5 #ifndef PACKAGE_VERSION
6 #define PACKAGE_VERSION "0.1.3-21 (r286)"
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 bam_mating(int argc, char *argv[]);
16 int bam_rmdup(int argc, char *argv[]);
17 int bam_rmdupse(int argc, char *argv[]);
18 int bam_flagstat(int argc, char *argv[]);
19 int bam_fillmd(int argc, char *argv[]);
21 int main_samview(int argc, char *argv[]);
22 int main_import(int argc, char *argv[]);
24 int faidx_main(int argc, char *argv[]);
25 int glf3_view_main(int argc, char *argv[]);
27 int bam_tagview(int argc, char *argv[])
35 fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
38 fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
40 header = bam_header_read(fp);
42 fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
45 tag[0] = argv[2][0]; tag[1] = argv[2][1];
46 b = (bam1_t*)calloc(1, sizeof(bam1_t));
47 while ((ret = bam_read1(fp, b)) >= 0) {
48 uint8_t *d = bam_aux_get(b, tag);
50 printf("%s\t%d\t", bam1_qname(b), b->core.flag);
51 if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
52 else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
53 else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
54 else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
55 else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
56 else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
60 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
61 free(b->data); free(b);
62 bam_header_destroy(header);
69 fprintf(stderr, "\n");
70 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
71 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
72 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
73 fprintf(stderr, "Command: import import from SAM (obsolete; use `view')\n");
74 fprintf(stderr, " view export to the text format\n");
75 fprintf(stderr, " sort sort alignment file\n");
76 fprintf(stderr, " merge merge multiple sorted alignment files\n");
77 fprintf(stderr, " pileup generate pileup output\n");
78 fprintf(stderr, " faidx index/extract FASTA\n");
80 fprintf(stderr, " tview text alignment viewer\n");
82 fprintf(stderr, " index index alignment\n");
83 fprintf(stderr, " fixmate fix mate information\n");
84 fprintf(stderr, " rmdup remove PCR duplicates\n");
85 fprintf(stderr, " glfview print GLFv3 file\n");
86 fprintf(stderr, " flagstat simple stats\n");
87 fprintf(stderr, " fillmd fill the MD tag and change identical base to =\n");
88 fprintf(stderr, "\n");
92 int main(int argc, char *argv[])
94 if (argc < 2) return usage();
95 if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
96 else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
97 else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
98 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
99 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
100 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
101 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
102 else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
103 else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
104 else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+1);
105 else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
106 else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
107 else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
108 else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
110 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
113 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);