void parse_lumpy(std::string lumpy_bede, std::vector<strvcfentry> & entries,
int min_number_supporting, double max_eval) {
size_t buffer_size = 2000000;
char*buffer = new char[buffer_size];
std::ifstream myfile;
myfile.open(lumpy_bede.c_str(), std::ifstream::in);
if (!myfile.good()) {
std::cout << "Lumpy Parser: could not open file: " << lumpy_bede.c_str()
<< std::endl;
exit(0);
}
int call_id=entries.size();
myfile.getline(buffer, buffer_size);
while (!myfile.eof()) {
int count = 0;
short type = -1;
double eval = 99;
strregion region;
int support = 0;
for (size_t i = 0;
i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n';
i++) {
if (count == 7 && buffer[i - 1] == '\t') {
eval = atof(&buffer[i]);
}
if (count >9 && strncmp(&buffer[i], "TYPE:", 5) == 0) {
//get type;
type = get_type(&buffer[i + 5]);
}
if (count > 10 && strncmp(&buffer[i], "STRANDS", 7) == 0) {
//get support val;
support = get_support(&buffer[i + 7]);
}
if (count > 10 && strncmp(&buffer[i], "MAX:", 4) == 0) {
//get positions;
region = get_coords(&buffer[i + 4]);
}
if (buffer[i] == '\t') {
count++;
}
}
//filter the parsed SV:
if (support > min_number_supporting && eval < max_eval) {
//std::cout<<eval<<" "<<type<<" "<<region.start.pos<<" "<<region.stop.pos<<std::endl;
//detect overlap with delly:
//if no overlap construct vcf entry for Lumpy:
entries.push_back(create_entry(region,eval,support,type,call_id));
call_id++;
}
myfile.getline(buffer, buffer_size);
}
myfile.close();
}
__initfunc(int pcwatchdog_init(void))
#endif
{
int i, found = 0;
revision = PCWD_REVISION_A;
printk("pcwd: v%s Ken Hollis ([email protected])\n", WD_VER);
/* Initial variables */
is_open = 0;
supports_temp = 0;
mode_debug = 0;
temp_panic = 0;
initial_status = 0x0000;
#ifndef PCWD_BLIND
for (i = 0; pcwd_ioports[i] != 0; i++) {
current_readport = pcwd_ioports[i];
if (pcwd_checkcard()) {
found = 1;
break;
}
}
if (!found) {
printk("pcwd: No card detected, or port not available.\n");
return(-EIO);
}
#endif
#ifdef PCWD_BLIND
current_readport = PCWD_BLIND;
#endif
get_support();
revision = get_revision();
if (revision == PCWD_REVISION_A)
printk("pcwd: PC Watchdog (REV.A) detected at port 0x%03x\n", current_readport);
else if (revision == PCWD_REVISION_C)
printk("pcwd: PC Watchdog (REV.C) detected at port 0x%03x (Firmware version: %s)\n",
current_readport, get_firmware());
else {
/* Should NEVER happen, unless get_revision() fails. */
printk("pcwd: Unable to get revision.\n");
return -1;
}
debug_off();
pcwd_showprevstate();
/* Disable the board */
if (revision == PCWD_REVISION_C) {
outb_p(0xA5, current_readport + 3);
outb_p(0xA5, current_readport + 3);
}
if (revision == PCWD_REVISION_A)
request_region(current_readport, 2, "PCWD Rev.A (Berkshire)");
else
request_region(current_readport, 4, "PCWD Rev.C (Berkshire)");
misc_register(&pcwd_miscdev);
if (supports_temp)
misc_register(&temp_miscdev);
return 0;
}
