7 bam_header_t *bam_header_dup(const bam_header_t *h0)
11 h = bam_header_init();
14 h->text = (char*)calloc(h->l_text + 1, 1);
15 memcpy(h->text, h0->text, h->l_text);
16 h->target_len = (uint32_t*)calloc(h->n_targets, 4);
17 h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
18 for (i = 0; i < h->n_targets; ++i) {
19 h->target_len[i] = h0->target_len[i];
20 h->target_name[i] = strdup(h0->target_name[i]);
25 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
28 fp = (samfile_t*)calloc(1, sizeof(samfile_t));
29 if (mode[0] == 'r') { // read
30 fp->type |= TYPE_READ;
31 if (mode[1] == 'b') { // binary
33 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
34 if (fp->x.bam == 0) goto open_err_ret;
35 fp->header = bam_header_read(fp->x.bam);
37 fp->x.tamr = sam_open(fn);
38 if (fp->x.tamr == 0) goto open_err_ret;
39 fp->header = sam_header_read(fp->x.tamr);
40 if (fp->header->n_targets == 0) { // no @SQ fields
41 if (aux) { // check if aux is present
42 bam_header_destroy(fp->header);
43 fp->header = sam_header_read2((const char*)aux);
45 if (fp->header->n_targets == 0)
46 fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
47 } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
49 } else if (mode[0] == 'w') { // write
50 fp->header = bam_header_dup((const bam_header_t*)aux);
51 if (mode[1] == 'b') { // binary
53 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
54 if (fp->x.bam == 0) goto open_err_ret;
55 bam_header_write(fp->x.bam, fp->header);
58 fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
59 if (fp->x.tamr == 0) goto open_err_ret;
61 if (strstr(mode, "h")) {
64 // parse the header text
65 alt = bam_header_init();
66 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
67 sam_header_parse(alt);
68 alt->l_text = 0; alt->text = 0;
69 // check if there are @SQ lines in the header
70 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
71 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
72 if (alt->n_targets != fp->header->n_targets)
73 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
74 } else { // then dump ->target_{name,len}
75 for (i = 0; i < fp->header->n_targets; ++i)
76 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
78 bam_header_destroy(alt);
89 void samclose(samfile_t *fp)
92 if (fp->header) bam_header_destroy(fp->header);
93 if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
94 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
95 else fclose(fp->x.tamw);
99 int samread(samfile_t *fp, bam1_t *b)
101 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
102 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
103 else return sam_read1(fp->x.tamr, fp->header, b);
106 int samwrite(samfile_t *fp, const bam1_t *b)
108 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
109 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
111 char *s = bam_format1(fp->header, b);
113 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
119 int sampileup(samfile_t *fp, int mask, int min_mapQ, bam_pileup_f func, void *func_data)
125 buf = bam_plbuf_init(func, func_data);
126 bam_plbuf_set_mask(buf, mask);
127 while ((ret = samread(fp, b)) >= 0)
128 if (b->core.qual >= min_mapQ)
129 bam_plbuf_push(b, buf);
130 bam_plbuf_push(0, buf);
131 bam_plbuf_destroy(buf);