ret == 0) { | |
69 fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION); | |
70 fprintf(stderr, "[%s] CMD:", __func__); | |
71 for (i = 0; i < argc; ++i) | |
72 fprintf(stderr, " %s", argv[i]); | |
73 fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime()); | |
74 } | |
75 return 0; | |
76 } |