9 bam_header_t *bam_header_dup(const bam_header_t *h0)
13 h = bam_header_init();
16 h->text = (char*)calloc(h->l_text + 1, 1);
17 memcpy(h->text, h0->text, h->l_text);
18 h->target_len = (uint32_t*)calloc(h->n_targets, 4);
19 h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
20 for (i = 0; i < h->n_targets; ++i) {
21 h->target_len[i] = h0->target_len[i];
22 h->target_name[i] = strdup(h0->target_name[i]);
24 if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
27 static void append_header_text(bam_header_t *header, char* text, int len)
29 int x = header->l_text + 1;
30 int y = header->l_text + len + 1; // 1 byte null
31 if (text == 0) return;
34 if (x < y) header->text = (char*)realloc(header->text, y);
35 strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
36 header->l_text += len;
37 header->text[header->l_text] = 0;
40 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
43 fp = (samfile_t*)calloc(1, sizeof(samfile_t));
44 if (mode[0] == 'r') { // read
45 fp->type |= TYPE_READ;
46 if (mode[1] == 'b') { // binary
48 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
49 if (fp->x.bam == 0) goto open_err_ret;
50 fp->header = bam_header_read(fp->x.bam);
52 fp->x.tamr = sam_open(fn);
53 if (fp->x.tamr == 0) goto open_err_ret;
54 fp->header = sam_header_read(fp->x.tamr);
55 if (fp->header->n_targets == 0) { // no @SQ fields
56 if (aux) { // check if aux is present
57 bam_header_t *textheader = fp->header;
58 fp->header = sam_header_read2((const char*)aux);
59 append_header_text(fp->header, textheader->text, textheader->l_text);
60 bam_header_destroy(textheader);
62 if (fp->header->n_targets == 0)
63 fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
64 } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
66 sam_header_parse_rg(fp->header);
67 } else if (mode[0] == 'w') { // write
68 fp->header = bam_header_dup((const bam_header_t*)aux);
69 if (mode[1] == 'b') { // binary
71 bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
73 fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
74 if (fp->x.bam == 0) goto open_err_ret;
75 bam_header_write(fp->x.bam, fp->header);
78 fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
79 if (fp->x.tamr == 0) goto open_err_ret;
80 if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
81 else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
82 else fp->type |= BAM_OFDEC<<2;
84 if (strstr(mode, "h")) {
87 // parse the header text
88 alt = bam_header_init();
89 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
90 sam_header_parse(alt);
91 alt->l_text = 0; alt->text = 0;
92 // check if there are @SQ lines in the header
93 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
94 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
95 if (alt->n_targets != fp->header->n_targets)
96 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
97 } else { // then dump ->target_{name,len}
98 for (i = 0; i < fp->header->n_targets; ++i)
99 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
101 bam_header_destroy(alt);
112 void samclose(samfile_t *fp)
115 if (fp->header) bam_header_destroy(fp->header);
116 if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
117 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
118 else fclose(fp->x.tamw);
122 int samread(samfile_t *fp, bam1_t *b)
124 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
125 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
126 else return sam_read1(fp->x.tamr, fp->header, b);
129 int samwrite(samfile_t *fp, const bam1_t *b)
131 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
132 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
134 char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
136 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
142 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
148 buf = bam_plbuf_init(func, func_data);
149 bam_plbuf_set_mask(buf, mask);
150 while ((ret = samread(fp, b)) >= 0)
151 bam_plbuf_push(b, buf);
152 bam_plbuf_push(0, buf);
153 bam_plbuf_destroy(buf);
158 char *samfaipath(const char *fn_ref)
161 if (fn_ref == 0) return 0;
162 fn_list = calloc(strlen(fn_ref) + 5, 1);
163 strcat(strcpy(fn_list, fn_ref), ".fai");
164 if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
165 if (access(fn_ref, R_OK) == -1) {
166 fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
168 fprintf(stderr, "[samfaipath] build FASTA index...\n");
169 if (fai_build(fn_ref) == -1) {
170 fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
171 free(fn_list); fn_list = 0;