#ifndef _NO_RAZF
#include "razf.h"
#else
+#ifdef _WIN32
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else
extern off_t ftello(FILE *stream);
extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif
#define RAZF FILE
#define razf_read(fp, buf, size) fread(buf, 1, size, fp)
#define razf_open(fn, mode) fopen(fn, mode)
#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
#define razf_tell(fp) ftello(fp)
#endif
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
struct __faidx_t {
RAZF *rz;
faidx1_t x;
k = kh_get(s, fai->hash, fai->name[i]);
x = kh_value(fai->hash, k);
+#ifdef _WIN32
+ fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
}
}
faidx_t *fai;
char *buf, *p;
int len, line_len, line_blen;
+#ifdef _WIN32
+ long offset;
+#else
long long offset;
+#endif
fai = (faidx_t*)calloc(1, sizeof(faidx_t));
fai->hash = kh_init(s);
buf = (char*)calloc(0x10000, 1);
while (!feof(fp) && fgets(buf, 0x10000, fp)) {
for (p = buf; *p && isgraph(*p); ++p);
*p = 0; ++p;
+#ifdef _WIN32
+ sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
fai_insert_index(fai, buf, len, line_len, line_blen, offset);
}
free(buf);
sprintf(str, "%s.fai", fn);
rz = razf_open(fn, "r");
if (rz == 0) {
- fprintf(stderr, "[fai_build] fail to open the FASTA file.\n");
+ fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",str);
free(str);
return -1;
}
fai = fai_build_core(rz);
razf_close(rz);
- fp = fopen(str, "w");
+ fp = fopen(str, "wb");
if (fp == 0) {
- fprintf(stderr, "[fai_build] fail to write FASTA index.\n");
+ fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
fai_destroy(fai); free(str);
return -1;
}
return 0;
}
+#ifdef _USE_KNETFILE
+FILE *download_and_open(const char *fn)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ uint8_t *buf;
+ FILE *fp;
+ knetFile *fp_remote;
+ const char *url = fn;
+ const char *p;
+ int l = strlen(fn);
+ for (p = fn + l - 1; p >= fn; --p)
+ if (*p == '/') break;
+ fn = p + 1;
+
+ // First try to open a local copy
+ fp = fopen(fn, "r");
+ if (fp)
+ return fp;
+
+ // If failed, download from remote and open
+ fp_remote = knet_open(url, "rb");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+ return NULL;
+ }
+ if ((fp = fopen(fn, "wb")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+ knet_close(fp_remote);
+ return NULL;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+
+ return fopen(fn, "r");
+}
+#endif
+
faidx_t *fai_load(const char *fn)
{
char *str;
faidx_t *fai;
str = (char*)calloc(strlen(fn) + 5, 1);
sprintf(str, "%s.fai", fn);
- fp = fopen(str, "r");
+
+#ifdef _USE_KNETFILE
+ if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
+ {
+ fp = download_and_open(str);
+ if ( !fp )
+ {
+ fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+ free(str);
+ return 0;
+ }
+ }
+ else
+#endif
+ fp = fopen(str, "rb");
if (fp == 0) {
fprintf(stderr, "[fai_load] build FASTA index.\n");
fai_build(fn);
- fp = fopen(str, "r");
+ fp = fopen(str, "rb");
if (fp == 0) {
fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
free(str);
return 0;
}
}
+
fai = fai_read(fp);
fclose(fp);
- fai->rz = razf_open(fn, "r");
+
+ fai->rz = razf_open(fn, "rb");
free(str);
if (fai->rz == 0) {
fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
l = 0;
s = (char*)malloc(end - beg + 2);
razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
- while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg)
+ while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
if (isgraph(c)) s[l++] = c;
s[l] = '\0';
*len = l;
return 0;
}
+int faidx_fetch_nseq(const faidx_t *fai)
+{
+ return fai->n;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+ int l;
+ char c;
+ khiter_t iter;
+ faidx1_t val;
+ char *seq=NULL;
+
+ // Adjust position
+ iter = kh_get(s, fai->hash, c_name);
+ if(iter == kh_end(fai->hash)) return 0;
+ val = kh_value(fai->hash, iter);
+ if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+ if(p_beg_i < 0) p_beg_i = 0;
+ else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+ if(p_end_i < 0) p_end_i = 0;
+ else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+ // Now retrieve the sequence
+ l = 0;
+ seq = (char*)malloc(p_end_i - p_beg_i + 2);
+ razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+ while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
+ if (isgraph(c)) seq[l++] = c;
+ seq[l] = '\0';
+ *len = l;
+ return seq;
+}
+
#ifdef FAIDX_MAIN
int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
#endif
projects / samtools.git / blobdiff