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
31 if (x < y) header->text = (char*)realloc(header->text, y);
32 strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
33 header->l_text += len;
34 header->text[header->l_text] = 0;
37 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
40 fp = (samfile_t*)calloc(1, sizeof(samfile_t));
41 if (mode[0] == 'r') { // read
42 fp->type |= TYPE_READ;
43 if (mode[1] == 'b') { // binary
45 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
46 if (fp->x.bam == 0) goto open_err_ret;
47 fp->header = bam_header_read(fp->x.bam);
49 fp->x.tamr = sam_open(fn);
50 if (fp->x.tamr == 0) goto open_err_ret;
51 fp->header = sam_header_read(fp->x.tamr);
52 if (fp->header->n_targets == 0) { // no @SQ fields
53 if (aux) { // check if aux is present
54 bam_header_t *textheader = fp->header;
55 fp->header = sam_header_read2((const char*)aux);
56 append_header_text(fp->header, textheader->text, textheader->l_text);
57 bam_header_destroy(textheader);
59 if (fp->header->n_targets == 0)
60 fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
61 } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
63 sam_header_parse_rg(fp->header);
64 } else if (mode[0] == 'w') { // write
65 fp->header = bam_header_dup((const bam_header_t*)aux);
66 if (mode[1] == 'b') { // binary
68 bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
70 fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
71 if (fp->x.bam == 0) goto open_err_ret;
72 bam_header_write(fp->x.bam, fp->header);
75 fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
76 if (fp->x.tamr == 0) goto open_err_ret;
78 if (strstr(mode, "h")) {
81 // parse the header text
82 alt = bam_header_init();
83 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
84 sam_header_parse(alt);
85 alt->l_text = 0; alt->text = 0;
86 // check if there are @SQ lines in the header
87 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
88 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
89 if (alt->n_targets != fp->header->n_targets)
90 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
91 } else { // then dump ->target_{name,len}
92 for (i = 0; i < fp->header->n_targets; ++i)
93 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
95 bam_header_destroy(alt);
106 void samclose(samfile_t *fp)
109 if (fp->header) bam_header_destroy(fp->header);
110 if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
111 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
112 else fclose(fp->x.tamw);
116 int samread(samfile_t *fp, bam1_t *b)
118 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
119 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
120 else return sam_read1(fp->x.tamr, fp->header, b);
123 int samwrite(samfile_t *fp, const bam1_t *b)
125 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
126 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
128 char *s = bam_format1(fp->header, b);
130 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
136 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
142 buf = bam_plbuf_init(func, func_data);
143 bam_plbuf_set_mask(buf, mask);
144 while ((ret = samread(fp, b)) >= 0)
145 bam_plbuf_push(b, buf);
146 bam_plbuf_push(0, buf);
147 bam_plbuf_destroy(buf);