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]);
26 static void append_header_text(bam_header_t *header, char* text, int len)
28 int x = header->l_text + 1;
29 int y = header->l_text + len + 1; // 1 byte null
30 if (text == 0) return;
33 if (x < y) header->text = (char*)realloc(header->text, y);
34 strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
35 header->l_text += len;
36 header->text[header->l_text] = 0;
39 samfile_t *samopen(const char *fn, const char *mode, const void *aux)
42 fp = (samfile_t*)calloc(1, sizeof(samfile_t));
43 if (mode[0] == 'r') { // read
44 fp->type |= TYPE_READ;
45 if (mode[1] == 'b') { // binary
47 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
48 if (fp->x.bam == 0) goto open_err_ret;
49 fp->header = bam_header_read(fp->x.bam);
51 fp->x.tamr = sam_open(fn);
52 if (fp->x.tamr == 0) goto open_err_ret;
53 fp->header = sam_header_read(fp->x.tamr);
54 if (fp->header->n_targets == 0) { // no @SQ fields
55 if (aux) { // check if aux is present
56 bam_header_t *textheader = fp->header;
57 fp->header = sam_header_read2((const char*)aux);
58 append_header_text(fp->header, textheader->text, textheader->l_text);
59 bam_header_destroy(textheader);
61 if (fp->header->n_targets == 0)
62 fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
63 } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
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;
78 if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
79 else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
80 else fp->type |= BAM_OFDEC<<2;
82 if (strstr(mode, "h")) {
85 // parse the header text
86 alt = bam_header_init();
87 alt->l_text = fp->header->l_text; alt->text = fp->header->text;
88 sam_header_parse(alt);
89 alt->l_text = 0; alt->text = 0;
90 // check if there are @SQ lines in the header
91 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
92 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
93 if (alt->n_targets != fp->header->n_targets)
94 fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
95 } else { // then dump ->target_{name,len}
96 for (i = 0; i < fp->header->n_targets; ++i)
97 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
99 bam_header_destroy(alt);
110 void samclose(samfile_t *fp)
113 if (fp->header) bam_header_destroy(fp->header);
114 if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
115 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
116 else fclose(fp->x.tamw);
120 int samread(samfile_t *fp, bam1_t *b)
122 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
123 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
124 else return sam_read1(fp->x.tamr, fp->header, b);
127 int samwrite(samfile_t *fp, const bam1_t *b)
129 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
130 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
132 char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
134 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
140 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
146 buf = bam_plbuf_init(func, func_data);
147 bam_plbuf_set_mask(buf, mask);
148 while ((ret = samread(fp, b)) >= 0)
149 bam_plbuf_push(b, buf);
150 bam_plbuf_push(0, buf);
151 bam_plbuf_destroy(buf);
156 char *samfaipath(const char *fn_ref)
159 if (fn_ref == 0) return 0;
160 fn_list = calloc(strlen(fn_ref) + 5, 1);
161 strcat(strcpy(fn_list, fn_ref), ".fai");
162 if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
163 if (access(fn_ref, R_OK) == -1) {
164 fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
166 fprintf(stderr, "[samfaipath] build FASTA index...\n");
167 if (fai_build(fn_ref) == -1) {
168 fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
169 free(fn_list); fn_list = 0;