5 #ifndef PACKAGE_VERSION
6 #define PACKAGE_VERSION "0.1.2-22"
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_flagstat(int argc, char *argv[]);
19 int faidx_main(int argc, char *argv[]);
20 int glf3_view_main(int argc, char *argv[]);
22 static int view_aux(const bam1_t *b, void *data)
24 bam_view1((bam_header_t*)data, b);
27 static int view_auxb(const bam1_t *b, void *data)
29 bam_write1((bamFile)data, b);
33 int bam_view(int argc, char *argv[])
35 bamFile fp, fpout = 0;
38 int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
39 while ((c = getopt(argc, argv, "bhH")) >= 0) {
41 case 'b': is_bam = 1; break;
42 case 'h': is_header = 1; break;
43 case 'H': is_headeronly = 1; break;
44 default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
48 fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
51 fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
53 header = bam_header_read(fp);
55 assert(fpout = bam_dopen(fileno(stdout), "w"));
56 bam_header_write(fpout, header);
58 if (is_header || is_headeronly) {
60 c = header->text[header->l_text-1];
61 header->text[header->l_text-1] = 0;
62 printf("%s", header->text);
64 header->text[header->l_text-1] = c;
65 for (i = 0; i < header->n_targets; ++i)
66 printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
68 bam_header_destroy(header);
73 if (optind + 1 == argc) {
74 b = (bam1_t*)calloc(1, sizeof(bam1_t));
75 while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
76 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
77 free(b->data); free(b);
81 idx = bam_index_load(argv[optind]);
82 for (i = optind + 1; i < argc; ++i) {
84 bam_parse_region(header, argv[i], &tid, &beg, &end);
85 if (tid < 0) return 0;
86 if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
87 else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
89 bam_index_destroy(idx);
91 bam_header_destroy(header);
93 if (is_bam) bam_close(fpout);
99 fprintf(stderr, "\n");
100 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
101 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
102 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
103 fprintf(stderr, "Command: import import from the text format\n");
104 fprintf(stderr, " view export to the text format\n");
105 fprintf(stderr, " sort sort alignment file\n");
106 fprintf(stderr, " merge merge multiple sorted alignment files\n");
107 fprintf(stderr, " pileup generate pileup output\n");
108 fprintf(stderr, " faidx index/extract FASTA\n");
110 fprintf(stderr, " tview text alignment viewer\n");
112 fprintf(stderr, " index index alignment\n");
113 fprintf(stderr, " fixmate fix mate information\n");
114 fprintf(stderr, " rmdup remove PCR duplicates\n");
115 fprintf(stderr, " glfview print GLFv2 file\n");
116 fprintf(stderr, " flagstat simple stats\n");
117 fprintf(stderr, "\n");
121 int main(int argc, char *argv[])
123 if (argc < 2) return usage();
124 if (strcmp(argv[1], "view") == 0) return bam_view(argc-1, argv+1);
125 else if (strcmp(argv[1], "import") == 0) return bam_taf2baf(argc-1, argv+1);
126 else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
127 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
128 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
129 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
130 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
131 else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
132 else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
133 else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
134 else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
136 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
139 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);