5 #ifndef PACKAGE_VERSION
6 #define PACKAGE_VERSION "0.1.3-6 (r244)"
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[]);
18 int bam_fillmd(int argc, char *argv[]);
20 int faidx_main(int argc, char *argv[]);
21 int glf3_view_main(int argc, char *argv[]);
23 static int view_aux(const bam1_t *b, void *data)
25 bam_view1((bam_header_t*)data, b);
28 static int view_auxb(const bam1_t *b, void *data)
30 bam_write1((bamFile)data, b);
34 int bam_view(int argc, char *argv[])
36 bamFile fp, fpout = 0;
39 int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
40 while ((c = getopt(argc, argv, "bhH")) >= 0) {
42 case 'b': is_bam = 1; break;
43 case 'h': is_header = 1; break;
44 case 'H': is_headeronly = 1; break;
45 default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
49 fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
52 fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
54 header = bam_header_read(fp);
56 fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
60 assert(fpout = bam_dopen(fileno(stdout), "w"));
61 bam_header_write(fpout, header);
63 if (is_header || is_headeronly) {
65 c = header->text[header->l_text-1];
66 header->text[header->l_text-1] = 0;
67 printf("%s", header->text);
69 header->text[header->l_text-1] = c;
70 for (i = 0; i < header->n_targets; ++i)
71 printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
73 bam_header_destroy(header);
78 if (optind + 1 == argc) {
79 b = (bam1_t*)calloc(1, sizeof(bam1_t));
80 while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
81 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
82 free(b->data); free(b);
86 idx = bam_index_load(argv[optind]);
87 for (i = optind + 1; i < argc; ++i) {
89 bam_parse_region(header, argv[i], &tid, &beg, &end);
91 fprintf(stderr, "[bam_view] fail to get the reference name. Abort!\n");
94 if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
95 else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
97 bam_index_destroy(idx);
99 bam_header_destroy(header);
101 if (is_bam) bam_close(fpout);
105 int bam_tagview(int argc, char *argv[])
108 bam_header_t *header;
113 fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
116 fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
118 header = bam_header_read(fp);
120 fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
123 tag[0] = argv[2][0]; tag[1] = argv[2][1];
124 b = (bam1_t*)calloc(1, sizeof(bam1_t));
125 while ((ret = bam_read1(fp, b)) >= 0) {
126 uint8_t *d = bam_aux_get(b, tag);
128 printf("%s\t%d\t", bam1_qname(b), b->core.flag);
129 if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
130 else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
131 else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
132 else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
133 else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
134 else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
138 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
139 free(b->data); free(b);
140 bam_header_destroy(header);
147 fprintf(stderr, "\n");
148 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
149 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
150 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
151 fprintf(stderr, "Command: import import from the text format\n");
152 fprintf(stderr, " view export to the text format\n");
153 fprintf(stderr, " sort sort alignment file\n");
154 fprintf(stderr, " merge merge multiple sorted alignment files\n");
155 fprintf(stderr, " pileup generate pileup output\n");
156 fprintf(stderr, " faidx index/extract FASTA\n");
158 fprintf(stderr, " tview text alignment viewer\n");
160 fprintf(stderr, " index index alignment\n");
161 fprintf(stderr, " fixmate fix mate information\n");
162 fprintf(stderr, " rmdup remove PCR duplicates\n");
163 fprintf(stderr, " glfview print GLFv3 file\n");
164 fprintf(stderr, " flagstat simple stats\n");
165 fprintf(stderr, " fillmd fill the MD tag and change identical base to =\n");
166 fprintf(stderr, "\n");
170 int main(int argc, char *argv[])
172 if (argc < 2) return usage();
173 if (strcmp(argv[1], "view") == 0) return bam_view(argc-1, argv+1);
174 else if (strcmp(argv[1], "import") == 0) return bam_taf2baf(argc-1, argv+1);
175 else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
176 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
177 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
178 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
179 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
180 else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
181 else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
182 else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
183 else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
184 else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
185 else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
187 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
190 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);