本文整理汇总了C++中Annotation::getCategoryOfSNP方法的典型用法代码示例。如果您正苦于以下问题：C++ Annotation::getCategoryOfSNP方法的具体用法？C++ Annotation::getCategoryOfSNP怎么用？C++ Annotation::getCategoryOfSNP使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Annotation的用法示例。
在下文中一共展示了Annotation::getCategoryOfSNP方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: getFstFromVCF
//.........这里部分代码省略.........
*pHetSets << "scaffold" << "\t" << "Start" << "\t" << "End" << "Set1_heterozygosity" << "\t" << "Set2_heterozygosity" << "\t" << "Set1_heterozygosity_Nei" << "\t" << "Set2_heterozygosity_Nei" << "\t" << "Set1_nucleotideDiversity_pi" << "\t" << "Set2_nucleotideDiversity_pi" << std::endl;
*pFst << "var_num" << "\t" << "scaffold" << "\t" << "Start" << "\t" << "End" << "\t" << "Fst" << "\t" << "Dxy_onlyVaiants" << "\t" << "Dxy_AllSites" << "\t" << "windowSize" << std::endl;
if (opt::regAbove > 0) *regionsAboveFstFile << "scaffold" << "\t" << "Start" << "\t" << "End" << std::endl;
} else {
*pHetSets << "Middle_SNP_position" << "\t" << "Set1_heterozygosity" << "\t" << "Set2_heterozygosity" << "\t" << "Set1_heterozygosity_Nei" << "\t" << "Set2_heterozygosity_Nei" << "\t" << "Set1_nucleotideDiversity_pi" << "\t" << "Set2_nucleotideDiversity_pi" << std::endl;
}
}
} else {
totalVariantNumber++;
std::vector<std::string> fields = split(line, '\t');
std::vector<std::string> info = split(fields[7], ';');
if (info[0] != "INDEL") { // Without indels
SetCounts counts = getVariantCountsForFst(fields,set1Loci,set2Loci);
//std::cerr << "Still here: " << counts.set1HaplotypeVariant.size() << "\t" << counts.set1individualsWithVariant.size() << "\t" << n1 << std::endl;
//std::cerr << "Still here: " << counts.set2HaplotypeVariant.size() << "\t" << counts.set2individualsWithVariant.size() << "\t" << n2 << std::endl;
//print_vector_stream(counts.set1HaplotypeVariant, std::cerr);
//print_vector_stream(counts.set1individualsWithVariant, std::cerr);
//print_vector_stream(counts.set2HaplotypeVariant, std::cerr);
if ((counts.set1Count > 0 || counts.set2Count > 0) && (counts.set1Count < n1 || counts.set2Count < n2)) {
countedVariantNumber++;
double FstNumerator = calculateFstNumerator(counts, n1, n2); fstNumerators.push_back(FstNumerator); fixedWindowFstNumVector.push_back(FstNumerator);
double FstDenominator = calculateFstDenominator(counts, n1, n2); fstDenominators.push_back(FstDenominator); fixedWindowFstDenomVector.push_back(FstDenominator);
assert(FstDenominator != 0);
double thisSNPDxy = calculateDxy(counts, n1, n2); DxyVector.push_back(thisSNPDxy); fixedWindowDxyVector.push_back(thisSNPDxy);
std::vector<double> thisSNPhet = getSetHeterozygozities(counts, n1, n2); heterozygositiesVector.push_back(thisSNPhet);
std::vector<double> thisSNPpis = calculatePiTwoSets(counts, n1, n2); fixedWindowPi1Vector.push_back(thisSNPpis[0]); fixedWindowPi2Vector.push_back(thisSNPpis[1]);
set1heterozygositiesPi.push_back(thisSNPpis[0]); set2heterozygositiesPi.push_back(thisSNPpis[1]);
// std::cerr << "Still here: " << thisSNPpis[0] << std::endl;
set1heterozygositiesSimple.push_back(thisSNPhet[0]); set2heterozygositiesSimple.push_back(thisSNPhet[1]); fixedWindowHet1Vector.push_back(thisSNPhet[0]);
set1heterozygositiesNei.push_back(thisSNPhet[2]); set2heterozygositiesNei.push_back(thisSNPhet[3]); fixedWindowHet2Vector.push_back(thisSNPhet[1]);
if (!opt::annotFile.empty()) {
string scaffold = fields[0]; string loc = fields[1]; // Scaffold
string SNPcategory = wgAnnotation.getCategoryOfSNP(scaffold, loc);
double thisSNPFst = FstNumerator/FstDenominator;
*snpCategoryFstFile << SNPcategory << "\t" << thisSNPFst << "\t" << thisSNPDxy << "\t" << scaffold << "\t" << loc << std::endl;
}
if (!opt::ancSets.empty()) {
double thisSNPFst = FstNumerator/FstDenominator;
if (thisSNPFst < 0) { thisSNPFst = 0; }
string AA = split(info[info.size()-1],'=')[1];
//std::cerr << "AA=" << " " << AA << std::endl;
FourSetCounts c;
if (AA == fields[3]) {
c = getFourSetVariantCounts(fields,set1Loci,set2Loci,ancSet1Loci,ancSet2Loci,"ref");
*ancSetsOutFile << fields[0] << "\t" << fields[1] << "\t" << c.set1daAF-c.set2daAF << "\t" << thisSNPFst << "\t";
if (c.set3daAF > 0 & c.set3daAF < 1) { *ancSetsOutFile << "1" << "\t"; } else { *ancSetsOutFile << "0" << "\t"; }
if (c.set4daAF > 0 & c.set4daAF < 1) { *ancSetsOutFile << "1" << std::endl; } else { *ancSetsOutFile << "0" << std::endl; }
} else if (AA == fields[4]) {
c = getFourSetVariantCounts(fields,set1Loci,set2Loci,ancSet1Loci,ancSet2Loci,"alt");
*ancSetsOutFile << fields[0] << "\t" << fields[1] << "\t" << c.set1daAF-c.set2daAF << "\t" << thisSNPFst << "\t";
if (c.set3daAF > 0 & c.set3daAF < 1) { *ancSetsOutFile << "1" << "\t"; } else { *ancSetsOutFile << "0" << "\t"; }
if (c.set4daAF > 0 & c.set4daAF < 1) { *ancSetsOutFile << "1" << std::endl; } else { *ancSetsOutFile << "0" << std::endl; }
// std::cerr << "AA=alt" << " " << c.set1daAF << " " << c.set2daAF << std::endl;
} else {
c = getFourSetVariantCounts(fields,set1Loci,set2Loci,ancSet1Loci,ancSet2Loci,"N");
*ancSetsOutFile << fields[0] << "\t" << fields[1] << "\t" << "-888" << "\t" << thisSNPFst << "\t";
if (c.set3AltAF > 0 & c.set3AltAF < 1) { *ancSetsOutFile << "1" << "\t"; } else { *ancSetsOutFile << "0" << "\t"; }
if (c.set4AltAF > 0 & c.set4AltAF < 1) { *ancSetsOutFile << "1" << std::endl; } else { *ancSetsOutFile << "0" << std::endl; }
}
}
std::vector<string> s = split(windowStartEnd, '\t');
if (s[0] == fields[0]) {