#include <string.h>
#include <stdlib.h>
#include <stdio.h>
+#include <stdint.h>
#include "faidx.h"
#include "khash.h"
typedef struct {
- uint64_t len:32, line_len:16, line_blen:16;
+ int32_t line_len, line_blen;
+ int64_t len;
uint64_t offset;
} faidx1_t;
KHASH_MAP_INIT_STR(s, faidx1_t)
#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;
{
char c, *name;
int l_name, m_name, ret;
- int len, line_len, line_blen, state;
+ int line_len, line_blen, state;
int l1, l2;
faidx_t *idx;
uint64_t offset;
+ int64_t len;
idx = (faidx_t*)calloc(1, sizeof(faidx_t));
idx->hash = kh_init(s);
return 0;
}
++l1; len += l2;
- if (l2 >= 0x10000) {
- fprintf(stderr, "[fai_build_core] line length exceeds 65535 in sequence '%s'.\n", name);
- free(name); fai_destroy(idx);
- return 0;
- }
if (state == 1) line_len = l1, line_blen = l2, state = 0;
else if (state == 0) {
if (l1 != line_len || l2 != line_blen) state = 2;
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",fn);
free(str);
return -1;
}
razf_close(rz);
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, "rb");
+
+#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, "rb");
free(str);
if (fai->rz == 0) {
char *fai_fetch(const faidx_t *fai, const char *str, int *len)
{
- char *s, *p, c;
- int i, l, k;
+ char *s, c;
+ int i, l, k, name_end;
khiter_t iter;
faidx1_t val;
khash_t(s) *h;
beg = end = -1;
h = fai->hash;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- iter = kh_get(s, h, s); /* get the ref_id */
- if (iter == kh_end(h)) {
- *len = 0;
- free(s); return 0;
- }
+ name_end = l = strlen(str);
+ s = (char*)malloc(l+1);
+ // remove space
+ for (i = k = 0; i < l; ++i)
+ if (!isspace(str[i])) s[k++] = str[i];
+ s[k] = 0; l = k;
+ // determine the sequence name
+ for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+ if (i >= 0) name_end = i;
+ if (name_end < l) { // check if this is really the end
+ int n_hyphen = 0;
+ for (i = name_end + 1; i < l; ++i) {
+ if (s[i] == '-') ++n_hyphen;
+ else if (!isdigit(s[i]) && s[i] != ',') break;
+ }
+ if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+ s[name_end] = 0;
+ iter = kh_get(s, h, s);
+ if (iter == kh_end(h)) { // cannot find the sequence name
+ iter = kh_get(s, h, str); // try str as the name
+ if (iter == kh_end(h)) {
+ *len = 0;
+ free(s); return 0;
+ } else s[name_end] = ':', name_end = l;
+ }
+ } else iter = kh_get(s, h, str);
val = kh_value(h, iter);
- if (i == k) { /* dump the whole sequence */
- beg = 0; end = val.len;
- } else {
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- beg = atoi(p);
- if (i < k) {
- p = s + i + 1;
- end = atoi(p);
- } else end = val.len;
- }
- if (beg > 0) --beg;
+ // parse the interval
+ if (name_end < l) {
+ for (i = k = name_end + 1; i < l; ++i)
+ if (s[i] != ',') s[k++] = s[i];
+ s[k] = 0;
+ beg = atoi(s + name_end + 1);
+ for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+ end = i < k? atoi(s + i + 1) : val.len;
+ if (beg > 0) --beg;
+ } else beg = 0, end = val.len;
if (beg >= val.len) beg = val.len;
if (end >= val.len) end = val.len;
if (beg > end) beg = end;
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