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SVDcalculator.cpp
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SVDcalculator.cpp
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#include "SVDcalculator.h"
#include "Eigen/Dense"
#include "libVcf/libVcfFile.h"
#include <Error.h>
#include <fstream>
#include <unordered_map>
#include <unordered_set>
using namespace libVcf;
using namespace Eigen;
SVDcalculator::SVDcalculator()
{
numIndividual = 0;
numMarker = 0;
}
SVDcalculator::~SVDcalculator() {}
int SVDcalculator::ReadVcf(const std::string &VcfPath,
std::vector<std::vector<char> >& genotype,
int & nSamples, int& nMarkers) {
try {
int maxPhred=255;
VcfFile *pVcf = new VcfFile;
pVcf->bSiteOnly = false;
pVcf->bParseGenotypes = false;
pVcf->bParseDosages = false;
pVcf->bParseValues = true;
pVcf->openForRead(VcfPath.c_str());
// check the sanity of data
if (pVcf->getSampleCount() == 0) {
throw VcfFileException("No individual genotype information exist in the input VCF file %s",
VcfPath.c_str());
}
std::unordered_set<std::string> acceptChr={"1","2","3","4","5","6","7","8","9","10",
"11","12","13","14","15","16","17","18","19","20",
"21","22",
"chr1", "chr2", "chr3","chr4","chr5","chr6","chr7","chr8", "chr9","chr10",
"chr11","chr12","chr13","chr14","chr15","chr16","chr17", "chr18","chr19",
"chr20","chr21","chr22"};
nSamples = pVcf->getSampleCount();
nMarkers = 0;
char refAllele;
char altAllele;
VcfMarker *pMarker = new VcfMarker;
String markerName;
String prevMarkerName;
while (pVcf->iterateMarker()) {//for each marker
pMarker = pVcf->getLastMarker();
markerName.printf("%s:%d", pMarker->sChrom.c_str(), pMarker->nPos);
if(prevMarkerName==markerName)
{
error("Duplicated Marker: %s",markerName.c_str());
}
if(pMarker->asFilters.Length()>1 || pMarker->asFilters[0]!="PASS")
{
warning("Skip filtered (%s) marker: %s",pMarker->asFilters[0].c_str(), markerName.c_str());
continue;
}
if(pMarker->asAlts.Length()>1)
{
warning("Skip non-Biallelic marker: %s",markerName.c_str());
continue;
}
if(pMarker->sRef.Length()>1 or pMarker->asAlts[0].Length()>1 )
{
warning("Skip non-SNP marker: %s",markerName.c_str());
continue;
}
if(acceptChr.find(std::string(pMarker->sChrom.c_str())) == acceptChr.end())
{
warning("Skip non-autosome marker: %s",markerName.c_str());
continue;
}
refAllele=pMarker->sRef[0];
altAllele=pMarker->asAlts[0][0];
int PLidx = pMarker->asFormatKeys.Find("PL");
int PLGLGTflag = 0;//0 for PL, 1 for GL, 2 for GT
if (PLidx < 0) {
PLidx = pMarker->asFormatKeys.Find("GL");
if (PLidx >= 0) PLGLGTflag = 1;//found GL
else {
PLidx = pMarker->asFormatKeys.Find("GT");
if(PLidx >= 0) PLGLGTflag = 2;//found GT
else throw VcfFileException("Cannot recognize GT, GL or PL key in FORMAT field");
}
}
int formatLength = pMarker->asFormatKeys.Length();
int idx11 = 0, idx12 = 1, idx22 = 2;
StringArray phred;
long phred11 = 0;
long phred12 = 0;
long phred22 = 0;
std::vector<char> perMarkerGeno(nSamples,-1);
int nMissingGenoSamples = 0;
for (int i = 0; i < nSamples; i++)//for each individual
{
if(nMarkers==0) Samples.push_back(pVcf->getSampleID(i).c_str());
if(PLGLGTflag==0)//found PL
{
phred.ReplaceTokens(pMarker->asSampleValues[PLidx + i * formatLength], ",");
if (phred.Length() == 3 && phred[0] != ".") {
phred11 = phred[idx11].AsInteger();
phred12 = phred[idx12].AsInteger();
phred22 = phred[idx22].AsInteger();
}
else nMissingGenoSamples++;
}
else if(PLGLGTflag == 1)//found GL
{
phred.ReplaceTokens(pMarker->asSampleValues[PLidx + i * formatLength], ",");
if (phred.Length() == 3 && phred[0] != ".") {
phred11 =
static_cast<int>(-10. * phred[idx11].AsDouble());
phred12 =
static_cast<int>(-10. * phred[idx12].AsDouble());
phred22 =
static_cast<int>(-10. * phred[idx22].AsDouble());
}
else nMissingGenoSamples++;
}
else//found GT
{
phred.ReplaceTokens(pMarker->asSampleValues[PLidx + i * formatLength], "|/");
if (phred.Length() == 3 && phred[0] != ".") {
long geno =
phred[0].AsInteger() + phred[1].AsInteger();
if (geno == 0) {
phred11 = 0;
phred12 = 30;
phred22 = 50;
} else if (geno == 1) {
phred11 = 50;
phred12 = 0;
phred22 = 50;
} else {
phred11 = 50;
phred12 = 30;
phred22 = 0;
}
}
else nMissingGenoSamples++;
}
if ((phred11 < 0) || (phred12 < 0) || (phred22 < 0)) {
error("Negative PL or Positive GL observed");
}
if (phred11 > maxPhred) phred11 = maxPhred;
if (phred12 > maxPhred) phred12 = maxPhred;
if (phred22 > maxPhred) phred22 = maxPhred;
//
// printf("phred scores are %f, %f, %f;\tphred11/12/22 %d, %d, %d\n", phred[idx11].AsDouble(), phred[idx12].AsDouble(), phred[idx22].AsDouble(),phred11,phred12,phred22);
int minGeno = -1;
long minPhred = maxPhred;
if(phred11 < minPhred)
{
minPhred = phred11;
minGeno = 0;
}
if(phred12 < minPhred)
{
minPhred = phred12;
minGeno = 1;
}
if(phred22 < minPhred)
{
minPhred = phred22;
minGeno = 2;
}
perMarkerGeno[i] = minGeno;
}
float genoMissingRate = static_cast<float>(nMissingGenoSamples) / nSamples;
if(genoMissingRate > 0.2f)
{
warning("Skip marker (%s) with high missing rate (%f > 0.2) in genotype fields.",markerName.c_str(), genoMissingRate);
continue;
}
genotype.push_back(perMarkerGeno);
chooseBed[pMarker->sChrom.c_str()][pMarker->nPos]=std::make_pair(refAllele,altAllele);
BedVec.push_back(region_t(pMarker->sChrom.c_str(),pMarker->nPos-1,pMarker->nPos));
nMarkers++;
prevMarkerName = markerName;
}
delete pVcf;
//delete pMarker;
}
catch (VcfFileException& e) {
error(e.what());
}
return 0;
}
void SVDcalculator::ProcessRefVCF(const std::string &VcfPath)
{
std::vector<std::vector<char> > genotype;//markers X samples
ReadVcf(VcfPath, genotype, numIndividual, numMarker);
MatrixXf genoMatrix(numMarker,numIndividual);
// std::cerr<<numMarker<<"\t"<<genotype.size()<<"\t"<<numIndividual<<"\t"<<genotype[0].size()<<std::endl;
notice("Number of Markers:%d",numMarker);
notice("Number of Individuals:%d",numIndividual);
if(numMarker < 5000 || numIndividual < 1000)
{
error("Insufficient available number of Markers(5000) or Individuals(1000)\n");
}
for (int i = 0; i <genotype.size() ; ++i) {//per marker
for (int j = 0; j <genotype[i].size() ; ++j) {//per sample
genoMatrix(i,j)=genotype[i][j];
}
}
genotype.clear();
VectorXf mu = genoMatrix.rowwise().mean();
for (int rowIdx = 0; rowIdx < numMarker; ++rowIdx) {
for (int colIdx = 0; colIdx < numIndividual; ++colIdx) {
genoMatrix(rowIdx,colIdx)-=mu(rowIdx);
}
Mu.push_back(mu(rowIdx));
}
JacobiSVD<MatrixXf> svd(genoMatrix, ComputeThinU | ComputeThinV);
auto matrixD = svd.singularValues().asDiagonal();
MatrixXf matrixUD = svd.matrixU() * matrixD;//marker X PC
UD.resize(matrixUD.rows(),std::vector<double>(matrixUD.cols(),0.f));
for (int rowIdx = 0; rowIdx <matrixUD.rows(); ++rowIdx) {
for (int colIdx = 0; colIdx <matrixUD.cols(); ++colIdx) {
UD[rowIdx][colIdx] = matrixUD(rowIdx,colIdx);
}
}
MatrixXf matrixV = svd.matrixV();
PC.resize(numIndividual,std::vector<double>(matrixUD.cols(),0.f));
for (int sampleIdx = 0; sampleIdx < numIndividual ; ++sampleIdx) {
for (int pcIdx = 0; pcIdx <matrixUD.cols() ; ++pcIdx) {
PC[sampleIdx][pcIdx] = matrixV(sampleIdx,pcIdx);
}
}
WriteSVD(VcfPath);
}
vector<vector<double>> SVDcalculator::GetUDMatrix() {
return UD;
}
vector<vector<double>> SVDcalculator::GetPCMatrix() {
return PC;
}
std::vector<PCtype> SVDcalculator::GetMuArray() {
return Mu;
}
BED SVDcalculator::GetchooseBed() {
return chooseBed;
}
vector<region_t> SVDcalculator::GetBedVec() {
return BedVec;
}
void SVDcalculator::WriteSVD(const std::string &Prefix) {
std::ofstream fMu(Prefix+".mu");
std::ofstream fUD(Prefix+".UD");
std::ofstream fPC(Prefix+".V");
std::ofstream fBed(Prefix+".bed");
std::string chr;
int beg(0),end(0);
for (int i = 0; i < numMarker; ++i) {
chr=BedVec[i].chr;
beg=BedVec[i].beg;
end=BedVec[i].end;
fMu<<chr+":"+std::to_string(end)<<"\t"<<Mu[i]<<std::endl;
fBed<<chr<<"\t"<<beg<<"\t"<<end<<"\t"<<chooseBed[chr][end].first<<"\t"<<chooseBed[chr][end].second<<std::endl;
for (int j = 0; j < 10/*UD[i].size()*/ ; ++j) {
fUD<<UD[i][j]<<"\t";
}
fUD<<std::endl;
}
for (int k = 0; k <numIndividual; ++k) {
fPC<<Samples[k]<<"\t";
for (int i = 0; i < 10/*PC[k].size()*/; ++i) {
fPC<<PC[k][i]<<"\t";
}
fPC<<std::endl;
}
fBed.close();
fMu.close();
fUD.close();
fPC.close();
}