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]);
22 if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
25 static void append_header_text(bam_header_t *header, char* text, int len)
27 int x = header->l_text + 1;
28 int y = header->l_text + len + 1; // 1 byte null
29 if (text == 0) return;
32 if (x < y) header->text = (char*)realloc(header->text, y);
33 strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
34 header->l_text += len;
35 header->text[header->l_text] = 0;
38 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
41 fp = (samfile_t*)calloc(1, sizeof(samfile_t));
42 if (mode[0] == 'r') { // read
43 fp->type |= TYPE_READ;
44 if (mode[1] == 'b') { // binary
46 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
47 if (fp->x.bam == 0) goto open_err_ret;
48 fp->header = bam_header_read(fp->x.bam);
50 fp->x.tamr = sam_open(fn);
51 if (fp->x.tamr == 0) goto open_err_ret;
52 fp->header = sam_header_read(fp->x.tamr);
53 if (fp->header->n_targets == 0) { // no @SQ fields
54 if (aux) { // check if aux is present
55 bam_header_t *textheader = fp->header;
56 fp->header = sam_header_read2((const char*)aux);
57 append_header_text(fp->header, textheader->text, textheader->l_text);
58 bam_header_destroy(textheader);
60 if (fp->header->n_targets == 0)
61 fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
62 } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
64 sam_header_parse_rg(fp->header);
65 } else if (mode[0] == 'w') { // write
66 fp->header = bam_header_dup((const bam_header_t*)aux);
67 if (mode[1] == 'b') { // binary
69 bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
71 fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
72 if (fp->x.bam == 0) goto open_err_ret;
73 bam_header_write(fp->x.bam, fp->header);
76 fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
77 if (fp->x.tamr == 0) goto open_err_ret;
79 if (strstr(mode, "h")) {
82 // parse the header text
83 alt = bam_header_init();
84 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
85 sam_header_parse(alt);
86 alt->l_text = 0; alt->text = 0;
87 // check if there are @SQ lines in the header
88 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
89 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
90 if (alt->n_targets != fp->header->n_targets)
91 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
92 } else { // then dump ->target_{name,len}
93 for (i = 0; i < fp->header->n_targets; ++i)
94 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
96 bam_header_destroy(alt);
107 void samclose(samfile_t *fp)
110 if (fp->header) bam_header_destroy(fp->header);
111 if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
112 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
113 else fclose(fp->x.tamw);
117 int samread(samfile_t *fp, bam1_t *b)
119 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
120 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
121 else return sam_read1(fp->x.tamr, fp->header, b);
124 int samwrite(samfile_t *fp, const bam1_t *b)
126 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
127 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
129 char *s = bam_format1(fp->header, b);
131 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
137 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
143 buf = bam_plbuf_init(func, func_data);
144 bam_plbuf_set_mask(buf, mask);
145 while ((ret = samread(fp, b)) >= 0)
146 bam_plbuf_push(b, buf);
147 bam_plbuf_push(0, buf);
148 bam_plbuf_destroy(buf);