//{{{void load_vid_data(struct vid_file *v)
void load_vid_data(struct vid_file *v)
{
if (v->vids != NULL)
errx(EX_SOFTWARE,
"VID data has already been loaded for file '%s'.", v->file_name);
v->vids = (uint32_t *) malloc(v->gqt_header->num_variants*sizeof(uint32_t));
if (!v->vids)
err(EX_OSERR, "malloc error");
if (v->type == VID_LOCAL) {
if (fseek(v->file.local, sizeof(struct gqt_file_header), SEEK_SET))
err(EX_IOERR,
"Error seeking to data in VID file '%s'.",
v->file_name);
size_t fr = fread(v->vids,
sizeof(uint32_t),
v->gqt_header->num_variants,
v->file.local);
check_file_read(v->file_name,
v->file.local,
v->gqt_header->num_variants,
fr);
} else {
if (knet_seek(v->file.remote,
sizeof(struct gqt_file_header),
SEEK_SET) == -1)
err(EX_IOERR,
"Error seeking to data in remote VID file '%s'.",
v->file_name);
size_t fr = knet_read(v->file.remote,
v->vids,
v->gqt_header->num_variants*sizeof(uint32_t));
check_remote_file_read(v->file_name,
v->gqt_header->num_variants*sizeof(uint32_t),
fr);
}
}
int main(void)
{
char *buf;
knetFile *fp;
int type = 4, l;
#ifdef _WIN32
knet_win32_init();
#endif
buf = calloc(0x100000, 1);
if (type == 0) {
fp = knet_open("knetfile.c", "r");
knet_seek(fp, 1000, SEEK_SET);
} else if (type == 1) { // NCBI FTP, large file
fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
knet_seek(fp, 2500000000ll, SEEK_SET);
l = knet_read(fp, buf, 255);
} else if (type == 2) {
fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
knet_seek(fp, 1000, SEEK_SET);
} else if (type == 3) {
fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
knet_seek(fp, 1000, SEEK_SET);
} else if (type == 4) {
fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
knet_read(fp, buf, 10000);
knet_seek(fp, 20000, SEEK_SET);
knet_seek(fp, 10000, SEEK_SET);
l = knet_read(fp, buf+10000, 10000000) + 10000;
}
if (type != 4 && type != 1) {
knet_read(fp, buf, 255);
buf[255] = 0;
printf("%s\n", buf);
} else write(fileno(stdout), buf, l);
knet_close(fp);
free(buf);
return 0;
}
static off_t net_seek(hFILE *fpv, off_t offset, int whence)
{
hFILE_net *fp = (hFILE_net *) fpv;
return knet_seek(fp->netfp, offset, whence);
}
