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HisMaker.cpp
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HisMaker.cpp
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// Application includes
#include "HisMaker.hh"
#include "Genotyper.hh"
#include "Genome.hh"
#include "Interval.hh"
#include "FastaParser.hh"
#include "VcfParser.hh"
#include "Math/Math.h"
#include "Math/SpecFuncMathCore.h"
#include <limits>
#include <iomanip>
#ifdef USE_YEPPP
#include <yepCore.h>
#include <yepMath.h>
#include <yepLibrary.h>
#endif
static const int N_CHROM_MAX = 20000;
double my_gaus(double *x_arr,double *par)
{
double con = par[0];
double mean = par[1];
double sigma = par[2];
double x = x_arr[0];
double d = (x - mean)/sigma;
return con*TMath::Exp(-0.5*d*d);
}
void normalize(TH1 *his,double max = 1,double min = -1,double norm = -1)
{
int nbins = his->GetNbinsX(),n = 0;
double sum = 0;
if (max >= 0 && max <= 1) {
int max_bin = int(max*nbins + 0.5);
for (int b = 1;b <= max_bin;b++) {
sum += his->GetBinContent(b);
n++;
}
}
if (min >= 0 && min <= 1) {
int min_bin = int(min*nbins + 0.5);
for (int b = min_bin;b <= nbins;b++) {
sum += his->GetBinContent(b);
n++;
}
}
if (sum > 0) {
if (norm > 0) his->Scale(norm*n/sum);
else his->Scale(1./sum);
}
}
HisMaker::HisMaker(string rootFile,Genome *genome) :
root_file_name(rootFile),
io(rootFile),
inv_vals(NULL),sqrt_vals(NULL),tfuncs(NULL),
gen_his_signal(NULL),
gen_his_distr(NULL),
gen_his_distr_all(NULL),
canv_view(NULL),
refGenome_(genome)
{}
HisMaker::HisMaker(string rootFile,int binSize,bool useGCcorr,
Genome *genome): root_file_name(rootFile),
io(rootFile),
chromosome_len(1),
gen_his_signal(NULL),
gen_his_distr(NULL),
gen_his_distr_all(NULL),
_mean(0), _sigma(0),
_mean_all(0),_sigma_all(0),
canv_view(NULL),
refGenome_(genome)
{
if (binSize <= 0) {
cerr<<"Bin size "<<binSize<<" is not valid."<<endl;
return;
}
bin_size = binSize;
inv_bin_size = 1./bin_size;
dir_name = getDirName(bin_size);
// Statistics on RD
rd_gc_name = "rd_gc_"; rd_gc_name += binSize;
rd_gc_xy_name = "rd_gc_xy_"; rd_gc_xy_name += binSize;
rd_gc_GC_name = "rd_gc_GC_"; rd_gc_GC_name += binSize;
rd_gc_xy_GC_name = "rd_gc_xy_GC_"; rd_gc_xy_GC_name += binSize;
// Statistics on partitioning
TString suff = "";
if (useGCcorr) suff = "_GC";
rd_level = new TH1D("rd_level" + suff,"RD level",401,-0.5,400.5);
rd_level_merge = new TH1D("rd_level_merge" + suff,"RD level after merge",
401,-0.5,400.5);
frag_len = new TH1D("frag_len" + suff,"Partitioning fragment length",
1000,0.5,1000.5);
dl = new TH1D("dl" + suff, "Delta RD level",401,-0.5,400.5);
dl2 = new TH2D("dl2" + suff,"Delta RD level",
601,-300.5,300.5,601,-300.5,300.5);
// Precalculating inverse
inv_vals = new double[N_INV];
for (int i = 0;i < N_INV;i++) inv_vals[i] = 0;
// recalculating sqrt
sqrt_vals = new double[N_SQRT];
for (int i = 0;i < N_SQRT;i++) sqrt_vals[i] = 0;
// Allocating t-cumulative functions
tfuncs = new TF1*[N_FUNC];
for (int i = 0;i < N_FUNC;i++) tfuncs[i] = NULL;
}
HisMaker::~HisMaker()
{
delete[] inv_vals;
delete[] sqrt_vals;
delete[] tfuncs;
}
TH1* HisMaker::getHistogram(TString name,TString alt_name)
{
io.file.cd();
TDirectory *d = NULL;
d = (TDirectory*)io.file.Get(dir_name);
if (!d) {
cerr<<"Can't find directory '"<<dir_name<<"'."<<endl;
return NULL;
}
d->cd();
TH1 *his = (TH1*)d->Get(name);
if (!his) {
his = (TH1*)d->Get(alt_name);
if (!his) return NULL;
}
gROOT->cd();
TH1 *ret = (TH1*)his->Clone(his->GetName());
return ret;
}
TH1* HisMaker::getHistogram(TString root_file,TString dir,
TString name,TString alt_name)
{
TFile file(root_file);
if (file.IsZombie()) {
cerr<<"Can't open file '"<<root_file<<"'."<<endl;
return NULL;
}
TDirectory *d = NULL;
if (dir.Length() > 0) {
d = (TDirectory*)file.Get(dir);
if (!d) {
cerr<<"Can't find directory '"<<dir<<"'."<<endl;
return NULL;
}
d->cd();
} else d = &file;
TH1 *his = (TH1*)d->Get(name);
if (!his) {
his = (TH1*)d->Get(alt_name);
if (!his) return NULL;
}
gROOT->cd();
TH1 *ret = (TH1*)his->Clone(his->GetName());
file.Close();
return ret;
}
bool HisMaker::writeH(bool useDir,
TH1 *his1,TH1 *his2,TH1 *his3,
TH1 *his4,TH1 *his5,TH1 *his6)
{
io.file.cd();
if (useDir) {
TDirectory *dir = (TDirectory*)io.file.Get(dir_name);
if (!dir) {
cout<<"Making directory "<<dir_name<<" ..."<<endl;
dir = io.file.mkdir(dir_name);
dir->Write(dir_name);
}
if (!dir) {
cerr<<"Can't find/create directory '"<<dir_name<<"'."<<endl;
return false;
}
dir->cd();
}
if (his1) his1->Write(his1->GetName(),TObject::kOverwrite);
if (his2) his2->Write(his2->GetName(),TObject::kOverwrite);
if (his3) his3->Write(his3->GetName(),TObject::kOverwrite);
if (his4) his4->Write(his4->GetName(),TObject::kOverwrite);
if (his5) his5->Write(his5->GetName(),TObject::kOverwrite);
if (his6) his6->Write(his6->GetName(),TObject::kOverwrite);
return true;
}
double HisMaker::getInverse(int n)
{
if (n <= 0) return 0;
if (n >= N_INV) return 1./n;
if (inv_vals[n] == 0) inv_vals[n] = 1./n;
return inv_vals[n];
}
double HisMaker::getSqrt(int n)
{
if (n <= 0) return 0;
if (n >= N_SQRT) return TMath::Sqrt(n);
if (sqrt_vals[n] == 0) sqrt_vals[n] = TMath::Sqrt(n);
return sqrt_vals[n];
}
TF1 *HisMaker::getTFunction(int n)
{
if (n < 1) return NULL;
if (n >= N_FUNC || tfuncs[n] == NULL) {
TString desc = "ROOT::Math::tdistribution_cdf(x,";
desc += n; desc += ")";
TString name = "tcum_";name += n;
TF1 *f = new TF1(name.Data(),desc.Data(),-100,100);
if (n < N_FUNC) tfuncs[n] = f;
return f;
}
return tfuncs[n];
}
void HisMaker::getAverageVariance(double *rd,int start,int stop,
double &average,double &variance,int &n)
{
average = variance = 0;
n = 0;
for (int b = start;b <= stop;b++) {
average += rd[b];
variance += rd[b]*rd[b];
n++;
}
double over_n = 1./n;
average *= over_n;
variance = variance*over_n - average*average;
}
double HisMaker::testRegion(double value,double m,double s,int n)
{
if (s == 0) s = 1;
TF1 *cum_t = getTFunction(n - 1);
if (cum_t == NULL) {
cerr<<"4: Can't find proper t-function."<<endl;
return 1;
}
double x = (value - m)/sqrt(s)*getSqrt(n);
double p = cum_t->Eval(x); if (x > 0) p = 1 - p;
return p;
}
double HisMaker::testTwoRegions(double m1,double s1,int n1,
double m2,double s2,int n2,
double scale)
{
if (s1 == 0) s1 = 1;
if (s2 == 0) s2 = 1;
double tmp1 = s1*getInverse(n1),tmp2 = s2*getInverse(n2);
double s = TMath::Sqrt(tmp1 + tmp2);
double t = (m1 - m2)/s;
double tmp = (tmp1 + tmp2)*(tmp1 + tmp2)*(n1 - 1)*(n2 - 1);
tmp /= tmp1*tmp1*(n2 - 1) + tmp2*tmp2*(n1 - 1);
int ndf = int(tmp + 0.5);
TF1* cum_t = getTFunction(ndf);
if (cum_t == NULL) {
cerr<<"2: Can't find proper t-function."<<endl;
return 1;
}
double ret = cum_t->Eval(t);
if (t > 0) ret = 1 - ret;
ret *= scale*inv_bin_size*getInverse(n1 + n2);
return ret;
}
double HisMaker::getEValue(double mean,double sigma,double *rd,
int start,int end)
{
int n = end - start + 1;
double aver = 0,s = 0, over_n = 1./n;
for (int b = start;b <= end;b++) {
aver += rd[b];
s += rd[b]*rd[b];
}
aver *= over_n;
s = TMath::Sqrt(s*over_n - aver*aver);
if (s == 0) s = sigma*TMath::Sqrt(aver/mean);
if (s == 0) s = 1;
TF1* cum = getTFunction(n - 1);
double x = (aver - mean)*getSqrt(n)/s;
double ret = cum->Eval(x);
if (x > 0) ret = 1 - ret;
ret *= GENOME_SIZE_NORMAL*inv_bin_size*getInverse(end - start + 1);
return ret;
}
bool HisMaker::sameLevel(double l1, double l2)
{
return (TMath::Abs(l1 - l2) < PRECISION);
}
bool HisMaker::getRegionLeft(double *level,int n_bins,int bin,
int &start,int &stop)
{
if (bin < 0 || bin >= n_bins) return false;
start = bin; stop = bin;
while (start >= 0 && sameLevel(level[start],level[stop])) start--;
start++;
return true;
}
bool HisMaker::getRegionRight(double *level,int n_bins,int bin,
int &start,int &stop)
{
if (bin < 0 || bin >= n_bins) return false;
start = bin; stop = start;
while (stop < n_bins && sameLevel(level[start],level[stop])) stop++;
stop--;
return true;
}
void HisMaker::view(string *files,int n_files,bool useATcorr,bool useGCcorr)
{
TTimer *timer = new TTimer("gSystem->ProcessEvents();",50,kFALSE);
TString input = "";
while (input != "exit" && input != "quit") {
TString chrom = "",start = "",end = "",option = "",tmp;
istringstream sin(input.Data());
sin>>tmp;
if (tmp == "execute") {
TString obj_class,class_fun,args;
sin>>obj_class>>class_fun>>args;
executeROOT(obj_class,class_fun,args);
} else if (tmp == "gview" || tmp == "all") {
generateView(useATcorr,useGCcorr);
} else if (parseInput(input,chrom,start,end,option)) {
if (option == "genotype") {
for (int i = 0;i < n_files;i++) {
Genotyper gen(this,files[i],bin_size);
gen.printGenotype(chrom.Data(),
start.Atoi(),end.Atoi(),useATcorr,useGCcorr);
}
} else if (option == "print") {
int s = start.Atoi(), e = end.Atoi();
printRegion(chrom,s,e,useATcorr,useGCcorr);
} else if (option == "baf") {
int s = start.Atoi(), e = end.Atoi();
generateViewBAF(chrom,s,e,useATcorr,useGCcorr);
} else {
int s = start.Atoi(), e = end.Atoi();
if (option.IsDigit())
generateView(chrom,s,e,useATcorr,useGCcorr,files,option.Atoi());
else
generateView(chrom,s,e,useATcorr,useGCcorr,files);
}
}
timer->TurnOn();
timer->Reset();
input = Getline(">");
input.ReplaceAll("\n","\0");
input = input.Remove(TString::kBoth,' ');
timer->TurnOff();
}
delete timer;
delete canv_view;
exit(0);
}
void interateOverPrimitives(TList *list)
{
}
void HisMaker::executeROOT(TString obj_class,TString class_fun,TString args)
{
if (!canv_view) return;
TIter i1(canv_view->GetListOfPrimitives());
while (TPad *pad = (TPad*)i1.Next()) {
pad->cd();
TIter i2(pad->GetListOfPrimitives());
while (TObject *obj = i2.Next())
if (obj->ClassName() == obj_class) obj->Execute(class_fun,args);
if (pad->ClassName() == obj_class) pad->Execute(class_fun,args);
pad->Update();
}
if (canv_view->ClassName() == obj_class) canv_view->Execute(class_fun,args);
canv_view->cd();
canv_view->Update();
}
void HisMaker::printRegion(TString chrom,int start,int end,
bool useATcorr,bool useGCcorr)
{
TString alt_chr = Genome::canonicalChromName(chrom.Data());
if (alt_chr == chrom) alt_chr = Genome::extendedChromName(chrom.Data());
TString name = getRawSignalName(chrom,bin_size);
TString alt_name = getRawSignalName(alt_chr,bin_size);
TString name_his = getSignalName(chrom,bin_size,false,false);
TString alt_name_his = getSignalName(alt_chr,bin_size,false,false);
TString name_corr = getSignalName(chrom,bin_size,useATcorr,useGCcorr);
TString alt_name_corr = getSignalName(alt_chr,bin_size,useATcorr,useGCcorr);
TString name_partition = getPartitionName(chrom,bin_size,
useATcorr,useGCcorr);
TString alt_name_part = getPartitionName(alt_chr,bin_size,
useATcorr,useGCcorr);
TString name_merge = name_partition + "_merge";
TString alt_name_merge = alt_name_part + "_merge";
TString dir = getDirName(bin_size);
TH1 *raw = getHistogram(root_file_name,dir,name, alt_name);
TH1 *his = getHistogram(root_file_name,dir,name_his, alt_name_his);
TH1 *hisc = getHistogram(root_file_name,dir,name_corr, alt_name_corr);
TH1 *hisp = getHistogram(root_file_name,dir,name_partition,alt_name_part);
TH1 *hism = getHistogram(root_file_name,dir,name_merge, alt_name_merge);
TH1 *his_gc = getHistogram(getGCName(chrom,bin_size));
if (!his_gc) his_gc = getHistogram(getGCName(alt_chr,bin_size));
if (his)
for (int i = 1;i <= his->GetNbinsX();i++) {
int s = his->GetBinLowEdge(i);
int e = s + his->GetBinWidth(i);
if ((s >= start || e >= start) && (e <= end || s <= end)) {
cout<<s<<"\t";
if (his) cout<<his->GetBinContent(i); else cout<<-1;
cout<<"\t";
if (hisc) cout<<hisc->GetBinContent(i); else cout<<-1;
cout<<"\t";
if (hisp) cout<<hisp->GetBinContent(i); else cout<<-1;
cout<<"\t";
if (hism) cout<<hism->GetBinContent(i); else cout<<-1;
cout<<"\t";
if (his_gc) cout<<his_gc->GetBinContent(i); else cout<<-1;
cout<<endl;
}
}
return;
}
void HisMaker::generateView(bool useATcorr,bool useGCcorr) // Global view
{
if (canv_view) {
delete canv_view;
canv_view = NULL;
}
if (!canv_view) {
TStyle *st = new TStyle("st","st");
st->SetOptStat(false); // No box with statistics
st->SetOptTitle(false); // No box with title
gROOT->SetStyle("st");
canv_view = new TCanvas("canv","canv",1400,850);
canv_view->SetFillColor(kWhite);
canv_view->SetBorderMode(0); // No borders
}
canv_view->Divide(6,4);
double mean,sigma;
TH1 *rd_his = getHistogram(getDistrName("chr1",bin_size,
useATcorr,useGCcorr));
getMeanSigma(rd_his,mean,sigma);
TString chroms[24] = {"chr1","chr2","chr3","chr4","chr5","chr6","chr7",
"chr8","chr9","chr10","chr11","chr12","chr13","chr14",
"chr15","chr16","chr17","chr18","chr19","chr20",
"chr21","chr22","chrX","chrY"};
for (int i = 0;i < 24;i++) {
TString chrom = chroms[i];
TString file_name = root_file_name;
TString alt_chr = Genome::canonicalChromName(chrom.Data());
if (alt_chr == chrom) alt_chr = Genome::extendedChromName(chrom.Data());
TString name = getRawSignalName(chrom,bin_size);
TString alt_name = getRawSignalName(alt_chr,bin_size);
TString name_his = getSignalName(chrom,bin_size,false,false);
TString alt_name_his = getSignalName(alt_chr,bin_size,false,false);
TString name_corr = getSignalName(chrom,bin_size,useATcorr,useGCcorr);
TString alt_name_corr = getSignalName(alt_chr,bin_size,useATcorr,useGCcorr);
TString name_partition = getPartitionName(chrom,bin_size,
useATcorr,useGCcorr);
TString alt_name_part = getPartitionName(alt_chr,bin_size,
useATcorr,useGCcorr);
TString name_merge = name_partition + "_merge";
TString alt_name_merge = alt_name_part + "_merge";
TString dir = getDirName(bin_size);
TH1 *raw = getHistogram(file_name,dir,name, alt_name);
TH1 *his = getHistogram(file_name,dir,name_his, alt_name_his);
TH1 *hisc = getHistogram(file_name,dir,name_corr, alt_name_corr);
TH1 *hisp = getHistogram(file_name,dir,name_partition,alt_name_part);
TH1 *hism = getHistogram(file_name,dir,name_merge, alt_name_merge);
TVirtualPad *pad = canv_view->cd(i + 1);
pad->SetFillColor(kWhite);
pad->SetLineColor(kWhite);
pad->SetFrameLineColor(kWhite);
pad->SetFrameBorderMode(0);
TString title = file_name; title.ReplaceAll(".root","");
drawHistograms(chrom,0,250e+6,0,title,pad,raw,his,hisc,hisp,hism);
if (hisc) {
hisc->GetYaxis()->SetRangeUser(0,2*mean);
hisc->SetLineWidth(1);
}
if (raw) raw->SetLineWidth(1);
if (his) his->SetLineWidth(1);
if (hisc) hisc->SetLineWidth(1);
if (hisp) hisp->SetLineWidth(1);
if (hism) hism->SetLineWidth(1);
if (!his || !hisc || !hisp || !hism) {
cout<<"For file '"<<file_name<<"'."<<endl;
if (!his)
cout<<"Can't find RD histogram for '"<<chrom<<"'."<<endl;
else if (!hisc)
cout<<"Can't find corrected RD histogram for '"<<chrom<<"'."<<endl;
else if (!hisp)
cout<<"Can't find partitioning histogram for '"<<chrom<<"'."<<endl;
else if (!hism)
cout<<"Can't find merging histogram for '"<<chrom<<"'."<<endl;
}
}
canv_view->cd(0);
canv_view->Update();
}
void HisMaker::generateView(TString chrom,int start,int end,
bool useATcorr,bool useGCcorr,
string *files,int win)
{
if (win <= 0) {
win = 3*(end - start + 1);
if (win < 10000) win = 10000;
}
int n_files = 1;
if (files != NULL) {
n_files = 0;
while (n_files < 16 && files[n_files].length() > 0)
n_files++;
}
if (!canv_view) {
TStyle *st = new TStyle("st","st");
st->SetOptStat(false); // No box with statistics
st->SetOptTitle(false); // No box with title
gROOT->SetStyle("st");
canv_view = new TCanvas("canv","canv",1400,850);
canv_view->SetFillColor(kWhite);
canv_view->SetBorderMode(0); // No borders
if (n_files == 2) canv_view->Divide(1,2);
else if (n_files == 3) canv_view->Divide(1,3);
//else if (n_files == 4) canv_view->Divide(2,2);
else if (n_files == 4) canv_view->Divide(1,4);
else if (n_files == 5 ||
n_files == 6) canv_view->Divide(2,3);
else if (n_files == 8) canv_view->Divide(2,4);
else if (n_files == 7 ||
n_files == 9) canv_view->Divide(3,3);
else if (n_files > 9) canv_view->Divide(4,4);
}
TString title = chrom; title += ":";
title += start; title += "-";
title += end;
canv_view->SetTitle(title);
TString alt_chr = Genome::canonicalChromName(chrom.Data());
if (alt_chr == chrom) alt_chr = Genome::extendedChromName(chrom.Data());
TString name = getRawSignalName(chrom,bin_size);
TString alt_name = getRawSignalName(alt_chr,bin_size);
TString name_his = getSignalName(chrom,bin_size,false,false);
TString alt_name_his = getSignalName(alt_chr,bin_size,false,false);
TString name_corr = getSignalName(chrom,bin_size,useATcorr,useGCcorr);
TString alt_name_corr = getSignalName(alt_chr,bin_size,useATcorr,useGCcorr);
TString name_partition = getPartitionName(chrom,bin_size,
useATcorr,useGCcorr);
TString alt_name_part = getPartitionName(alt_chr,bin_size,
useATcorr,useGCcorr);
TString name_merge = name_partition + "_merge";
TString alt_name_merge = alt_name_part + "_merge";
for (int i = 0;i < n_files;i++) {
TString file_name = root_file_name;
if (files) file_name = files[i];
TString dir = getDirName(bin_size);
TH1 *raw = getHistogram(file_name,dir,name, alt_name);
TH1 *his = getHistogram(file_name,dir,name_his, alt_name_his);
TH1 *hisc = getHistogram(file_name,dir,name_corr, alt_name_corr);
TH1 *hisp = getHistogram(file_name,dir,name_partition,alt_name_part);
TH1 *hism = getHistogram(file_name,dir,name_merge, alt_name_merge);
TVirtualPad *pad = canv_view->cd(i + 1);
pad->SetFillColor(kWhite);
pad->SetLineColor(kWhite);
pad->SetFrameLineColor(kWhite);
pad->SetFrameBorderMode(0);
TString title = file_name; title.ReplaceAll(".root","");
//if (his)
drawHistograms(chrom,start,end,win,title,pad,raw,his,hisc,hisp,hism);
if (!his || !hisc || !hisp || !hism) {
cout<<"For file '"<<file_name<<"'."<<endl;
if (!his)
cout<<"Can't find RD histogram for '"<<chrom<<"'."<<endl;
else if (!hisc)
cout<<"Can't find corrected RD histogram for '"<<chrom<<"'."<<endl;
else if (!hisp)
cout<<"Can't find partitioning histogram for '"<<chrom<<"'."<<endl;
else if (!hism)
cout<<"Can't find merging histogram for '"<<chrom<<"'."<<endl;
}
}
canv_view->cd(0);
canv_view->Update();
}
void HisMaker::generateViewBAF(TString chrom,int start,int end,
bool useATcorr,bool useGCcorr)
{
int win = 1*(end - start + 1);
if (win < 10000) win = 10000;
if (canv_view) delete canv_view;
TStyle *st = new TStyle("st","st");
st->SetOptStat(false); // No box with statistics
st->SetOptTitle(false); // No box with title
gROOT->SetStyle("st");
canv_view = new TCanvas("canv","canv",900,900);
canv_view->SetFillColor(kWhite);
canv_view->SetBorderMode(0); // No borders
canv_view->Divide(1,2);
TString title = chrom; title += ":";
title += start; title += "-";
title += end;
canv_view->SetTitle(title);
TString alt_chr = Genome::canonicalChromName(chrom.Data());
if (alt_chr == chrom) alt_chr = Genome::extendedChromName(chrom.Data());
TString name = getRawSignalName(chrom,bin_size);
TString alt_name = getRawSignalName(alt_chr,bin_size);
TString name_his = getSignalName(chrom,bin_size,false,false);
TString alt_name_his = getSignalName(alt_chr,bin_size,false,false);
TString name_corr = getSignalName(chrom,bin_size,useATcorr,useGCcorr);
TString alt_name_corr = getSignalName(alt_chr,bin_size,useATcorr,useGCcorr);
TString name_partition = getPartitionName(chrom,bin_size,
useATcorr,useGCcorr);
TString alt_name_part = getPartitionName(alt_chr,bin_size,
useATcorr,useGCcorr);
TString name_merge = name_partition + "_merge";
TString alt_name_merge = alt_name_part + "_merge";
TString file_name = root_file_name;
TString dir = getDirName(bin_size);
TH1 *raw = getHistogram(file_name,dir,name, alt_name);
TH1 *his = getHistogram(file_name,dir,name_his, alt_name_his);
TH1 *hisc = getHistogram(file_name,dir,name_corr, alt_name_corr);
TH1 *hisp = getHistogram(file_name,dir,name_partition,alt_name_part);
TH1 *hism = getHistogram(file_name,dir,name_merge, alt_name_merge);
TVirtualPad *pad = canv_view->cd(1);
pad->SetFillColor(kWhite);
pad->SetLineColor(kWhite);
pad->SetFrameLineColor(kWhite);
pad->SetFrameBorderMode(0);
title = file_name; title.ReplaceAll(".root","");
drawHistograms(chrom,start,end,win,title,pad,raw,his,hisc,hisp,hism);
if (hisc) {
double mean,sigma;
TH1 *rd_his = getHistogram(getDistrName("chr1",bin_size,
useATcorr,useGCcorr));
getMeanSigma(rd_his,mean,sigma);
hisc->GetYaxis()->SetRangeUser(0,2*mean);
hisc->SetLineWidth(1);
}
pad = canv_view->cd(2);
pad->SetFillColor(kWhite);
pad->SetLineColor(kWhite);
pad->SetFrameLineColor(kWhite);
pad->SetFrameBorderMode(0);
title = "BAF";
stringstream sn;
sn<<"snp_"<<chrom;
io.file.cd();
TTree *vcftree = (TTree*)io.file.Get(sn.str().c_str());
if (!vcftree) {
cerr<<"Can't find VCF tree for chromosome '"<<chrom<<"' in file '"
<<root_file_name<<"'."<<endl;
return;
}
if(vcftree) drawHistogramsBAF(chrom,start,end,win,title,pad,his,vcftree);
delete vcftree;
canv_view->cd(0);
canv_view->Update();
}
void HisMaker::drawHistogramsBAF(TString chrom,int start,int end,
int win,TString title,
TVirtualPad *pad,
TH1 *main,TTree *vcftree)
{
int s = start - win, e = end + win;
main->Draw();
main->GetXaxis()->SetRangeUser(s,e);
main->GetXaxis()->SetTitle(chrom);
main->GetYaxis()->SetRangeUser(0,1.05);
main->GetYaxis()->SetTitle(title);
main->SetLineWidth(3);
main->SetLineWidth(0);
vcftree->SetMarkerSize(0.2);
vcftree->SetMarkerStyle(21);
vcftree->SetMarkerColor(kBlue);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==1 && (flag&2)","same");
vcftree->SetMarkerColor(kCyan);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==1 && !(flag&2)","same");
vcftree->SetMarkerColor(kRed);
vcftree->Draw("nref/(nref+nalt):position","_gt%4==2 && (flag&2)","same");
vcftree->SetMarkerColor(kOrange);
vcftree->Draw("nref/(nref+nalt):position","_gt%4==2 && !(flag&2)","same");
vcftree->SetMarkerColor(kGreen);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==0 && (flag&2)","same");
vcftree->SetMarkerColor(kYellow);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==0 && !(flag&2)","same");
vcftree->SetMarkerColor(kBlack);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==3 && (flag&2)","same");
vcftree->SetMarkerColor(kGray);
vcftree->Draw("nalt/(nref+nalt):position","_gt%4==3 && !(flag&2)","same");
}
void HisMaker::genotype(string *files,int n_files,
bool useATcorr,bool useGCcorr)
{
Genotyper **gs = new Genotyper*[n_files];
for (int i = 0;i < n_files;i++)
gs[i] = new Genotyper(this,files[i],bin_size);
TTimer *timer = new TTimer("gSystem->ProcessEvents();",50,kFALSE);
TString input = "";
while (input != "exit" && input != "quit") {
TString chrom = "",start = "",end = "",option = "";
if (parseInput(input,chrom,start,end,option)) {
if (option == "view") {
generateView(chrom,start.Atoi(),end.Atoi(),useATcorr,useGCcorr,files);
} else {
for (int i = 0;i < n_files;i++)
gs[i]->printGenotype(chrom.Data(),
start.Atoi(),end.Atoi(),
useATcorr,useGCcorr);
}
}
timer->TurnOn();
timer->Reset();
input = Getline(">");
input.ReplaceAll("\n","\0");
input = input.Remove(TString::kBoth,' ');
timer->TurnOff();
}
for (int i = 0;i < n_files;i++) delete gs[i];
delete[] gs;
delete timer;
exit(0);
}
void HisMaker::pe_for_file(string file,string *bams,int n_bams,
double over,double qual)
{
static const int max_len = 2500;
static const int max_ses = 10000;
int ses[max_ses];
ifstream fin(file.c_str());
char *str = new char[max_len];
string type(""), coor(""),tmp("");
while (!fin.eof()) {
fin.getline(str,max_len);
istringstream sin(str);
if (sin>>type && sin>>coor) {
//cout<<"type = "<<type<<"\t"<<"coor = "<<coor<<endl;
int n_pe = 0;
TString input(coor);
if (type == "deletion") input.Append(" del");
if (type == "duplication") input.Append(" tdup");
n_pe = extract_pe(input,bams,n_bams,over,qual,false,ses);
if (n_pe == 0) cout<<str<<"\t"<<n_pe<<endl;
else {
int n = max_ses; if (2*n_pe < n) n = 2*n_pe;
int s = ses[0], e = ses[1];
for (int i = 2;i < n;i++) {
if (ses[i] > s) s = ses[i];
i++;
if (ses[i] < e) e = ses[i];
}
TString chrom(""),start(""),end(""),option(""),new_coor("");
if (!parseInput(input,chrom,start,end,option)) { continue; }
new_coor = chrom; new_coor += ":"; new_coor += s;
new_coor += "-"; new_coor += e;
cout<<type<<"\t"<<new_coor;
//if (sin>>tmp) cout<<"\t"<<e - s;
while (sin>>tmp) cout<<"\t"<<tmp;
cout<<"\t"<<n_pe<<endl;
}
}
}
return;
}
void HisMaker::pe(string *bams,int n_bams,double over,double qual)
{
TTimer *timer = new TTimer("gSystem->ProcessEvents();",50,kFALSE);
TString input = "";
while (input != "exit" && input != "quit") {
int i = 0,n = input.Length();
//cout<<"Working on => '"<<input<<"' ..."<<endl;
extract_pe(input,bams,n_bams,over,qual,true);
timer->TurnOn();
timer->Reset();
input = Getline(">");
input.ReplaceAll("\n","\0");
input = input.Remove(TString::kBoth,' ');
timer->TurnOff();
}
delete timer;
exit(0);
}
int HisMaker::extract_pe(TString input,
string *bams,int n_bams,double over,double qual,
bool do_print,int *ses)
{
int ret = 0;
TString chrom = "",start = "",end = "",option = "";
if (!parseInput(input,chrom,start,end,option)) { return ret; }
int MIN_WIN = 2000,MAX_WIN = 20000;
map<string,int> qual_hash;
int s = start.Atoi(), e = end.Atoi(), l = e - s + 1;
bool forDel = option.Contains("del", TString::kIgnoreCase);
bool forTdup = option.Contains("tdup",TString::kIgnoreCase);
if (forDel || forTdup) {
int win = l;
if (win < MIN_WIN) win = MIN_WIN;
if (win > MAX_WIN) win = MAX_WIN;
int srange = s - win,erange = e + win;
qual_hash.clear();
for (int f = 0;f < n_bams;f++) {
if (do_print) cout<<"\t"<<bams[f]<<endl;
AliParser *parser = new AliParser(bams[f].c_str(),true);
int chr_index = parser->scrollTo(chrom.Data(),srange);
if (chr_index < 0) {
chrom.ToUpper();
if (chrom(0,3) == "CHR") chrom = chrom(3,2);
else if (chrom(0,5) == "CHROM") chrom = chrom(5,2);
chr_index = parser->scrollTo(chrom.Data(),srange);
if (chr_index < 0) {
cerr<<"Nowhere to scroll."<<endl;
delete parser;
continue;
}
}
while (parser->parseRecord()) {
if (parser->isUnmapped() || parser->isNextUnmapped()) continue;
int frg_len = parser->getFragmentLength();
int rs = parser->getStart(), re = parser->getEnd();
if (parser->getChromosomeIndex() != chr_index ||
rs > erange) break;
int fs,fe;
bool go_further = false;
if (frg_len > 0)
if ((forDel &&
!parser->isReversed() && parser->isNextReversed()) ||
(forTdup &&
parser->isReversed() && !parser->isNextReversed())) {
fs = rs;
fe = fs + frg_len;
go_further = true;
}
if (frg_len < 0)
if ((forDel &&
parser->isReversed() && !parser->isNextReversed()) ||
(forTdup &&
!parser->isReversed() && parser->isNextReversed())) {
fe = re;
fs = fe + frg_len;
go_further = true;
}
if (!go_further) continue;
int fl = fe - fs + 1;
int smax = s; if (fs > smax) smax = fs;
int emin = e; if (fe < emin) emin = fe;
int o = emin - smax + 1;
if (o < over*l || o < over*fl) continue;
string name = parser->getQueryName();
map<string,int>::iterator iter = qual_hash.find(name);
if (iter == qual_hash.end()) { // First read
qual_hash[name] = parser->getQuality();
} else { // Second read
int other_qual = iter->second;
if (other_qual >= qual && parser->getQuality() >= qual) {
if (do_print) cout<<input<<" "
<<parser->getQueryName()<<" "<<fs<<" "<<fe<<" "
<<other_qual<<" "<<parser->getQuality()<<endl;
if (ses) {
ses[2*ret] = fs;
ses[2*ret + 1] = fe;
}
ret++;
}
}
}
delete parser;
}
}
return ret;
}
bool HisMaker::parseInput(TString &input,TString &chrom,
TString &start,TString &end,TString &option)
{
if (input.Length() <= 0) return false;
int i = 0;
chrom = start = end = option = "";
while (i < input.Length() && input[i] == ' ') i++; // Space
while (i < input.Length() && input[i] != ':' && input[i] != ' ')
chrom += input[i++]; i++;
while (i < input.Length() && input[i] == ' ') i++; // Space
while (i < input.Length() && input[i] != '-' && input[i] != ' ')
start += input[i++]; i++;
while (i < input.Length() && input[i] == ' ') i++; // Space
while (i < input.Length() && input[i] != ' ')
end += input[i++];
while (i < input.Length() && input[i] == ' ') i++; // Space
while (i < input.Length() && input[i] != ' ')
option += input[i++];
TString s = "", e = "", o = "";
bool ret = true;
if (!start.IsDigit() && start.Length() > 1) {
s = start(0,start.Length() - 1);
char z = start[start.Length() - 1];
if (s.IsDigit()) {
if (z == 'M' || z == 'm') s += "000000";
else if (z == 'K' || z == 'k') s += "000";
else s += z;
}
} else s = start;
if (!s.IsDigit()) {
cout<<"Invalid start '"<<start<<"'."<<endl;
ret = false;
}
start = s;
if (!end.IsDigit() && end.Length() > 1) {
e = end(0,end.Length() - 1);
char z = end[end.Length() - 1];
if (e.IsDigit()) {
if (z == 'M' || z == 'm') e += "000000";
else if (z == 'K' || z == 'k') e += "000";
else e += z;
}
} else e = end;
if (!e.IsDigit()) {
cout<<"Invalid end '"<<end<<"'."<<endl;
ret = false;
}
end = e;
if (!option.IsDigit() && option.Length() > 1) {
o = option(0,option.Length() - 1);
char z = option[option.Length() - 1];
if (o.IsDigit()) {
if (z == 'M' || z == 'm') o += "000000";
else if (z == 'K' || z == 'k') o += "000";
else o += z;
option = o;
}
}