#include <string.h>
+#include <unistd.h>
+#include "faidx.h"
#include "sam.h"
#define TYPE_BAM 1
int i;
h = bam_header_init();
*h = *h0;
- h->hash = 0;
+ h->hash = h->dict = h->rg2lib = 0;
h->text = (char*)calloc(h->l_text + 1, 1);
memcpy(h->text, h0->text, h->l_text);
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
h->target_len[i] = h0->target_len[i];
h->target_name[i] = strdup(h0->target_name[i]);
}
- if (h0->rg2lib) h->rg2lib = bam_strmap_dup(h0->rg2lib);
return h;
}
static void append_header_text(bam_header_t *header, char* text, int len)
{
samfile_t *fp;
fp = (samfile_t*)calloc(1, sizeof(samfile_t));
- if (mode[0] == 'r') { // read
+ if (strchr(mode, 'r')) { // read
fp->type |= TYPE_READ;
- if (mode[1] == 'b') { // binary
+ if (strchr(mode, 'b')) { // binary
fp->type |= TYPE_BAM;
fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
if (fp->x.bam == 0) goto open_err_ret;
if (aux) { // check if aux is present
bam_header_t *textheader = fp->header;
fp->header = sam_header_read2((const char*)aux);
+ if (fp->header == 0) goto open_err_ret;
append_header_text(fp->header, textheader->text, textheader->l_text);
bam_header_destroy(textheader);
}
fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
- sam_header_parse_rg(fp->header);
- } else if (mode[0] == 'w') { // write
+ } else if (strchr(mode, 'w')) { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
- if (mode[1] == 'b') { // binary
+ if (strchr(mode, 'b')) { // binary
char bmode[3];
- bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
fp->type |= TYPE_BAM;
fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
if (fp->x.bam == 0) goto open_err_ret;
// open file
fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
if (fp->x.tamr == 0) goto open_err_ret;
- if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
- else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+ if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
+ else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
else fp->type |= BAM_OFDEC<<2;
// write header
- if (strstr(mode, "h")) {
+ if (strchr(mode, 'h')) {
int i;
bam_header_t *alt;
// parse the header text
bam_destroy1(b);
return 0;
}
+
+char *samfaipath(const char *fn_ref)
+{
+ char *fn_list = 0;
+ if (fn_ref == 0) return 0;
+ fn_list = calloc(strlen(fn_ref) + 5, 1);
+ strcat(strcpy(fn_list, fn_ref), ".fai");
+ if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+ if (access(fn_ref, R_OK) == -1) {
+ fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+ } else {
+ fprintf(stderr, "[samfaipath] build FASTA index...\n");
+ if (fai_build(fn_ref) == -1) {
+ fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+ free(fn_list); fn_list = 0;
+ }
+ }
+ }
+ return fn_list;
+}