#include <string.h>
+#include <unistd.h>
+#include "faidx.h"
#include "sam.h"
#define TYPE_BAM 1
// 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;
+ else fp->type |= BAM_OFDEC<<2;
// write header
if (strstr(mode, "h")) {
int i;
if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
else {
- char *s = bam_format1(fp->header, b);
+ char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
int l = strlen(s);
fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
free(s);
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;
+}