-int glf3_view_main(int argc, char *argv[]);
-
-int bam_tagview(int argc, char *argv[])
-{
- bamFile fp;
- bam_header_t *header;
- bam1_t *b;
- char tag[2];
- int ret;
- if (argc < 3) {
- fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
- return 1;
- }
- fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
- assert(fp);
- header = bam_header_read(fp);
- if (header == 0) {
- fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
- return 1;
- }
- tag[0] = argv[2][0]; tag[1] = argv[2][1];
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
- while ((ret = bam_read1(fp, b)) >= 0) {
- uint8_t *d = bam_aux_get(b, tag);
- if (d) {
- printf("%s\t%d\t", bam1_qname(b), b->core.flag);
- if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
- else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
- else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
- else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
- else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
- else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
- else printf("\n");
- }
- }
- if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
- free(b->data); free(b);
- bam_header_destroy(header);
- bam_close(fp);
- return 0;
-}