5 #ifndef PACKAGE_VERSION
6 #define PACKAGE_VERSION "0.1.1"
9 int bam_taf2baf(int argc, char *argv[]);
10 int bam_pileup(int argc, char *argv[]);
11 int bam_merge(int argc, char *argv[]);
12 int bam_index(int argc, char *argv[]);
13 int bam_sort(int argc, char *argv[]);
14 int bam_tview_main(int argc, char *argv[]);
15 int faidx_main(int argc, char *argv[]);
17 static int view_aux(const bam1_t *b, void *data)
19 bam_view1((bam_header_t*)data, b);
22 static int view_auxb(const bam1_t *b, void *data)
24 bam_write1((bamFile)data, b);
28 int bam_view(int argc, char *argv[])
30 bamFile fp, fpout = 0;
33 int ret, c, is_bam = 0;
34 while ((c = getopt(argc, argv, "b")) >= 0) {
36 case 'b': is_bam = 1; break;
37 default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
41 fprintf(stderr, "Usage: samtools view [-b] <in.bam> [<region> [...]]\n");
44 fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
46 header = bam_header_read(fp);
48 assert(fpout = bam_dopen(fileno(stdout), "w"));
49 bam_header_write(fpout, header);
51 if (optind + 1 == argc) {
52 b = (bam1_t*)calloc(1, sizeof(bam1_t));
53 while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
54 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
55 free(b->data); free(b);
59 idx = bam_index_load(argv[optind]);
60 for (i = optind + 1; i < argc; ++i) {
62 bam_parse_region(header, argv[i], &tid, &beg, &end);
63 if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
64 else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
66 bam_index_destroy(idx);
68 bam_header_destroy(header);
70 if (is_bam) bam_close(fpout);
76 fprintf(stderr, "\n");
77 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
78 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
79 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
80 fprintf(stderr, "Command: import import from the text format\n");
81 fprintf(stderr, " view export to the text format\n");
82 fprintf(stderr, " sort sort alignment file\n");
83 fprintf(stderr, " merge merge multiple sorted alignment files\n");
84 fprintf(stderr, " pileup generate pileup output\n");
85 fprintf(stderr, " faidx index/extract FASTA\n");
87 fprintf(stderr, " tview text alignment viewer\n");
89 fprintf(stderr, " index index alignment\n");
90 fprintf(stderr, "\n");
94 int main(int argc, char *argv[])
96 if (argc < 2) return usage();
97 if (strcmp(argv[1], "view") == 0) return bam_view(argc-1, argv+1);
98 else if (strcmp(argv[1], "import") == 0) return bam_taf2baf(argc-1, argv+1);
99 else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
100 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
101 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
102 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
103 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
105 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
108 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);