- if (is_bam) {
- assert(fpout = bam_dopen(fileno(stdout), "w"));
- bam_header_write(fpout, header);
- }
- if (is_header || is_headeronly) {
- int i, c;
- c = header->text[header->l_text-1];
- header->text[header->l_text-1] = 0;
- printf("%s", header->text);
- if (c) putchar(c);
- header->text[header->l_text-1] = c;
- for (i = 0; i < header->n_targets; ++i)
- printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
- if (is_headeronly) {
- bam_header_destroy(header);
- bam_close(fp);
- return 0;
- }
- }
- if (optind + 1 == argc) {
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
- while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
- if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
- free(b->data); free(b);
- } else {
- int i;
- bam_index_t *idx;
- idx = bam_index_load(argv[optind]);
- for (i = optind + 1; i < argc; ++i) {
- int tid, beg, end;
- bam_parse_region(header, argv[i], &tid, &beg, &end);
- if (tid < 0) {
- fprintf(stderr, "[bam_view] fail to get the reference name. Abort!\n");
- return 1;
- }
- if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
- else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
+ 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");