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msGenotyper.cpp
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msGenotyper.cpp
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#include <iostream>
#include <set>
#include <map>
#include <string>
#include <ctime>
#include <math.h>
#include <vector>
#include <numeric>
#include <sstream>
#include <fstream>
#include <ios>
#include <assert.h>
#include <sys/stat.h>
#include <seqan/file.h>
#include <seqan/find.h>
#include <seqan/basic.h>
#include <seqan/vcf_io.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <liblinear.hpp>
namespace msGenotyper
{
#define Malloc(type,n) (type *)malloc((n)*sizeof(type))
namespace io = boost::iostreams;
using namespace std;
using namespace seqan;
//structure to store read information
struct AttributeLine {
string PnId;
float numOfRepeats;
float ratioBf;
float ratioAf;
unsigned locationShift;
unsigned mateEditDist;
float purity;
float ratioOver20In;
int label;
double pValue;
} ;
//For storing marker information
struct Marker {
string chrom;
int start;
int end;
string motif;
float refRepeatNum;
} ;
//For storing number of members in each class and their pValue-sum
struct LabelProps {
Pair<int, double> p1;
Pair<int, double> p2;
Pair<int, double> p3;
} ;
//For storing marker values
struct MarkerStats
{
model* regressionModel;
LabelProps slippCount;
double slippage;
unsigned nAlleles;
double stutter;
double stepSum;
std::set<float> alleles;
std::set<float> trueAlleles;
double posSlippSum;
double negSlippSum;
};
//For storing all possible genotypes, their pValues, the chosen genotype, its pValue, all alleles with their frequencies and number of reads available for the decision
struct GenotypeInfo {
String<Pair<float> > genotypes;
String<long double> pValues;
Pair<float> genotype;
double pValue;
int numOfReads;
map<float, int> alleleToFreq; //This maps from reported alleles to their frequencies
double pValueSum;
double fullMotifSlippageSum;
} ;
struct MakeGenotypesRet {
std::set<Pair<float> > genotypesSet;
String<Pair<float> > genotypes;
};
//So I can map from Markers
bool operator<(const Marker & left, const Marker & right)
{
return left.start < right.start;
}
//stores various marker specific values
map<Marker, MarkerStats> markerToStats;
//for debugging purposes
bool useGeom = true;
//Parameter, problem and model structs to use in training of logistic regression model and computing pValues
parameter param;
problem prob;
problem probBig; //problem structure including reads with label = 2 to use for predict function
model* model_;
double bias = -1;
//Fills in the x-part of a problem structure from an AttributeLine structure
void fillProblemX(int idx, AttributeLine currentLine, problem& myProb)
{
myProb.x[idx][0].index = 1;
myProb.x[idx][0].value = currentLine.ratioBf;
myProb.x[idx][1].index = 2;
myProb.x[idx][1].value = currentLine.ratioAf;
myProb.x[idx][2].index = 3;
myProb.x[idx][2].value = currentLine.locationShift;
myProb.x[idx][3].index = 4;
myProb.x[idx][3].value = currentLine.mateEditDist;
myProb.x[idx][4].index = 5;
myProb.x[idx][4].value = currentLine.purity;
myProb.x[idx][5].index = 6;
myProb.x[idx][5].value = currentLine.ratioOver20In;
myProb.x[idx][6].index = -1; // This is to indicate that there aren't any more attributes to read in.
myProb.x[idx][6].value = 0;
}
double getPval(Marker marker, AttributeLine currentLine)
{
double predict_label;
model* model_ = markerToStats[marker].regressionModel;
double *prob_estimates = (double *) malloc(2*sizeof(double));
problem prob_;
prob_.bias = -1;
prob_.l = 1;
prob_.n = 6;
prob_.x = (feature_node **) malloc(prob_.l * sizeof(feature_node *));
prob_.x[0] = (feature_node *) malloc(10 * sizeof(feature_node));
fillProblemX(0, currentLine, prob_);
predict_label = predict_probability(model_,prob_.x[0],prob_estimates);
return prob_estimates[0];
}
//Parses one line from attribute file by filling up and returning an AttributeLine, also initializes markerToStats map labelProps using the labels
AttributeLine parseNextLine(float winner, float second, bool is_gz, ifstream& attributeFile, io::filtering_istream& attributeFile_gz, Marker& marker, string PnId, map<Pair<string,Marker>, GenotypeInfo>& PnAndMarkerToGenotype, String<string> firstLine, bool useFirstLine, bool useModelAndLabels, bool enoughReads)
{
PnAndMarkerToGenotype[Pair<string,Marker>(PnId, marker)].genotype = Pair<float>(winner,second);
AttributeLine currentLine;
currentLine.PnId = PnId;
string tmp;
if (useFirstLine)
{
lexicalCast(currentLine.numOfRepeats, firstLine[0]);
lexicalCast(currentLine.ratioBf,firstLine[1]);
lexicalCast(currentLine.ratioAf,firstLine[2]);
lexicalCast(currentLine.locationShift,firstLine[3]);
lexicalCast(currentLine.mateEditDist,firstLine[4]);
lexicalCast(currentLine.purity,firstLine[5]);
lexicalCast(currentLine.ratioOver20In,firstLine[6]);
}
else
{
if (is_gz)
{
attributeFile_gz >> currentLine.numOfRepeats;
attributeFile_gz >> currentLine.ratioBf;
attributeFile_gz >> currentLine.ratioAf;
attributeFile_gz >> currentLine.locationShift;
attributeFile_gz >> currentLine.mateEditDist;
attributeFile_gz >> currentLine.purity;
attributeFile_gz >> currentLine.ratioOver20In;
attributeFile_gz >> tmp; //repeatSeqFromRead
}
else
{
attributeFile >> currentLine.numOfRepeats;
attributeFile >> currentLine.ratioBf;
attributeFile >> currentLine.ratioAf;
attributeFile >> currentLine.locationShift;
attributeFile >> currentLine.mateEditDist;
attributeFile >> currentLine.purity;
attributeFile >> currentLine.ratioOver20In;
attributeFile >> tmp; //repeatSeqFromRead
}
}
if (!useModelAndLabels)
currentLine.pValue = 0.95;
else
currentLine.pValue = getPval(marker, currentLine);
if (enoughReads)
PnAndMarkerToGenotype[Pair<string,Marker>(PnId, marker)].pValueSum += currentLine.pValue;
//Check if the read is a result of a full motif slippage
float diff1 = fabs(winner-currentLine.numOfRepeats), diff2 = fabs(second-currentLine.numOfRepeats);
if (std::min(diff1,diff2)>=0.9)
{
PnAndMarkerToGenotype[Pair<string,Marker>(PnId, marker)].fullMotifSlippageSum += currentLine.pValue;
//Check whether slippage removed or added repeat
if (diff1 < diff2)
{
if (winner > currentLine.numOfRepeats)
markerToStats[marker].negSlippSum += currentLine.pValue;
else
markerToStats[marker].posSlippSum += currentLine.pValue;
}
else
{
if (second > currentLine.numOfRepeats)
markerToStats[marker].negSlippSum += currentLine.pValue;
else
markerToStats[marker].posSlippSum += currentLine.pValue;
}
}
//Determining the initial label of the read
if (diff1 <= 0.05 || diff2 <= 0.05)
{
currentLine.label = 1;
++markerToStats[marker].slippCount.p1.i1;
if (enoughReads)
markerToStats[marker].slippCount.p1.i2 += currentLine.pValue;
}
else
{
if (fabs(currentLine.numOfRepeats - (winner - 1)) <= 0.05 || fabs(currentLine.numOfRepeats - (second - 1)) <= 0.05)
{
currentLine.label = 2;
++markerToStats[marker].slippCount.p2.i1;
if (enoughReads)
markerToStats[marker].slippCount.p2.i2 += currentLine.pValue;
markerToStats[marker].stepSum += (float)marker.motif.size();
}
else
{
currentLine.label = -1;
++markerToStats[marker].slippCount.p3.i1;
if (enoughReads)
markerToStats[marker].slippCount.p3.i2 += currentLine.pValue;
if (fmod(diff1,1.0)<0.05)
{
if (fmod(diff2,1.0)<0.05)
markerToStats[marker].stepSum += round(std::min(diff1,diff2) * (float)marker.motif.size());
else
markerToStats[marker].stepSum += round(diff1 * (float)marker.motif.size());
}
else
{
if (fmod(diff2,1.0)<0.05)
markerToStats[marker].stepSum += round(diff2 * (float)marker.motif.size());
else
markerToStats[marker].stepSum += round(std::min(diff1,diff2) * (float)marker.motif.size());
}
}
}
return currentLine;
}
MakeGenotypesRet makeGenotypes(std::set<float> alleles, float refAllele)
{
String<Pair<float> > genotypes;
String<float> alleleString;
std::set<Pair<float> > genotypeSet;
std::set<float>::reverse_iterator allelesBegin = alleles.rend();
float closestToRef = *alleles.rbegin();
float minDistToRef = fabs(closestToRef-refAllele);
unsigned refIdx = 0;
for (std::set<float>::reverse_iterator alleleIt = alleles.rbegin(); alleleIt!=allelesBegin; ++alleleIt)
{
appendValue(alleleString, *alleleIt);
if (fabs(*alleleIt-refAllele)<minDistToRef)
{
closestToRef = *alleleIt;
minDistToRef = fabs(*alleleIt-refAllele);
refIdx = length(alleleString)-1;
}
}
//Put reference allele at end of alleleString
erase(alleleString, refIdx);
appendValue(alleleString, closestToRef);
for (unsigned i=0; i<length(alleleString); ++i)
{
appendValue(genotypes,Pair<float>(alleleString[i],alleleString[i]));
genotypeSet.insert(Pair<float>(alleleString[i],alleleString[i]));
if (i == (length(alleleString)-1))
break;
for (unsigned j=i+1; j<length(alleleString); ++j)
{
appendValue(genotypes,Pair<float>(alleleString[j],alleleString[i]));
genotypeSet.insert(Pair<float>(alleleString[j],alleleString[i]));
}
}
reverse(genotypes);
MakeGenotypesRet returnValue;
returnValue.genotypes = genotypes;
returnValue.genotypesSet = genotypeSet;
return returnValue;
}
int findMinIndex(String<long double> probs)
{
int minIndex = 0;
long double minValue = probs[0];
for (unsigned i = 1; i<length(probs); ++i)
{
if (probs[i]<minValue)
{
minIndex=i;
minValue=probs[i];
}
}
return minIndex;
}
float dgeom(int diff, double psucc)
{
if (diff < 0)
return 0;
double p = psucc;
for (int i = 0; i < diff; i++)
{
p = p*(1-psucc);
}
return p;
}
float dpois(int step, float lambda) {
if (step < 0)
return 0;
float p = exp(-1*lambda);
for (int i = 0; i < step; i++) {
p = p*lambda;
p = p/(i+1);
}
return p;
}
Pair<GenotypeInfo, bool> determineGenotype(String<AttributeLine> reads, double markerSlippage, String<Pair<float> > genotypes, int numberOfAlleles, int motifLength, double psucc, double posSlippProb, double negSlippProb)
{
GenotypeInfo returnValue;
returnValue.pValueSum = 0;
returnValue.genotypes = genotypes;
returnValue.numOfReads = length(reads);
Pair<float> genotypeToCheck;
AttributeLine readToCheck;
String<long double> probs;
double errorProbSum = 0;
resize(probs, length(genotypes));
bool isHomo, enoughDistance = true;
float diff, diff2, lambda = std::max((double)0.001,markerSlippage), posNegSlipp = 1, posNegSlipp2 = 1;
int indexOfWinner, indexOfSecond;
for (unsigned i=0; i<length(genotypes); ++i)
{
probs[i] = 0;
genotypeToCheck = genotypes[i];
isHomo = genotypeToCheck.i1 == genotypeToCheck.i2;
for (unsigned j=0; j<length(reads); ++j)
{
posNegSlipp = 1;
posNegSlipp2 = 1;
readToCheck = reads[j];
if (i == 0)
{
++returnValue.alleleToFreq[readToCheck.numOfRepeats];
if (length(reads) >= 10)
returnValue.pValueSum += readToCheck.pValue;
}
if (isHomo)
{
if (readToCheck.numOfRepeats - genotypeToCheck.i1 < -0.9)
posNegSlipp = negSlippProb;
if (readToCheck.numOfRepeats - genotypeToCheck.i1 > 0.9)
posNegSlipp = posSlippProb;
diff = fabs(readToCheck.numOfRepeats - genotypeToCheck.i1);
if (useGeom)
probs[i] += -(double)10*log10(readToCheck.pValue * dgeom(static_cast<int>(roundf((diff-(float)floor(diff))*motifLength)), psucc) * dpois(floor(diff), lambda) * posNegSlipp + ((double)(1.0-readToCheck.pValue)/(double)numberOfAlleles));
else
probs[i] += -(double)10*log10(readToCheck.pValue * dpois(ceil(diff), lambda) * posNegSlipp + ((double)(1.0-readToCheck.pValue)/(double)numberOfAlleles));
}
else
{
if (readToCheck.numOfRepeats - genotypeToCheck.i1 < -0.9)
posNegSlipp = negSlippProb;
if (readToCheck.numOfRepeats - genotypeToCheck.i1 > 0.9)
posNegSlipp = posSlippProb;
if (readToCheck.numOfRepeats - genotypeToCheck.i2 < -0.9)
posNegSlipp2 = negSlippProb;
if (readToCheck.numOfRepeats - genotypeToCheck.i2 > 0.9)
posNegSlipp2 = posSlippProb;
diff = fabs(readToCheck.numOfRepeats - genotypeToCheck.i1);
diff2 = fabs(readToCheck.numOfRepeats - genotypeToCheck.i2);
if (useGeom)
probs[i] += -(double)10*log10(readToCheck.pValue * 0.5 * (dgeom(static_cast<int>(roundf((diff-(float)floor(diff))*motifLength)), psucc) * dpois(floor(diff), lambda) * posNegSlipp + dgeom(static_cast<int>(roundf((diff2-(float)floor(diff2))*motifLength)), psucc) * dpois(floor(diff2), lambda) * posNegSlipp2) + ((double)(1.0-readToCheck.pValue)/(double)numberOfAlleles));
else
probs[i] += -(double)10*log10(readToCheck.pValue * 0.5 * (dpois(ceil(diff), lambda) * posNegSlipp + dpois(ceil(diff2), lambda) * posNegSlipp2) + ((double)(1.0-readToCheck.pValue)/(double)numberOfAlleles));
}
}
}
returnValue.pValues = probs;
indexOfWinner = findMinIndex(probs);
if (length(probs)>1)
{
String<long double> probsCopy = probs;
erase(probsCopy,indexOfWinner);
indexOfSecond = findMinIndex(probsCopy);
enoughDistance = round(probsCopy[indexOfSecond]-probs[indexOfWinner]) > 10;
}
returnValue.genotype = genotypes[indexOfWinner];
returnValue.pValue = probs[indexOfWinner];
for (unsigned j=0; j<length(reads); ++j)
{
readToCheck = reads[j];
if ((readToCheck.numOfRepeats != returnValue.genotype.i1) && (readToCheck.numOfRepeats != returnValue.genotype.i2))
errorProbSum += readToCheck.pValue;
}
return Pair<GenotypeInfo, bool>(returnValue, enoughDistance);
}
unsigned getChrLength(string chrom)
{
if (chrom.compare("chr1") == 0)
return 248956422;
if (chrom.compare("chr2") == 0)
return 242193529;
if (chrom.compare("chr3") == 0)
return 198295559;
if (chrom.compare("chr4") == 0)
return 190214555;
if (chrom.compare("chr5") == 0)
return 181538259;
if (chrom.compare("chr6") == 0)
return 170805979;
if (chrom.compare("chr7") == 0)
return 159345973;
if (chrom.compare("chr8") == 0)
return 145138636;
if (chrom.compare("chr9") == 0)
return 138394717;
if (chrom.compare("chr10") == 0)
return 133797422;
if (chrom.compare("chr11") == 0)
return 135086622;
if (chrom.compare("chr12") == 0)
return 133275309;
if (chrom.compare("chr13") == 0)
return 114364328;
if (chrom.compare("chr14") == 0)
return 107043718;
if (chrom.compare("chr15") == 0)
return 101991189;
if (chrom.compare("chr16") == 0)
return 90338345;
if (chrom.compare("chr17") == 0)
return 83257441;
if (chrom.compare("chr18") == 0)
return 80373285;
if (chrom.compare("chr19") == 0)
return 58617616;
if (chrom.compare("chr20") == 0)
return 64444167;
if (chrom.compare("chr21") == 0)
return 46709983;
if (chrom.compare("chr22") == 0)
return 50818468;
else
return 0;
}
//Write all sorts of info to the header of the vfc file I pass to the function
void makeVcfHeader(VcfFileOut& out, String<string> PnIds, string chrom)
{
appendValue(contigNames(context(out)), chrom);
//Add IDs of all PNs to the header
for (unsigned i = 0; i<length(PnIds); ++i)
appendValue(sampleNames(context(out)), PnIds[i]);
unsigned chromLength = getChrLength(chrom);
string contigString = "<ID=" + chrom + ",length=" + to_string((long long unsigned int)chromLength) + ">";
//Complicated way of getting todays date
time_t rawtime;
tm* timeinfo;
char buffer [80];
time(&rawtime);
timeinfo = localtime(&rawtime);
strftime(buffer,10,"%Y%m%d",timeinfo);
string date = buffer;
VcfHeader header;
appendValue(header, VcfHeaderRecord("fileformat", "VCFv4.2"));
appendValue(header, VcfHeaderRecord("fileDate", date));
appendValue(header, VcfHeaderRecord("source", "PopSTR"));
appendValue(header, VcfHeaderRecord("source_bin", "/odinn/tmp/snaedisk/190423_popSTRfreeze/binary/computeReadAttributes"));
appendValue(header, VcfHeaderRecord("source_bin", "/odinn/tmp/snaedisk/190423_popSTRfreeze/binary/computePnSlippage"));
appendValue(header, VcfHeaderRecord("source_bin", "/odinn/tmp/snaedisk/190423_popSTRfreeze/binary/msGenotyper"));
appendValue(header, VcfHeaderRecord("reference", "/odinn/data/reference/Homo_sapiens-deCODE-hg38/Sequence/WholeGenomeFasta/genome.fa"));
appendValue(header, VcfHeaderRecord("contig", contigString));
appendValue(header, VcfHeaderRecord("INFO", "<ID=RefLen,Number=A,Type=Integer,Description=\"Length of the reference allele\">"));
appendValue(header, VcfHeaderRecord("INFO", "<ID=Motif,Number=1,Type=String,Description=\"Microsatellite repeat motif\">"));
appendValue(header, VcfHeaderRecord("FORMAT", "<ID=GT,Number=1,Type=String,Description=\"Genotype\">"));
appendValue(header, VcfHeaderRecord("FORMAT", "<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">"));
appendValue(header, VcfHeaderRecord("FORMAT", "<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth\">"));
appendValue(header, VcfHeaderRecord("FORMAT", "<ID=PL,Number=G,Type=Integer,Description=\"PHRED-scaled genotype likelihoods\">"));
writeHeader(out, header);
}
//Clear a stringstream and a string, I use this a lot in fillRecordMarker/Pn, so a function seemed appropriate
void stringClear(stringstream& ss, CharString& str)
{
ss.str("");
ss.clear();
clear(str);
}
Pair<int> findGenotypeIndices(GenotypeInfo& genotype, std::set<float>& allelesAtMarker)
{
Pair<int> gtIdxs = Pair<int>(0,0);
unsigned idx = 1;
float currentAllele;
std::set<float>::iterator allEnd = allelesAtMarker.end();
for (std::set<float>::iterator allIt = allelesAtMarker.begin(); allIt!=allEnd; ++allIt)
{
currentAllele = *allIt;
if (currentAllele == genotype.genotype.i1)
gtIdxs.i1 = idx;
if (currentAllele == genotype.genotype.i2)
gtIdxs.i2 = idx;
idx++;
}
return gtIdxs;
}
VcfRecord fillRecordMarker(Marker marker, std::set<float> allelesAtThisMarker)
{
int refLength = marker.end - (marker.start-1);
VcfRecord record;
record.rID = 0;
record.beginPos = marker.start-1;
stringstream ss;
ss << record.beginPos+1;
CharString str = ss.str();
record.id = marker.chrom + ":" + toCString(str) + ":M";
//Get ref seq using crop_fasta and set as record.ref
string refSeq;
FILE * stream;
char buffer[256];
stringstream cmdStream;
cmdStream << "/odinn/users/snaedisk/bin/crop_fasta /odinn/data/reference/Homo_sapiens-deCODE-hg38/Sequence/WholeGenomeFasta/genome.fa " << marker.chrom << ":" << toCString(str) << "-" << marker.end;
string cmd = cmdStream.str();
cmd.append(" 2>&1");
stream = popen(cmd.c_str(), "r");
if (stream) {
while (!feof(stream))
if (fgets(buffer, 256, stream) != NULL)
{
buffer[strcspn(buffer, "\n")] = 0;
refSeq.append(buffer);
}
pclose(stream);
}
//Set reference allele and delete it from allele set
stringClear(ss,str);
record.ref = refSeq;
allelesAtThisMarker.erase(marker.refRepeatNum);
record.qual = record.MISSING_QUAL();
record.info = "RefLen=";
ss << refLength;
str = ss.str();
append(record.info,str);
stringClear(ss,str);
append(record.info,";");
append(record.info,"Motif=");
append(record.info,marker.motif);
record.format = "GT:AD:DP:PL";
//Loop over all alternative alleles and add them to ALT field in record
float currentAllele;
std::set<float>::iterator allEnd = allelesAtThisMarker.end();
for (std::set<float>::iterator allIt = allelesAtThisMarker.begin(); allIt!=allEnd; ++allIt)
{
append(record.alt, "<");
currentAllele = *allIt;
ss << currentAllele;
str = ss.str();
append(record.alt, str);
append(record.alt, ">,");
stringClear(ss,str);
}
if (allelesAtThisMarker.size() > 0)
eraseBack(record.alt);
else
record.alt = ".";
return record;
}
//Fill up the PN-specific fields in the VCF-record.
void fillRecordPn(GenotypeInfo genotype, VcfRecord& record, MakeGenotypesRet genotypesAtThisMarker, std::set<float>& allelesAtMarker, Marker& marker)
{
unsigned indexOfCurrGt;
while (genotypesAtThisMarker.genotypesSet.find(genotype.genotype)== genotypesAtThisMarker.genotypesSet.end() && length(genotype.genotypes)>1)
{
indexOfCurrGt = findMinIndex(genotype.pValues);
erase(genotype.pValues,indexOfCurrGt);
erase(genotype.genotypes,indexOfCurrGt);
indexOfCurrGt = findMinIndex(genotype.pValues);
genotype.genotype = genotype.genotypes[indexOfCurrGt];
genotype.pValue = genotype.pValues[indexOfCurrGt];
}
float refAllele = marker.refRepeatNum;
//Remove ref allele from set.
allelesAtMarker.erase(refAllele);
stringstream ss;
CharString str = ss.str();
CharString gtInfo; //First I make the string containing the genotype info
Pair<int> gtIdxs = findGenotypeIndices(genotype, allelesAtMarker);
ss << gtIdxs.i1;
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,"/");
ss << gtIdxs.i2;
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,":");
//Add alleleDepth count for the ref allele
if (genotype.alleleToFreq.count(refAllele)==0)
append(gtInfo,"0,"); //No reads supporting ref allele
else
{
ss << genotype.alleleToFreq[refAllele];
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,",");
}
//Remove ref allele from set before looping over
allelesAtMarker.erase(refAllele);
//Add allele depth counts for other alleles
for (auto const & allele : allelesAtMarker)
{
if (genotype.alleleToFreq.count(allele) == 0)
append(gtInfo,"0,");
else
{
ss << genotype.alleleToFreq[allele];
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,",");
}
}
//put ref allele back in set after looping over
allelesAtMarker.insert(refAllele);
unsigned possibleGenotypes = 0;
for (unsigned i=0; i<allelesAtMarker.size(); ++i)
{
possibleGenotypes += i+1;
}
if (length(genotypesAtThisMarker.genotypes) != possibleGenotypes)
cerr << "ATTENTION: number of genotypes considered is wrong. It should be: " << possibleGenotypes << " but it is:" << length(genotypesAtThisMarker.genotypes) << endl;
eraseBack(gtInfo);
append(gtInfo,":");
//Add readDepth to gtInfo
ss << genotype.numOfReads;
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,":");
Pair<float> genotypeToLookFor;
Pair<float> genotypeToCompare;
int index;
long double numerator;
long double denominator;
int pl;
for (unsigned i=0; i<length(genotypesAtThisMarker.genotypes); ++i)
{
index = -1;
genotypeToLookFor = genotypesAtThisMarker.genotypes[i];
if (genotypeToLookFor == genotype.genotype)
{
ss << 0;
str = ss.str();
append(gtInfo,str);
}
else
{
for (unsigned j=0; j<length(genotype.genotypes); ++j)
{
genotypeToCompare=genotype.genotypes[j];
if (genotypeToCompare == genotypeToLookFor)
{
index = j;
break;
}
}
if (index == -1)
{
ss << 255;
str = ss.str();
append(gtInfo,str);
}
else
{
numerator = genotype.pValues[index];
denominator = genotype.pValue;
pl = round(numerator-denominator);
pl = std::min(255,pl);
if (pl<0)
pl = 255;
ss << pl;
str = ss.str();
append(gtInfo,str);
}
}
stringClear(ss,str);
append(gtInfo,",");
}
eraseBack(gtInfo);
//When the genotype info string is ready I append it to the stringset of charstrings
appendValue(record.genotypeInfos, gtInfo);
}
double computeAlleleDist(String<Pair<float> > genotypes, map<float,int> allelesToFreq, int pnsAtMarker)
{
float genotype1, genotype2;
double freq1, freq2;
double currVal;
double totalSum = 0;
int indicator;
for (unsigned i=0; i<length(genotypes); ++i)
{
indicator = 0;
genotype1 = genotypes[i].i1;
genotype2 = genotypes[i].i2;
float n1 = fabs(genotype1-genotype2);
float n2 = ceil(fabs(genotype1-genotype2));
float n3 = n1-n2;
if (n3 == 0)
indicator = 1;
freq1 = (double)allelesToFreq[genotype1]/(double)(2*pnsAtMarker);
freq2 = (double)allelesToFreq[genotype2]/(double)(2*pnsAtMarker);
currVal = (double)indicator*freq1*freq2;
if (genotype1 != genotype2)
currVal = 2*currVal;
totalSum += currVal;
}
return totalSum;
}
//Count number of words in a sentence, use to parse input from attribute file
Pair<int, String<string> > countNumberOfWords(string sentence)
{
int numberOfWords = 0;
String<string> words;
resize(words, 9);
int currentWordLength;
if (!isspace(sentence[0]))
{
numberOfWords++;
words[0] = sentence[0];
}
for (unsigned i = 1; i < sentence.length(); i++)
{
if ((!isspace(sentence[i])) && (isspace(sentence[i-1])))
{
numberOfWords++;
words[numberOfWords-1] = sentence[i];
}
else
{
if (!isspace(sentence[i]))
words[numberOfWords-1].push_back(sentence[i]);
}
}
resize(words, numberOfWords);
return Pair<int, String<string> >(numberOfWords, words);
}
String<Pair<int, string> > readMarkers(CharString & markerFile)
{
ifstream markerStream(toCString(markerFile));
if(markerStream.fail())
cout << "Unable to locate markerList @ " << markerFile << endl;
String<Pair<int, string> > markerList;
string motif;
int startPos;
while (true)
{
markerStream >> startPos;
markerStream >> motif;
if (markerStream.eof() || motif.length() == 0)
break;
Pair<int, string> currPair = Pair<int, string>(startPos, motif);
appendValue(markerList, currPair);
}
markerStream.close();
cout << "Finished reading " << length(markerList) << " markers.\n";
return markerList;
}
//Read in data from markerSlippageFile
void readMarkerSlippage(CharString markerSlippageFile, CharString iterationNumber, CharString regressionModelDirectory, CharString intervalIndex)
{
string prevItNum;
int itNum = 0;
lexicalCast(itNum, iterationNumber);
--itNum;
prevItNum = to_string(itNum);
append(markerSlippageFile, prevItNum);
append(markerSlippageFile, "_");
append(markerSlippageFile, intervalIndex);
ifstream markerSlippageIn(toCString(markerSlippageFile));
double currMarkSlipp, currMarkStutt, currPosSlippProb, currNegSlippProb;
int nPns, nAlleles;
Marker currMarker;
CharString currMarkerModelDir = regressionModelDirectory;
while (true)
{
markerSlippageIn >> currMarker.chrom;
markerSlippageIn >> currMarker.start;
markerSlippageIn >> currMarker.end;
markerSlippageIn >> currMarker.motif;
markerSlippageIn >> currMarker.refRepeatNum;
markerSlippageIn >> currMarkSlipp;
markerSlippageIn >> nPns;
markerSlippageIn >> nAlleles;
markerSlippageIn >> currMarkStutt;
markerSlippageIn >> currPosSlippProb;
markerSlippageIn >> currNegSlippProb;
if (markerSlippageIn.eof())
break;
markerToStats[currMarker].nAlleles = nAlleles;
markerToStats[currMarker].stutter = currMarkStutt;
markerToStats[currMarker].slippage = currMarkSlipp;
append(currMarkerModelDir, "/model_");
append(currMarkerModelDir, to_string(currMarker.start));
append(currMarkerModelDir, "_");
append(currMarkerModelDir, currMarker.motif);
const char *model_in_file = toCString(currMarkerModelDir);
markerToStats[currMarker].regressionModel = load_model(model_in_file);
currMarkerModelDir = regressionModelDirectory;
}
cout << "Finished reading marker slippage." << endl;
markerSlippageIn.close();
}
map<string, Pair<double, int> > readPnSlippage(CharString pnSlippagePath, CharString iterationNumber, String<string> & PnIds)
{
string PnId;
int nMarkers;
double currPnSlipp;
string prevItNum;
int itNum = 0;
lexicalCast(itNum, iterationNumber);
--itNum;
prevItNum = to_string(itNum);
map<string, Pair<double, int> > pnToSize;
append(pnSlippagePath, "_");
append(pnSlippagePath, prevItNum);
ifstream pnSlippageFile(toCString(pnSlippagePath));
while (true)
{
pnSlippageFile >> PnId;
pnSlippageFile >> currPnSlipp;
pnSlippageFile >> nMarkers;
if (pnSlippageFile.eof() || PnId.length() == 0)
break;
pnToSize[PnId].i1= currPnSlipp;
pnToSize[PnId].i2 = nMarkers;
appendValue(PnIds, PnId);
}
cout << "Finished reading pn Slippage, number of pns:" << pnToSize.size() << endl;
assert (pnToSize.size() == length(PnIds));
pnSlippageFile.close();
return pnToSize;
}
inline bool exists(const std::string& name)
{
struct stat buffer;
return (stat (name.c_str(), &buffer) == 0);
}
Pair<double, int> estimateSlippage(String<string> PnIds, map<Pair<string,Marker>, GenotypeInfo> PnAndMarkerToGenotype, Marker marker, CharString currItNum, map<string, Pair<double, int> > pnToSize)
{
int nMissing = 0, nAvailable;
vector<double> weights;
vector<double> slippFragments;
double currPnSlipp, currPvalSum = 0, weightSum = 0, fullMotifSlippageSum = 0, result, currMarkSlipp;
if (atoi(toCString(currItNum)) == 1)
{
for (unsigned i = 0; i<length(PnIds); ++i)
{
if ((PnAndMarkerToGenotype.count(Pair<string,Marker>(PnIds[i], marker)) == 0) || (PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i], marker)].pValueSum == 0))
continue;
fullMotifSlippageSum += PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i], marker)].fullMotifSlippageSum;
currPvalSum += PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i],marker)].pValueSum;
}
currMarkSlipp = 0.5*(fullMotifSlippageSum/currPvalSum);
}
else
currMarkSlipp = markerToStats[marker].slippage;
for (unsigned i = 0; i<length(PnIds); ++i)
{
if ((PnAndMarkerToGenotype.count(Pair<string,Marker>(PnIds[i], marker)) == 0) || (PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i], marker)].pValueSum == 0))
{
weights.push_back(0);
++nMissing;
continue;
}
if (pnToSize[PnIds[i]].i1 == 0)
currPnSlipp = 0.001;
else
currPnSlipp = pnToSize[PnIds[i]].i1;
currPvalSum = PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i],marker)].pValueSum;
weights.push_back(currPvalSum/((currPnSlipp+currMarkSlipp)*(1-(currPnSlipp+currMarkSlipp))));
}
weightSum = accumulate(weights.begin(),weights.end(),0.0);
nAvailable = length(PnIds) - nMissing;
for (unsigned i = 0; i<length(PnIds); ++i)
{
if ((PnAndMarkerToGenotype.count(Pair<string,Marker>(PnIds[i], marker)) == 0) || (PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i], marker)].pValueSum == 0))
{
slippFragments.push_back(0);
continue;
}
if (pnToSize[PnIds[i]].i1 == 0)
currPnSlipp = 0.001;
else
currPnSlipp = pnToSize[PnIds[i]].i1;
fullMotifSlippageSum = PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i], marker)].fullMotifSlippageSum;
currPvalSum = PnAndMarkerToGenotype[Pair<string,Marker>(PnIds[i],marker)].pValueSum;
slippFragments.push_back((weights[i]/weightSum)*((fullMotifSlippageSum/currPvalSum)-currPnSlipp));
}
result = std::max(0.0,accumulate(slippFragments.begin(),slippFragments.end(),0.0));
cout << "Slippage rate: " << result << endl;
return Pair<double, int>(result, nAvailable);
}
Pair<bool> genotypeIsConfident(GenotypeInfo& genotypeInfo)
{
bool A1ok = false, A2ok = false;
if (genotypeInfo.alleleToFreq[genotypeInfo.genotype.i1]>=3 && (double)genotypeInfo.alleleToFreq[genotypeInfo.genotype.i1]/(double)genotypeInfo.numOfReads >=0.25)
A1ok = true;
if (genotypeInfo.alleleToFreq[genotypeInfo.genotype.i2]>=3 && (double)genotypeInfo.alleleToFreq[genotypeInfo.genotype.i2]/(double)genotypeInfo.numOfReads >=0.25)
A2ok = true;
return Pair<bool>(A1ok, A2ok);
}
//For storing command line arguments
struct MsGenotyperOptions
{
CharString attDirChromNum, pnSlippageFile, markerList, intervalIndex, markerSlippageFile, regressionModelDirectory, iterationNumber, vcfOutputDirectory, vcfFileName;
unsigned firstPnIdx;
} ;
ArgumentParser::ParseResult parseCommandLine(MsGenotyperOptions & options, int argc, char const ** argv)
{
ArgumentParser parser("msGenotyper");
setShortDescription(parser, "Microsatellite genotyper");
setVersion(parser, "1.3");
setDate(parser, "June 2019");
addUsageLine(parser, "\\fI-AD\\fP attributesDirectory/chromNum \\fI-PNS\\fP pnSlippageFile \\fI-ML\\fP markerList \\fI-I\\fP intervalIndex \\fI-MS\\fP markerSlippageFile \\fI-MD\\fP regressionModelDirectory \\fI-IN\\fP iterationNumber \\fI-FP\\fP firstPnIdx \\fI-VD\\fP vcfOutputDirectory \\fI-VN\\fP vcfFileName ");
addDescription(parser, "Performs genptyping for all PNs in the pnSlippageFile over all markers in the markerFile. The genotypes are written to a file specified by the user.");
addOption(parser, ArgParseOption("AD", "attributesDirectory/chromNum", "Path to attributes files for the markers being genotyped.", ArgParseArgument::INPUT_FILE, "IN-DIR"));
setRequired(parser, "attributesDirectory/chromNum");
addOption(parser, ArgParseOption("PNS", "pnSlippageFile", "A file containing slippage rates for the pns to be genotyped.", ArgParseArgument::INPUT_FILE, "IN-FILE"));
setRequired(parser, "pnSlippageFile");
addOption(parser, ArgParseOption("ML", "markerList", "List of markers to genotype.", ArgParseArgument::INPUT_FILE, "IN-FILE"));
setRequired(parser, "markerList");
addOption(parser, ArgParseOption("I", "intervalIndex", "Index of the interval being processed", ArgParseArgument::STRING, "INDEX"));
setRequired(parser, "intervalIndex");
addOption(parser, ArgParseOption("MS", "markerSlippageFile", "A file containing estimated slippage rates for the microsatellites.", ArgParseArgument::OUTPUT_FILE, "OUT-FILE"));
setRequired(parser, "markerSlippageFile");
addOption(parser, ArgParseOption("MD", "regressionModelDirectory", "A directory where logistic regression models for all markers in the markerList are stored", ArgParseArgument::INPUTPREFIX, "IN-DIR"));
setRequired(parser, "regressionModelDirectory");
addOption(parser, ArgParseOption("IN", "iterationNumber", "Index of the iteration being performed, 1-based.", ArgParseArgument::STRING, "INDEX"));
setRequired(parser, "iterationNumber");
addOption(parser, ArgParseOption("FP", "firstPnIdx", "Index of first Pn in pnList within the attributeFile.", ArgParseArgument::INTEGER, "INTEGER"));
setRequired(parser, "firstPnIdx");
//Used if this is the final iteration
addOption(parser, ArgParseOption("VD", "vcfOutputDirectory", "A directory to write the vcf file to.", ArgParseArgument::OUTPUT_FILE, "OUT-DIR"));
addOption(parser, ArgParseOption("VN", "vcfFileName", "Name of vcf output file.", ArgParseArgument::OUTPUT_FILE, "OUT-FILE"));
ArgumentParser::ParseResult res = parse(parser, argc, argv);
if (res != ArgumentParser::PARSE_OK)