double LocalCorrTrack(int pos1, int pos2, bool cmpl1, bool cmpl2, bool rnd){
if(!outLC) return 0;
if(smoothProf1==0) getMem(smoothProf1,profWithFlanksLength+10, "storeCorrTrack");
if(lcTmp==0) getMem(lcTmp,profWithFlanksLength+10, "storeCorrTrack");
calcSmoothProfile(0, cmpl1); // calculate smooth ptrofile c=\int f*\rho for the second profile (y)
memcpy(smoothProf1,LCorrelation.re,profWithFlanksLength*sizeof(double));
calcSmoothProfile(1, cmpl2); // calculate smooth profile for the first profile (x)
smoothProf2=LCorrelation.re;
double av=0;
double sd=track1->sd0*track2->sd0;
for(int i=LFlankProfSize; i<profWithFlanksLength-RFlankProfSize; i++){
double x=smoothProf1[i] /profWithFlanksLength; //the smoothed profile for x
double y=smoothProf2[i] /profWithFlanksLength; //the smoothed profile for y
double lc=0; //local correlation
// int ax=bTrack1.getBVal(pos1+i-LFlankProfSize,cmpl1);
// int ay=bTrack2.getBVal(pos2+i-LFlankProfSize,cmpl2);
// if(ax==NA || ay==NA) {lcTmp[i]=NA; continue;}
// double x0=(ax==NA)?0: bTrack1.getVal(ax), y0=(ay==NA)?0: bTrack2.getVal(ay);
// lc=0.5*(x0*y+y0*x);
lc=x*y/sd;
lc=normLC(lc);
lcTmp[i]=lc; av+=lc; // We use wCorrelation.im as a tmp buffer
dHist.add(lc,rnd ? 1:0);
}
av/=profileLength;
if(!rnd) addLCProf(lcTmp,pos1);
return av;
}
//==================== Make correlation track
double storeCorrTrack(int pos, bool cmpl1, bool cmpl2){
if(outWIG==NONE) return 0;
getMem0(corr2,profWithFlanksLength+10, "storeCorrTrack");
kern->fx.re[0]=kern->fx.re0;
kern->fy.re[0]=kern->fy.re0;
kern->ft.re[0]=kern->ft.re0;
calcSmoothProfile(1, cmpl2);
memcpy(corr2,wCorrelation.re,profWithFlanksLength*sizeof(double));
calcSmoothProfile(0, cmpl1);
double av=0;
double sd=bTrack1.sd0*bTrack2.sd0;
for(int i=LFlankProfSize; i<profWithFlanksLength-RFlankProfSize; i++){
double x=wCorrelation.re[i]/profWithFlanksLength;
double y=corr2[i] /profWithFlanksLength;
if((outWIG & WIG_CENTER) == WIG_CENTER) {x-=bTrack1.av0; y-=bTrack2.av0;}
if((outWIG & WIG_MULT) == WIG_MULT) wCorrelation.re[i]=x*y/sd;
if((outWIG & WIG_SUM ) == WIG_SUM ){
double xx=kern->fx.datRe[i], yy=kern->fy.datRe[i];
if((outWIG & WIG_CENTER) == WIG_CENTER) {xx-=bTrack1.av0; yy-=bTrack2.av0;}
wCorrelation.re[i]=0.5*(xx*x+yy*y)/sd;
av+=wCorrelation.re[i];
}
}
av/=profileLength;
wigCorr.addArray(wCorrelation.re+LFlankProfSize,pos);
return av;
}
void smooth(const char *fname){
outLC=1;
initOutLC();
int l=profileLength;
bTrack *tr=new bTrack(fname);
for(int i=0,k=0; i<l; i+=wProfStep,k++){
double d;
d=100.*k/(l/wProfStep);
if(k%10000 ==0) verb("\nSmooother: %4.1f%% (%6i/%i) ",d,k,l/wProfStep);
else if(k%1000 ==0) verb(".");
double *pr1=tr->getProfile(i,0); // decode the first profile. Decoder uses hasCompl and complFg flags and combines profiles
if(smoothProf==0) getMem(smoothProf,profWithFlanksLength+10, "storeCorrTrack");
if(smTmp==0) getMem(smTmp,profWithFlanksLength+10, "storeCorrTrack");
kern->fftx(pr1,0);
calcSmoothProfile(&(kern->fx),0, 0); // calculate smooth ptrofile c=\int f*\rho
addLCProf(LCorrelation.re,i);
}
char pfil[4096],wfil[4096];
makeFileName(pfil,trackPath,fname);
char *s=strrchr(pfil,'/'); if(s==0) s=wfil;
s=strrchr(s,'.'); if(s) *s=0;
sprintf(wfil,"%s_sm.bgr",pfil);
//================ normalize
double tt=0,ee=0,dd=0,nn=0;
for(int i=0; i<l; i++) {
double x=lcProfile->get(i);
ee+=x; nn++; dd+=x*x;
}
tt=ee; ee/=nn; dd=dd/nn-ee*ee; dd=sqrt(dd);
for(int i=0; i<l; i++) {
double x=lcProfile->get(i);
if(smoothZ){if((x-ee)/dd < smoothZ) x=0;}
else {x=x*tr->total/tt/binSize;}
lcProfile->set(i,x);
}
FILE *f=gopen(wfil,"w");
char b[4096]; strcpy(b,fname);
s=strrchr(b,'.'); if(s) *s=0;
s=strchr(b,'/'); if(s==0) s=b;
fprintf(f,"track type=bedGraph name=\"%s_Sm\" description=\"Smoothed track. Width=%.0f\"\n",s, kernelSigma);
verb("\n Write Smooth profile...\n");
writeBedGr(f,lcProfile, NA, NA);
verb(" Done\n");
}
//============= calculate smoothed profile c=\int f*\rho
void calcSmoothProfile(int k, bool cmpl){
Fourier *fx= (k==1) ? &kern->fy: &kern->fx;
calcSmoothProfile(fx,k,cmpl);
}