void outputBlocks(const std::string& outDir, PermVec& blocks,
BlockGroups& groups, int blockSize)
{
makeDirectory(outDir);
std::string permsFile = outDir + "/genomes_permutations.txt";
std::string coordsFile = outDir + "/blocks_coords.txt";
std::string statsFile = outDir + "/coverage_report.txt";
PermVec outPerms = filterBySize(blocks, groups, blockSize, true);
renumerate(outPerms);
outputPermutation(outPerms, permsFile);
outputCoords(outPerms, coordsFile);
outputStatistics(outPerms, statsFile);
}
int cyusb_open(void)
{
int fd1;
int r;
fd1 = open("/etc/cyusb.conf", O_RDONLY);
if ( fd1 < 0 ) {
printf("/etc/cyusb.conf file not found. Exiting\n");
return -1;
}
else {
close(fd1);
parse_configfile(); /* Parses the file and stores critical information inside exported data structures */
}
r = libusb_init(NULL);
if (r) {
printf("Error in initializing libusb library...\n");
return -2;
}
r = renumerate();
return r;
}
int main(int argc, char **argv)
{
if(argc <= 1)
usage();
int ret = 0;
libusb_init(NULL);
libusb_device_handle *dev = libusb_open_device_with_vid_pid(NULL, 0x601a, 0x4760);
if(dev == NULL)
{
printf("Cannot open device\n");
return -1;
}
if(libusb_claim_interface(dev, 0) != 0)
{
printf("Cannot claim interface\n");
libusb_close(dev);
return -2;
}
enum
{
OPT_ADDR = 0x100, OPT_LENGTH, OPT_UPLOAD, OPT_CPUINFO, OPT_DOWNLOAD,
OPT_START1, OPT_WAIT, OPT_RENUMERATE, OPT_START2, OPT_FLUSH_CACHES,
OPT_S1_ADDR, OPT_STAGE1
};
unsigned long last_length = 0;
unsigned long s1_addr = 0x80000000;
while(1)
{
static struct option long_options[] =
{
{"help", no_argument, 0, 'h'},
{"cpuinfo", no_argument, 0, OPT_CPUINFO},
{"addr", required_argument, 0, OPT_ADDR},
{"length", required_argument, 0, OPT_LENGTH},
{"upload", required_argument, 0, OPT_UPLOAD},
{"download", required_argument, 0, OPT_DOWNLOAD},
{"start1", required_argument, 0, OPT_START1},
{"wait", required_argument, 0, OPT_WAIT},
{"renumerate", no_argument, 0, OPT_RENUMERATE},
{"start2", required_argument, 0, OPT_START2},
{"flush-caches", no_argument, 0, OPT_FLUSH_CACHES},
{"s1-addr", required_argument, 0, OPT_S1_ADDR},
{"stage1", required_argument, 0, OPT_STAGE1},
{0, 0, 0, 0}
};
int c = getopt_long(argc, argv, "hv", long_options, NULL);
char *end = 0;
unsigned long param;
if(c == OPT_ADDR || c == OPT_LENGTH || c == OPT_START1 || c == OPT_WAIT
|| c == OPT_S1_ADDR)
{
param = strtoul(optarg, &end, 0);
if(*end)
{
printf("Invalid argument '%s'\n", optarg);
ret = 1;
break;
}
}
if(c == -1)
break;
switch(c)
{
default:
case -1:
break;
case 'h':
usage();
break;
case 'v':
g_verbose = true;
break;
case OPT_ADDR:
ret = jz_set_addr(dev, param);
break;
case OPT_LENGTH:
last_length = param;
ret = jz_set_length(dev, param);
break;
case OPT_UPLOAD:
ret = jz_upload(dev, optarg, last_length);
break;
case OPT_DOWNLOAD:
ret = jz_download(dev, optarg);
break;
case OPT_CPUINFO:
ret = jz_cpuinfo(dev);
break;
case OPT_START1:
ret = jz_start1(dev, param);
break;
case OPT_WAIT:
if(g_verbose)
printf("Wait for %lu seconds...\n", param);
sleep(param);
break;
case OPT_RENUMERATE:
ret = renumerate(&dev);
break;
case OPT_START2:
ret = jz_start2(dev, param);
break;
case OPT_FLUSH_CACHES:
ret = jz_flush_caches(dev);
break;
case OPT_S1_ADDR:
s1_addr = param;
break;
case OPT_STAGE1:
ret = jz_stage1(dev, s1_addr, optarg);
break;
}
if(ret != 0)
break;
}
if(optind != argc)
{
printf("Error: extra arguments on command line\n");
ret = 1;
}
libusb_close(dev);
libusb_exit(NULL);
return ret;
}
