#include "khash.h"
#include "ksort.h"
#include "bam_endian.h"
+#ifdef _USE_KNETFILE
#include "knetfile.h"
+#endif
/*!
@header
FILE *fp;
char *fnidx, *fn;
- if (strstr(_fn, "ftp://") == _fn) {
+ if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
const char *p;
int l = strlen(_fn);
for (p = _fn + l - 1; p >= _fn; --p)
} else return 0;
}
+#ifdef _USE_KNETFILE
static void download_from_remote(const char *url)
{
const int buf_size = 1 * 1024 * 1024;
uint8_t *buf;
knetFile *fp_remote;
int l;
- if (strstr(url, "ftp://") != url) return;
+ if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
l = strlen(url);
for (fn = (char*)url + l - 1; fn >= url; --fn)
if (*fn == '/') break;
fclose(fp);
knet_close(fp_remote);
}
+#else
+static void download_from_remote(const char *url)
+{
+ return;
+}
+#endif
bam_index_t *bam_index_load(const char *fn)
{
bam_index_t *idx;
idx = bam_index_load_local(fn);
- if (idx == 0 && strstr(fn, "ftp://") == fn) {
+ if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
char *fnidx = calloc(strlen(fn) + 5, 1);
strcat(strcpy(fnidx, fn), ".bai");
fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
return (rend > beg && rbeg < end);
}
-int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+// bam_fetch helper function retrieves
+pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off)
{
uint16_t *bins;
int i, n_bins, n_off;
}
free(bins);
{
- bam1_t *b;
- int l, ret, n_seeks;
- uint64_t curr_off;
- b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
+ int l;
ks_introsort(off, n_off, off);
// resolve completely contained adjacent blocks
for (i = 1, l = 0; i < n_off; ++i)
n_off = l + 1;
#endif
}
+ bam_destroy1(b);
+ }
+ *cnt_off = n_off;
+ return off;
+}
+
+int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
+{
+ int n_off;
+ pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
+ if (off == 0) return 0;
+ {
// retrive alignments
+ uint64_t curr_off;
+ int i, ret, n_seeks;
n_seeks = 0; i = -1; curr_off = 0;
+ bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
for (;;) {
if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
if (i == n_off - 1) break; // no more chunks