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msGenotyperDefault.cpp
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msGenotyperDefault.cpp
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#include <iostream>
#include <set>
#include <map>
#include <string>
#include <ctime>
#include <math.h>
#include <limits.h>
#include <unistd.h>
#include <vector>
#include <numeric>
#include <sstream>
#include <fstream>
#include <ios>
#include <stdio.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/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <liblinear.hpp>
namespace msGenotyperDefault
{
#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 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;
bool hasManyAlleles;
} ;
//For storing command line arguments
struct MsGenotyperOptions
{
CharString attDirChromNum, pnSlippageFile, markerSlippageFile, vcfOutputDirectory, vcfFileName, markerList, intervalIndex;
unsigned firstPnIdx;
} ;
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;
}
//Sums the pValues of reads and counts the number of reads for each type of label at every marker, also stores the current slippage rate value for each marker
map<Marker, Pair<LabelProps,double> > markerToLabelsAndSlipp;
//Stores the slippage rate value for each PN - read from input file.
map<string, double> pnToSize;
//Maps from pnId to reads and labels for one marker, is cleared for each marker
map<string, String<Pair<float> > > pnToLabels;
//Map from marker to (average stepsize)%period
map<Marker, double> markerToStepSum;
//Map from marker to pValue sums of full motif slippage events adding and removing motifs (for estimating posNegSlipp parameter in genotyping formula)
map<Marker, Pair<double> > markerToPosNegSums;
//Map from marker to alleles that I have found more than 3 reads of with freq > 25% in a single PN
map<Marker, std::set<float> > markerToTrueAlleles;
//Map from marker to map from alleles to counts of occasions when they have been < 25 percent of the reads
map<Marker, map<float, Pair<unsigned> > > markerToRareAlleles;
//USE FOR FILTERING: Map from a marker to number of reads at marker, number of samples with reads at marker, number of reads at marker not supporting assigned genotype and number of samples with reads from more than 3 alleles.
map<Marker, int[5]> markerToReadStats;
//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;
ArgumentParser::ParseResult parseCommandLine(MsGenotyperOptions & options, int argc, char const ** argv)
{
ArgumentParser parser("msGenotyperDefault");
setShortDescription(parser, "Microsatellite genotyper");
setVersion(parser, "1.3");
setDate(parser, "June 2019");
addUsageLine(parser, "\\fI-ADCN\\fP attributesDirectory/chromNum \\fI-PNS\\fP pnSlippageFile \\fI-MS\\fP markerSlippageFile \\fI-VD\\fP vcfOutputDirectory \\fI-VN\\fP vcfFileName \\fI-ML\\fP markerList \\fI-I\\fP intervalIndex \\fI-FP\\fP firstPnIdx");
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("ADCN", "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("MS", "markerSlippageFile", "A file containing slippage rates for the microsatellites.", ArgParseArgument::OUTPUT_FILE, "OUT-FILE"));
setRequired(parser, "markerSlippageFile");
addOption(parser, ArgParseOption("VD", "vcfOutputDirectory", "A directory to write the vcf file to.", ArgParseArgument::OUTPUT_FILE, "OUT-DIR"));
setRequired(parser, "vcfOutputDirectory");
addOption(parser, ArgParseOption("VN", "vcfFileName", "Name of vcf output file.", ArgParseArgument::OUTPUT_FILE, "OUT-FILE"));
setRequired(parser, "vcfFileName");
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");
setDefaultValue(parser, "intervalIndex", "1");
addOption(parser, ArgParseOption("FP", "firstPnIdx", "Index of first Pn in pnList within the attributeFile.", ArgParseArgument::INTEGER, "INTEGER"));
setRequired(parser, "firstPnIdx");
ArgumentParser::ParseResult res = parse(parser, argc, argv);
if (res != ArgumentParser::PARSE_OK)
return res;
getOptionValue(options.attDirChromNum, parser, "attributesDirectory/chromNum");
getOptionValue(options.pnSlippageFile, parser, "pnSlippageFile");
getOptionValue(options.markerSlippageFile, parser, "markerSlippageFile");
getOptionValue(options.vcfOutputDirectory, parser, "vcfOutputDirectory");
getOptionValue(options.vcfFileName, parser, "vcfFileName");
getOptionValue(options.markerList, parser, "markerList");
getOptionValue(options.intervalIndex, parser, "intervalIndex");
getOptionValue(options.firstPnIdx, parser, "firstPnIdx");
return ArgumentParser::PARSE_OK;
}
//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;
}
//Parses one line from attribute file by filling up and returning an AttributeLine, also initializes markerToLabelsAndSlipp map using the labels
AttributeLine parseNextLine(String<string> & read, Pair<float> winnerSecond, bool enoughReads, Marker& marker, string PnId, map<Pair<string,Marker>, GenotypeInfo>& PnAndMarkerToGenotype)
{
PnAndMarkerToGenotype[Pair<string,Marker>(PnId, marker)].genotype = winnerSecond;
AttributeLine currentLine;
currentLine.PnId = PnId;
lexicalCast(currentLine.numOfRepeats, read[0]);
lexicalCast(currentLine.ratioBf, read[1]);
lexicalCast(currentLine.ratioAf, read[2]);
lexicalCast(currentLine.locationShift, read[3]);
lexicalCast(currentLine.mateEditDist, read[4]);
lexicalCast(currentLine.purity, read[5]);
lexicalCast(currentLine.ratioOver20In, read[6]);
++PnAndMarkerToGenotype[Pair<string,Marker>(PnId, marker)].alleleToFreq[currentLine.numOfRepeats];
currentLine.pValue = 0.95;
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(winnerSecond.i1-currentLine.numOfRepeats), diff2 = fabs(winnerSecond.i2-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 (winnerSecond.i1 > currentLine.numOfRepeats)
markerToPosNegSums[marker].i2 += currentLine.pValue;
else
markerToPosNegSums[marker].i1 += currentLine.pValue;
}
else
{
if (winnerSecond.i2 > currentLine.numOfRepeats)
markerToPosNegSums[marker].i2 += currentLine.pValue;
else
markerToPosNegSums[marker].i1 += currentLine.pValue;
}
}
//Determining the initial label of the read
if ((fabs(currentLine.numOfRepeats - winnerSecond.i1) <= 0.05) || (fabs(currentLine.numOfRepeats - winnerSecond.i2) <= 0.05))
{
currentLine.label = 1;
++markerToLabelsAndSlipp[marker].i1.p1.i1;
if (enoughReads)
markerToLabelsAndSlipp[marker].i1.p1.i2 += currentLine.pValue;
}
else
{
if ((fabs(currentLine.numOfRepeats - (winnerSecond.i1 - 1)) <= 0.05) || (fabs(currentLine.numOfRepeats - (winnerSecond.i2 - 1)) <= 0.05))
{
currentLine.label = 2;
++markerToLabelsAndSlipp[marker].i1.p2.i1;
if (enoughReads)
markerToLabelsAndSlipp[marker].i1.p2.i2 += currentLine.pValue;
markerToStepSum[marker] += (float)marker.motif.size();
}
else
{
currentLine.label = -1;
++markerToLabelsAndSlipp[marker].i1.p3.i1;
if (enoughReads)
markerToLabelsAndSlipp[marker].i1.p3.i2 += currentLine.pValue;
float diff1, diff2;
diff1 = fabs(currentLine.numOfRepeats - winnerSecond.i1);
diff2 = fabs(currentLine.numOfRepeats - winnerSecond.i2);
if (fmod(diff1,1.0)<0.05)
{
if (fmod(diff2,1.0)<0.05)
markerToStepSum[marker] += round(std::min(diff1,diff2) * (float)marker.motif.size());
else
markerToStepSum[marker] += round(diff1 * (float)marker.motif.size());
}
else
{
if (fmod(diff2,1.0)<0.05)
markerToStepSum[marker] += round(diff2 * (float)marker.motif.size());
else
markerToStepSum[marker] += 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 mean) {
if (step < 0)
return 0;
float p = exp(-1*mean);
for (int i = 0; i < step; i++) {
p = p*mean;
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, Marker& thisMarker)
{
GenotypeInfo returnValue;
returnValue.pValueSum = 0;
returnValue.fullMotifSlippageSum = 0;
returnValue.genotypes = genotypes;
returnValue.numOfReads = length(reads);
Pair<float> genotypeToCheck;
AttributeLine readToCheck;
std::set<float> currentGenotype, newGenotypeSet;
String<long double> probs;
double lengthSlippage;
resize(probs, length(genotypes));
bool isHomo;
float posNegSlipp = 1, posNegSlipp2 = 1, lambda = std::max((double)0.001,markerSlippage), diff, diff2;
int indexOfWinner;
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)
{
if (length(reads) >= 10)
returnValue.pValueSum += readToCheck.pValue;
}
if (readToCheck.label == 1)
currentGenotype.insert(readToCheck.numOfRepeats);
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);
returnValue.genotype = genotypes[indexOfWinner];
returnValue.pValue = probs[indexOfWinner];
newGenotypeSet.insert(returnValue.genotype.i1);
newGenotypeSet.insert(returnValue.genotype.i2);
for (unsigned j=0; j<length(reads); ++j)
{
readToCheck = reads[j];
float diff1 = fabs(returnValue.genotype.i1-readToCheck.numOfRepeats), diff2 = fabs(returnValue.genotype.i2-readToCheck.numOfRepeats);
if (std::min(diff1,diff2)>=0.9)
{
returnValue.fullMotifSlippageSum += readToCheck.pValue;
if (diff1 < diff2)
{
if (returnValue.genotype.i1 > readToCheck.numOfRepeats)
markerToPosNegSums[thisMarker].i2 += readToCheck.pValue;
else
markerToPosNegSums[thisMarker].i1 += readToCheck.pValue;
}
else
{
if (returnValue.genotype.i2 > readToCheck.numOfRepeats)
markerToPosNegSums[thisMarker].i2 += readToCheck.pValue;
else
markerToPosNegSums[thisMarker].i1 += readToCheck.pValue;
}
}
}
if (newGenotypeSet == currentGenotype)
return Pair<GenotypeInfo, bool>(returnValue, false);
else
return Pair<GenotypeInfo, bool>(returnValue, true);
}
void relabelReads(String<AttributeLine>& readsToRelabel, int start, int end, Pair<float> newGenotype, Marker & marker)
{
int numOfReads = end - start;
for (unsigned i=start; i<end; ++i)
{
string pnId = readsToRelabel[i].PnId;
if ((fabs(readsToRelabel[i].numOfRepeats - newGenotype.i1)<=0.05) || (fabs(readsToRelabel[i].numOfRepeats - newGenotype.i2)<=0.05))
{
readsToRelabel[i].label = 1;
++markerToLabelsAndSlipp[marker].i1.p1.i1;
if (numOfReads >= 10)
markerToLabelsAndSlipp[marker].i1.p1.i2 += readsToRelabel[i].pValue;
}
else
{
if ((fabs(readsToRelabel[i].numOfRepeats - (newGenotype.i1 - 1))<=0.05) || (fabs(readsToRelabel[i].numOfRepeats - (newGenotype.i2 - 1))<=0.05))
{
readsToRelabel[i].label = 2;
++markerToLabelsAndSlipp[marker].i1.p2.i1;
markerToStepSum[marker] += (float)marker.motif.size();
if (numOfReads >= 10)
markerToLabelsAndSlipp[marker].i1.p2.i2 += readsToRelabel[i].pValue;
}
else
{
readsToRelabel[i].label = -1;
++markerToLabelsAndSlipp[marker].i1.p3.i1;
if (numOfReads >= 10)
markerToLabelsAndSlipp[marker].i1.p3.i2 += readsToRelabel[i].pValue;
float diff1, diff2;
diff1 = fabs(readsToRelabel[i].numOfRepeats - newGenotype.i1);
diff2 = fabs(readsToRelabel[i].numOfRepeats - newGenotype.i2);
if (fmod(diff1,1.0)<0.05)
{
if (fmod(diff2,1.0)<0.05)
markerToStepSum[marker] += round(std::min(diff1,diff2) * (float)marker.motif.size());
else
markerToStepSum[marker] += round(diff1 * (float)marker.motif.size());
}
else
{
if (fmod(diff2,1.0)<0.05)
markerToStepSum[marker] += round(diff2 * (float)marker.motif.size());
else
markerToStepSum[marker] += round(std::min(diff1,diff2) * (float)marker.motif.size());
}
}
}
}
}
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, string binPath)
{
std::size_t found = binPath.find_last_of("/\\");
std::string binDir = binPath.substr(0,found);
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) + ">";
string pnSlippPath = binDir + "/computePnSlippage";
string computeReadAttsPath = binDir + "/computeReadAttributes";
//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", computeReadAttsPath));
//appendValue(header, VcfHeaderRecord("source_bin", pnSlippPath));
appendValue(header, VcfHeaderRecord("source_bin", binPath));
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("INFO", "<ID=nReads,Number=A,Type=Integer,Description=\"Total number of reads\">"));
appendValue(header, VcfHeaderRecord("INFO", "<ID=nNonSupportReads,Number=A,Type=Integer,Description=\"Number of reads not supporting genotype\">"));
appendValue(header, VcfHeaderRecord("INFO", "<ID=nPnsWithReads,Number=A,Type=Integer,Description=\"Number of samples with available reads\">"));
appendValue(header, VcfHeaderRecord("INFO", "<ID=nMoreThan2alleles,Number=A,Type=Integer,Description=\"Number of samples with reads supporting more then two alleles\">"));
appendValue(header, VcfHeaderRecord("FILTER", "<ID=gqDepth, Description=\"Marker has an allele occurring at a < 25% per individual frequency in more than 30% of samples\">"));
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=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">"));
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, map<Pair<int, string>, Triple<double, double, string> > & markerToSlippStuttAndRefSeq)
{
int refLength = marker.end - (marker.start-1);
bool hasRareAllele = false;
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";
Pair<int, string> sAndM = Pair<int, string>(marker.start, marker.motif);
record.ref = markerToSlippStuttAndRefSeq[sAndM].i3;
allelesAtThisMarker.erase(marker.refRepeatNum);
record.qual = record.MISSING_QUAL();
record.info = "RefLen=";
stringClear(ss,str);
ss << refLength;
str = ss.str();
append(record.info,str);
stringClear(ss,str);
append(record.info,";Motif=");
append(record.info,marker.motif);
record.format = "GT:AD:DP:GQ:PL";
//Loop over all alternative alleles and add them to ALT field in record
float currentAllele;
for (auto allele : allelesAtThisMarker)
{
append(record.alt, "<");
currentAllele = allele;
ss << currentAllele;
str = ss.str();
append(record.alt, str);
append(record.alt, ">,");
stringClear(ss,str);
//Check if there is a rare allele at this marker (<25% of reads in 30% of the samples containing it.)
//cout << currentAllele << "\t" << markerToRareAlleles[marker][currentAllele].i1 << "/(" << markerToRareAlleles[marker][currentAllele].i2 << " + " << markerToRareAlleles[marker][currentAllele].i1 << ")\n";
if ((double)markerToRareAlleles[marker][currentAllele].i1/(double)(markerToRareAlleles[marker][currentAllele].i2 + markerToRareAlleles[marker][currentAllele].i1) > 0.3)
hasRareAllele = true;
}
//Have to check if ref allele is low freq in all PNS it's in as well
if ((double)markerToRareAlleles[marker][marker.refRepeatNum].i1/(double)(markerToRareAlleles[marker][marker.refRepeatNum].i2 + markerToRareAlleles[marker][marker.refRepeatNum].i1) > 0.3)
hasRareAllele = true;
if (hasRareAllele)
record.filter = "gqDepth";
else
record.filter = ".";
if (allelesAtThisMarker.size() > 0)
eraseBack(record.alt);
else
record.alt = ".";
return record;
}
void fillRecordReadStats(VcfRecord& record, Marker& marker)
{
stringstream ss;
append(record.info,";nReads=");
ss << markerToReadStats[marker][0];
CharString str = ss.str();
append(record.info,str);
stringClear(ss,str);
append(record.info,";nNonSupportReads=");
ss << markerToReadStats[marker][3];
str = ss.str();
append(record.info,str);
stringClear(ss,str);
append(record.info,";nPnsWithReads=");
ss << markerToReadStats[marker][1];
str = ss.str();
append(record.info,str);
stringClear(ss,str);
append(record.info,";nMoreThan2alleles=");
ss << markerToReadStats[marker][2];
str = ss.str();
append(record.info,str);
stringClear(ss,str);
}
//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, gtInfo, PLscores;
Pair<int> gtIdxs = findGenotypeIndices(genotype, allelesAtMarker);
//ss << genotype.genotype.i1;
ss << gtIdxs.i1;
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,"/");
//ss << genotype.genotype.i2;
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,",");
}
//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, pl, gq=255;
long double numerator, denominator;
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(PLscores,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(PLscores,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(PLscores,str);
if (pl < gq)
gq = pl;
}
}
stringClear(ss,str);
append(PLscores,",");
}
eraseBack(PLscores);
ss << gq;
str = ss.str();
append(gtInfo,str);
stringClear(ss,str);
append(gtInfo,":");
append(gtInfo,PLscores);
//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);
}
void readPnSlippage(CharString & pnSlippageFile, String<string> & PnIds)
{
ifstream pnSlippageStream(toCString(pnSlippageFile));
if(pnSlippageStream.fail())
{
cerr << "Unable to locate pnSlippageFile @ " << pnSlippageFile << endl;
return;
}
string PnId;
int nMarkers;
double currPnSlipp;
while (!pnSlippageStream.eof())
{
pnSlippageStream >> PnId;
pnSlippageStream >> currPnSlipp;
pnToSize[PnId]= currPnSlipp;
appendValue(PnIds,PnId);
}
eraseBack(PnIds);
pnSlippageStream.close();
}
void readMarkers(CharString & markerFile, map<Pair<int, string>, Triple<double, double, string> > & markerToSlippStuttAndRefSeq)
{
ifstream markerStream(toCString(markerFile));
if(markerStream.fail())
{
cerr << "Unable to locate markerList @ " << markerFile << endl;
return;
}
string line;
while (getline(markerStream, line))
{
istringstream iss(line);
string col1, motif, refSeq;
int startPos, col3;
double slipp, stutt;
iss >> col1 >> startPos >> col3 >> motif >> refSeq >> slipp >> stutt;
Pair<int, string> currPair = Pair<int, string>(startPos, motif);
markerToSlippStuttAndRefSeq[currPair] = Triple<double, double, string>(slipp, stutt, refSeq);
}
markerStream.close();
return;
}
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, int currItNum)
{
int nMissing = 0, nAvailable;
vector<double> weights;
vector<double> slippFragments;
double currPnSlipp, currPvalSum = 0, weightSum = 0, fullMotifSlippageSum = 0, result, currMarkSlipp;
if (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 = markerToLabelsAndSlipp[marker].i2;
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]] == 0)
currPnSlipp = 0.001;
else
currPnSlipp = pnToSize[PnIds[i]];
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]] == 0)
currPnSlipp = 0.001;