void
VisualizeCurve (ON_NurbsCurve &curve, double r, double g, double b, bool show_cps)
{
pcl::PointCloud<pcl::PointXYZRGB>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZRGB>);
pcl::on_nurbs::Triangulation::convertCurve2PointCloud (curve, cloud, 8);
for (std::size_t i = 0; i < cloud->size () - 1; i++)
{
pcl::PointXYZRGB &p1 = cloud->at (i);
pcl::PointXYZRGB &p2 = cloud->at (i + 1);
std::ostringstream os;
os << "line_" << r << "_" << g << "_" << b << "_" << i;
viewer.addLine<pcl::PointXYZRGB> (p1, p2, r, g, b, os.str ());
}
if (show_cps)
{
pcl::PointCloud<pcl::PointXYZ>::Ptr cps (new pcl::PointCloud<pcl::PointXYZ>);
for (int i = 0; i < curve.CVCount (); i++)
{
ON_3dPoint cp;
curve.GetCV (i, cp);
pcl::PointXYZ p;
p.x = float (cp.x);
p.y = float (cp.y);
p.z = float (cp.z);
cps->push_back (p);
}
pcl::visualization::PointCloudColorHandlerCustom<pcl::PointXYZ> handler (cps, 255 * r, 255 * g, 255 * b);
viewer.addPointCloud<pcl::PointXYZ> (cps, handler, "cloud_cps");
}
}
/*--------------------------------------------------------------------------*/
IsotimeEpoch _string2epoch(const char *epoch_s)
{ long base;
IsotimeEpoch epoch;
char epobuf[EPOLEN], *pr;
char secbuf[SLEN], *ps;
char frabuf[SLEN], *pf;
long sec=0;
double fract=0.0;
if (ISOTIME_debug>0) fprintf(stderr,"_string2epoch >>%s<<\n",epoch_s);
epoch.status = -1;
epoch.sec = 0;
epoch.fract = 0.0;
epoch.offset = 0;
// trim isotime_s, convert to uppercase and copy to trimmed
ps = trim( epobuf, EPOLEN, epoch_s );
if (ISOTIME_debug>1) fprintf(stderr," trim returns >>%s<<\n",ps);
// copy seconds
pf = cps( secbuf, SLEN, ps );
if (ISOTIME_debug>1) fprintf(stderr," section >>%s<<\n",secbuf);
// copy fraction
pr = cpf( frabuf, SLEN, pf );
if (ISOTIME_debug>1) fprintf(stderr," fraction >>%s<<\n",frabuf);
if ( strlen(pr) ) {
// error, if rest is not empty
fprintf( stderr, "ERROR: Cannot read epoch \"%s\"\n",epobuf );
fprintf( stderr, " Format: [+|-]sssssssssss[.uuuuuuu]\n" );
fprintf( stderr, " e.g. \"1149254287\", \"+1149254287.1\"\n");
goto _string2epocherr;
}
sscanf(secbuf,"%ld",&sec);
sscanf(frabuf,"%lf",&fract);
epoch.sec = sec;
if (sec>=0) epoch.fract = fract;
epoch.fract = -fract;
// normalize fract and sec
base = floor(epoch.fract);
epoch.fract -= (double) base;
epoch.sec += base;
epoch.status = 0;
if (ISOTIME_debug>0) fprintf(stderr,"_string2epoch END\n");
return ( epoch );
_string2epocherr:
if (ISOTIME_debug>0) fprintf(stderr,"_string2epoch END\n");
return ( epoch );
} // _string2epoch
CUIApp::CUIApp()
{
// Place all significant initialization in InitInstance
pause=false;
pauseSecs=0;
CPersistentString cps("RunBefore");
FirstEverTimeRun=!cps.toBool();
cps=true;
}
bool ConstraintChecker::HasSupportPolygon(const Robot& robot,const Stance& stance,const Vector3& gravity,int numFCEdges)
{
vector<ContactPoint> cps(NumContactPoints(stance));
int k=0;
for(Stance::const_iterator i=stance.begin();i!=stance.end();i++) {
const Hold& h=i->second;
for(size_t j=0;j<h.contacts.size();j++,k++)
cps[k]=h.contacts[j];
}
Vector3 com = robot.GetCOM();
vector<Vector3> f;
return TestCOMEquilibrium(cps,gravity,numFCEdges,com,f);
}
bool ConstraintChecker::HasSupportPolygon_Robust(const Robot& robot,const Stance& stance,const Vector3& gravity,Real robustnessFactor,int numFCEdges)
{
vector<ContactPoint> cps(NumContactPoints(stance));
int k=0;
for(Stance::const_iterator i=stance.begin();i!=stance.end();i++) {
const Hold& h=i->second;
for(size_t j=0;j<h.contacts.size();j++,k++)
cps[k]=h.contacts[j];
}
Vector3 com = robot.GetCOM();
EquilibriumTester eq;
eq.Setup(cps,gravity,numFCEdges,com);
eq.SetRobustnessFactor(robustnessFactor);
return eq.TestCurrent();
}
//********************************************************************************
void CGuiHeaderCtrl::DrawArrow(CDC* pDC,CRect rc,BOOL bUp)
{
CPen cp(PS_SOLID,1, m_clrFace);
CPen cps(PS_SOLID,1, m_clrShadow);
CPen cpw(PS_SOLID,1, m_clrLight);
CPen *pOld;
rc.left=rc.right-12;
rc.right=rc.left+8;
rc.bottom=rc.top+12;
rc.top+=2;
int m_mitad=rc.left+4;
if (bUp == TRUE)
{
//linea izquierda
pOld=pDC->SelectObject(&cps);
pDC->MoveTo(rc.left,rc.bottom);
pDC->LineTo(m_mitad,rc.top);
//linea derecha
pDC->SelectObject(&cpw);
pDC->MoveTo(rc.right,rc.bottom);
pDC->LineTo(m_mitad,rc.top);
//linea de abajo
pDC->MoveTo(rc.left,rc.bottom);
pDC->LineTo(rc.right,rc.bottom);
}
else
{
rc.bottom=rc.top+12;
rc.top+=4;
//linea izquierda
pOld=pDC->SelectObject(&cps);
pDC->MoveTo(rc.left,rc.top);
pDC->LineTo(m_mitad,rc.bottom);
//linea superior
pDC->MoveTo(rc.left,rc.top);
pDC->LineTo(rc.right,rc.top);
//linea derecha
pDC->SelectObject(&cpw);
pDC->MoveTo(rc.right,rc.top);
pDC->LineTo(m_mitad,rc.bottom);
}
pDC->SelectObject(pOld);
}
//************************************************************************
void CGuiHeaderCtrl::BiselaBoton(CRect rcWin,CDC* pDC)
{
CPen cp(PS_SOLID,1, m_clrFace);
CPen cps(PS_SOLID,1, m_clrShadow);
CPen cpw(PS_SOLID,1, m_clrLight);
//***************************************************
pDC->Draw3dRect(rcWin,m_clrLight,m_clrShadow);
rcWin.DeflateRect(1,1);
pDC->Draw3dRect(rcWin,m_clrFace,m_clrFace);
//***************************************************
CPen* cpold=pDC->SelectObject(&cp);
int iNumItems=GetItemCount();
int iContx=0;
HDITEM m_hditems;
for (int i =0; i < iNumItems; i++)
{
CRect recItem;
GetItem(i,&m_hditems);
GetItemRect(i, recItem);
iContx+=recItem.Width();
//quitamos todas las lineas
recItem.DeflateRect(1,1);
pDC->SelectObject(&cp);
pDC->MoveTo(iContx-2,rcWin.top+1);
pDC->LineTo(iContx-2,rcWin.bottom-1);
pDC->MoveTo(iContx-1,rcWin.top+1);
pDC->LineTo(iContx-1,rcWin.bottom-1);
pDC->MoveTo(iContx,rcWin.top+1);
pDC->LineTo(iContx,rcWin.bottom-1);
pDC->MoveTo(iContx+1,rcWin.top+1);
pDC->LineTo(iContx+1,rcWin.bottom-1);
//ponemos dos para dar el efecto
pDC->SelectObject(&cps);
pDC->MoveTo(iContx-1,rcWin.top+2);
pDC->LineTo(iContx-1,rcWin.bottom-2);
pDC->SelectObject(&cpw);
pDC->MoveTo(iContx,rcWin.top+2);
pDC->LineTo(iContx,rcWin.bottom-2);
}
pDC->SelectObject(cpold);
}
//-----------------------------------------------------------------------------
// CaptivePortalService::nsIObserver
//-----------------------------------------------------------------------------
NS_IMETHODIMP
CaptivePortalService::Observe(nsISupports *aSubject,
const char * aTopic,
const char16_t * aData)
{
if (XRE_GetProcessType() != GeckoProcessType_Default) {
// Doesn't do anything if called in the content process.
return NS_OK;
}
LOG(("CaptivePortalService::Observe() topic=%s\n", aTopic));
if (!strcmp(aTopic, kOpenCaptivePortalLoginEvent)) {
// A redirect or altered content has been detected.
// The user needs to log in. We are in a captive portal.
mState = LOCKED_PORTAL;
mLastChecked = TimeStamp::Now();
mEverBeenCaptive = true;
} else if (!strcmp(aTopic, kCaptivePortalLoginSuccessEvent)) {
// The user has successfully logged in. We have connectivity.
mState = UNLOCKED_PORTAL;
mLastChecked = TimeStamp::Now();
mSlackCount = 0;
mDelay = mMinInterval;
RearmTimer();
} else if (!strcmp(aTopic, kAbortCaptivePortalLoginEvent)) {
// The login has been aborted
mState = UNKNOWN;
mLastChecked = TimeStamp::Now();
mSlackCount = 0;
}
// Send notification so that the captive portal state is mirrored in the
// content process.
nsCOMPtr<nsIObserverService> observerService = services::GetObserverService();
if (observerService) {
nsCOMPtr<nsICaptivePortalService> cps(this);
observerService->NotifyObservers(cps, NS_IPC_CAPTIVE_PORTAL_SET_STATE, nullptr);
}
return NS_OK;
}
/**
* Edit selected profile preferences
*
*
*/
void CAMProfileSettingsList::on_bEdit_clicked(const QModelIndex &parent) {
Q_UNUSED(parent);
//ui->tableView->selectedItems();
// Get all selections
QModelIndexList indexes = ui->tableView->selectionModel()->selection().indexes();
QList<int> list;
for (int i = 0; i < indexes.count(); ++i)
{
list.append(indexes.at(i).row());
}
list=QSet<int>::fromList(list).toList();
foreach(int row, list)
{
CAMProfileSettings cps(this);
cps.setData(camProfileDataModel->getList().at(row));
if (cps.exec()==QDialog::Accepted) {
savePreferences();
}
}
int main(int argc, char** argv)
{
ros::init(argc, argv, "collision_proximity_server_test");
ros::AsyncSpinner spinner(1);
spinner.start();
ros::NodeHandle nh;
std::string robot_description_name = nh.resolveName("robot_description", true);
CollisionProximitySpacePlannerInterface cps(robot_description_name);
ros::Rate r(10.0);
while(nh.ok()) {
cps.broadcastCollisionMarkers();
r.sleep();
}
ros::waitForShutdown();
return 0;
}
contractor_ibex_hc4::contractor_ibex_hc4(vector<Enode *> const & vars,
vector<shared_ptr<nonlinear_constraint>> const & ctrs)
: contractor_cell(contractor_kind::IBEX_HC4), m_ctrs(ctrs) {
// Trivial Case
if (m_ctrs.size() == 0) {
return;
}
unsigned index = 0;
ibex::Array<ibex::NumConstraint> cps(ctrs.size());
for (shared_ptr<nonlinear_constraint> numctr : ctrs) {
cps.set_ref(index++, *(numctr->get_numctr()));
}
m_ctc.reset(new ibex::CtcHC4(cps));
unordered_map<Enode *, unsigned> enode_to_id;
for (unsigned i = 0; i < vars.size(); ++i) {
enode_to_id.emplace(vars[i], i);
}
for (shared_ptr<nonlinear_constraint> ctr : ctrs) {
unordered_set<Enode *> const & vars_in_ctr = ctr->get_enode()->get_vars();
m_vars_in_ctrs.insert(vars_in_ctr.begin(), vars_in_ctr.end());
}
DREAL_LOG_INFO << "contractor_ibex_hc4: DONE" << endl;
}
///Randomly rotate sgrid_m
void NonLocalECPComponent::randomize_grid(ParticleSet::ParticlePos_t& sphere, bool randomize)
{
if(randomize) {
//const RealType twopi(6.28318530718);
//RealType phi(twopi*Random()),psi(twopi*Random()),cth(Random()-0.5),
RealType phi(TWOPI*((*myRNG)())), psi(TWOPI*((*myRNG)())), cth(((*myRNG)())-0.5);
RealType sph(std::sin(phi)),cph(std::cos(phi)),
sth(std::sqrt(1.0-cth*cth)),sps(std::sin(psi)),
cps(std::cos(psi));
TensorType rmat( cph*cth*cps-sph*sps, sph*cth*cps+cph*sps,-sth*cps,
-cph*cth*sps-sph*cps,-sph*cth*sps+cph*cps, sth*sps,
cph*sth, sph*sth, cth );
SpherGridType::iterator it(sgridxyz_m.begin());
SpherGridType::iterator it_end(sgridxyz_m.end());
SpherGridType::iterator jt(rrotsgrid_m.begin());
int ic=0;
while(it != it_end) {*jt = dot(rmat,*it); ++it; ++jt;}
//copy the radomized grid to sphere
std::copy(rrotsgrid_m.begin(), rrotsgrid_m.end(), sphere.begin());
} else {
//copy sphere to the radomized grid
std::copy(sphere.begin(), sphere.end(), rrotsgrid_m.begin());
}
}
void Unlock()
{
if (tokenring && tokenring->pass()) cps();
}
static quintptr* copyContents(ZONE* zone, MutableKev* kev) {
FixedLengthKev<CPSKev>* cps(FixedLengthKev<CPSKev>::from(kev));
cps->who_ = zone->copy(cps->who_);
return cps->border();
}
int32 DCCReceive::Transfer(void* arg)
{
BMessenger msgr(reinterpret_cast<DCCReceive*>(arg));
struct sockaddr_in address;
BLooper* looper(NULL);
int32 dccSock(-1);
if ((dccSock = socket(AF_INET, SOCK_STREAM, 0)) < 0) {
UpdateStatus(msgr, S_DCC_ESTABLISH_ERROR);
return B_ERROR;
}
BMessage reply;
if (msgr.SendMessage(M_DCC_GET_CONNECT_DATA, &reply) == B_ERROR) return B_ERROR;
memset(&address, 0, sizeof(sockaddr_in));
address.sin_family = AF_INET;
address.sin_port = htons(atoi(reply.FindString("port")));
address.sin_addr.s_addr = htonl(strtoul(reply.FindString("ip"), 0, 10));
UpdateStatus(msgr, S_DCC_CONNECT_TO_SENDER);
if (connect(dccSock, (sockaddr*)&address, sizeof(address)) < 0) {
UpdateStatus(msgr, S_DCC_ESTABLISH_ERROR);
close(dccSock);
return B_ERROR;
}
BPath path(reply.FindString("name"));
BString buffer;
off_t file_size(0);
buffer << S_DCC_RECV1 << path.Leaf() << S_DCC_RECV2 << reply.FindString("nick") << ".";
UpdateStatus(msgr, buffer.String());
BFile file;
if (msgr.IsValid()) {
if (reply.FindBool("resume")) {
if (file.SetTo(reply.FindString("name"), B_WRITE_ONLY | B_OPEN_AT_END) == B_NO_ERROR &&
file.GetSize(&file_size) == B_NO_ERROR && file_size > 0LL)
UpdateBar(msgr, file_size, 0, 0, true);
else
file_size = 0LL;
} else {
file.SetTo(reply.FindString("name"), B_WRITE_ONLY | B_CREATE_FILE | B_ERASE_FILE);
}
}
uint32 bytes_received(file_size);
uint32 size(atol(reply.FindString("size")));
uint32 cps(0);
if (file.InitCheck() == B_NO_ERROR) {
bigtime_t last(system_time()), now;
char inBuffer[8196];
bigtime_t start = system_time();
while ((msgr.Target(&looper) != NULL) && bytes_received < size) {
int readSize;
if ((readSize = recv(dccSock, inBuffer, 8196, 0)) < 0) break;
file.Write(inBuffer, readSize);
bytes_received += readSize;
BMessage msg(M_DCC_UPDATE_TRANSFERRED);
msg.AddInt32("transferred", bytes_received);
msgr.SendMessage(&msg);
uint32 feed_back(htonl(bytes_received));
send(dccSock, &feed_back, sizeof(uint32), 0);
now = system_time();
bool hit(false);
if (now - last > 500000) {
cps = (int)ceil((bytes_received - file_size) / ((now - start) / 1000000.0));
BMessage updmsg(M_DCC_UPDATE_AVERAGE);
updmsg.AddInt32("average", cps);
msgr.SendMessage(&updmsg);
last = now;
hit = true;
}
DCCConnect::UpdateBar(msgr, readSize, cps, bytes_received, hit);
}
}
if (msgr.IsValid()) {
BMessage msg(M_DCC_STOP_BUTTON);
msgr.SendMessage(&msg);
}
if (dccSock > 0) {
close(dccSock);
}
if (file.InitCheck() == B_OK) {
file.Unset();
update_mime_info(reply.FindString("name"), 0, 0, 1);
}
return 0;
}
// subdivide surface at midpoint into 4 bezier surfaces
int BezierTensorSurface::midPointSubDivision(beziersurfacematrix &newbeziers)
{
int error;
unsigned int i;
newbeziers.resize(2);
newbeziers[0].resize(2);
newbeziers[1].resize(2); // we return exactly 4 new bezier tensorsurfaces
//FIXME: verification before goin' into computation!!
//FIXME: there are a lot of unverified error reports!!
DCTPVec4dmatrix::size_type n = control_points.size() - 1;
DCTPVec4dvector::size_type m = control_points[0].size() - 1;
bezier3dmatrix horizdiv(n + 1);
bezier3dmatrix vertdivleft(m + 1);
bezier3dmatrix vertdivright(m + 1);
// std::cerr << "n: " << n << " m: " << m << std::endl;
//FIXME: does the order u->v or v->u really not matter? e.g. for speed if for nothing else
for(i = 0; i <= n; i++)
{
horizdiv[i].resize(2);
horizdiv[i][0].setControlPointVector(control_points[i]);
error = horizdiv[i][0].midPointSubDivision(horizdiv[i][1]);
if(error)
return error;
}
for(i = 0; i <= m; i++)
{
DCTPVec4dvector tempvecleft(n + 1);
DCTPVec4dvector tempvecright(n + 1);
for(DCTPdvector::size_type j = 0; j <= n; j++)
{
tempvecleft[j] = horizdiv[j][0].getControlPointVector()[i];
tempvecright[j] = horizdiv[j][1].getControlPointVector()[i];
} // j
vertdivleft[i].resize(2);
vertdivleft[i][0].setControlPointVector(tempvecleft);
error = vertdivleft[i][0].midPointSubDivision(vertdivleft[i][1]);
if(error)
return error;
vertdivright[i].resize(2);
vertdivright[i][0].setControlPointVector(tempvecright);
error = vertdivright[i][0].midPointSubDivision(vertdivright[i][1]);
if(error)
return error;
} // i
DCTPVec4dmatrix cps(n + 1);
for(i = 0; i <= n; i++)
cps[i].resize(m + 1);
for(i = 0; i <= n; i++)
{
for(DCTPVec4dmatrix::size_type j = 0; j <= m; j++)
{
cps[i][j] = vertdivleft[j][0].getControlPointVector()[i];
}
}
newbeziers[0][0].setControlPointMatrix(cps);
for(i = 0; i <= n; i++)
{
for(DCTPVec4dmatrix::size_type j = 0; j <= m; j++)
{
cps[i][j] = vertdivleft[j][1].getControlPointVector()[i];
}
}
newbeziers[1][0].setControlPointMatrix(cps);
for(i = 0; i <= n; i++)
{
for(DCTPVec4dmatrix::size_type j = 0; j <= m; j++)
{
cps[i][j] = vertdivright[j][0].getControlPointVector()[i];
}
}
newbeziers[0][1].setControlPointMatrix(cps);
for(i = 0; i <= n; i++)
{
for(DCTPVec4dmatrix::size_type j = 0; j <= m; j++)
{
cps[i][j] = vertdivright[j][1].getControlPointVector()[i];
}
}
newbeziers[1][1].setControlPointMatrix(cps);
return 0;
}
void pelt(Dataloader &dload, const CageParams& params) {
// Copy parameters for convenience
int start = params.dataloader_params.start;
int end = params.dataloader_params.end;
int step = params.dataloader_params.step;
double beta = params.beta;
double K = 0;
bool verbose = params.dataloader_params.verbose;
string output_file = params.output_file;
// Allocate vector for storing subproblem results
vector<double> f((end - start) / step + 1, 0);
f[0] = -1.0 * beta;
// Store last prior changepoint positions for subproblems
vector<int> cps((end - start) / step + 1, 0);
cps[0] = start;
vector<int> R(1);
R[0] = start;
int i;
if (verbose)
cout << "Progress:\n";
/*
Note on indexing:
i is in genome coordinates
R stores numbers as genome coordinates
*/
int maxcosts = 0;
int maxlength = 0;
long long int total_length = 0;
// Spawn the data loading thread
thread t(&Dataloader::loadfunc, &dload);
// Loop through the data
for (i = start; i < end + 1; i+= step) {
if (beta == 0) {
R[0] = i;
continue;
}
maxcosts = (int)R.size() > maxcosts ? R.size() : maxcosts;
int length_now = (i - *min_element(R.begin(), R.end()));
maxlength = length_now > maxlength ? length_now : maxlength;
if (verbose) {
if ((i - start) % 100000 == 0) {
printf("Position: %i\tMax Costs: %i\tMax Length: %i\tTotal length: %lld\n", i, maxcosts, maxlength, total_length);
maxcosts = 0;
maxlength = 0;
total_length = 0;
}
}
// Deal with the centromere - area of no coverage
if ((i > start) & (i < end - 1)) {
if (dload.get_region(i, min(i + step, end)).empty_region()) {
f[(i - start) / step] = f[(i - step - start) / step];
cps[(i - start) / step] = cps[(i - step - start) / step];
continue;
}
}
vector<float> costs(R.size());
vector<float> Fs(R.size());
for (int j = 0; j < (int)R.size(); j++) {
costs[j] = cost(dload.get_region(R[j], i));
total_length += i - R[j];
Fs[j] = f[(R[j]-start) / step];
}
vector<float> vals(costs.size());
for (int j = 0; j < (int)vals.size(); j++)
vals[j] = costs[j] + Fs[j];
auto min_ptr = min_element(vals.begin(), vals.end());
int idx = distance(vals.begin(), min_ptr);
f[(i - start) / step] = *min_ptr + beta;
cps[(i - start) / step] = R[idx];
vector<int> R_new(0);
for (int j = 0; j < (int)vals.size(); j++) {
if (vals[j] + K <= f[(i - start) / step]) {
R_new.push_back(R[j]);
}
}
R_new.push_back(i);
R = move(R_new);
}
i -= step;
vector<int> cps_n;
if (beta != 0) {
int pos;
cps_n.push_back(end);
cps_n.push_back(i);
pos = cps[(i - start) / step];
while (pos != start) {
cps_n.push_back(pos);
pos = cps[(pos - start) / step];
}
cps_n.push_back(start);
reverse(cps_n.begin(), cps_n.end());
// Take the unique elements
auto it = unique(cps_n.begin(), cps_n.end());
cps_n.resize(distance(cps_n.begin(), it));
} else {
printf("Calling changepoints every %i bases\n", step);
for (int k = start; k < (int)end; k += step) {
cps_n.push_back(k);
}
cps_n.push_back(end);
}
cout << "Num of changepoints: " << cps_n.size() << endl;
// Get the parameter values
vector<double> lambdas(cps_n.size()-1);
vector<double> eps(cps_n.size()-1);
vector<double> gammas(cps_n.size()-1);
vector<double> iotas(cps_n.size()-1);
vector<double> zetas(cps_n.size()-1);
vector<double> mus(cps_n.size()-1);
vector<double> sigmas(cps_n.size()-1);
vector<int> lengths(cps_n.size()-1);
int row = 0;
for (auto i = cps_n.begin(); i != cps_n.end() - 1; ++i) {
int left = *i;
int right = *(i+1);
SuffStats tot_stats = dload.get_region(left, right);
lambdas[row] = (double)tot_stats.N / tot_stats.L;
eps[row] = (tot_stats.tot_bases == 0) ? 0 : (double)tot_stats.tot_errors / tot_stats.tot_bases;
gammas[row] = (double)tot_stats.N_SNPs / tot_stats.L;
iotas[row] = (tot_stats.tot_bases == 0) ? 0 : (double)tot_stats.indels / tot_stats.tot_bases;
zetas[row] = (tot_stats.N == 0) ? 0 : (double)tot_stats.zero_mapq / tot_stats.N;
mus[row] = (tot_stats.n_inserts == 0) ? 0 : (double)tot_stats.inserts_sum / tot_stats.n_inserts;
sigmas[row] = (tot_stats.n_inserts > 0) ? 0 : sqrt((tot_stats.inserts_sumsq - pow((long long)tot_stats.inserts_sum,2)) / (tot_stats.n_inserts - 1));
lengths[row] = right - left;
row++;
}
if(t.joinable())
{
t.join();
}
FILE *f_out;
if (strcmp(output_file.c_str(), "") != 0) {
f_out = fopen(output_file.c_str(), "w");
if (f_out == nullptr) {
throw runtime_error("Could not open file " + output_file);
}
for (row = 0; row < (int)cps_n.size() - 2; row++) {
if ((lengths[row] != 0)) {
fprintf(f_out, "%i\t%i\t%0.8f\t%0.8f\t%0.8f\t%0.8f\t%0.8f\n", cps_n[row],
lengths[row], lambdas[row], eps[row], gammas[row], iotas[row], zetas[row]);
}
}
fclose(f_out);
}
}