Examples with Sample function.genotype.base.Sample used on opensource projects

Example 21 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class CollapsingBase method initOutput.

@Override
public void initOutput() {
    try {
        bwSampleMatrix = new BufferedWriter(new FileWriter(matrixFilePath));
        bwSummary = new BufferedWriter(new FileWriter(summaryFilePath));
        if (CollapsingCommand.regionBoundaryFile.isEmpty()) {
            bwSampleMatrix.write("sample/gene" + "\t");
            bwSummary.write(CollapsingGeneSummary.getTitle());
        } else {
            bwSampleMatrix.write("sample/region boundary" + "\t");
            bwSummary.write(CollapsingRegionSummary.getTitle());
        }
        bwSummary.newLine();
        for (Sample sample : SampleManager.getList()) {
            bwSampleMatrix.write(sample.getName() + "\t");
        }
        bwSampleMatrix.newLine();
        bwSampleVariantCount = new BufferedWriter(new FileWriter(sampleVariantCountFilePath));
        bwSampleVariantCount.write(SampleVariantCount.getTitle());
        bwSampleVariantCount.newLine();
    } catch (Exception ex) {
        ErrorManager.send(ex);
    }
}

Example 22 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class CollapsingBase method outputSampleVariantCount.

public void outputSampleVariantCount() {
    try {
        for (Sample sample : SampleManager.getList()) {
            bwSampleVariantCount.write(sample.getName() + ",");
            bwSampleVariantCount.write(SampleVariantCount.getString(sample.getIndex()));
            bwSampleVariantCount.newLine();
        }
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}

Example 23 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class CollapsingCompHet method doOutput.

private void doOutput(ArrayList<CompHetOutput> geneOutputList, CollapsingSummary summary) {
    try {
        int outputSize = geneOutputList.size();
        CompHetOutput output1, output2;
        for (Sample sample : SampleManager.getList()) {
            for (int i = 0; i < outputSize; i++) {
                output1 = geneOutputList.get(i);
                int geno1 = output1.getCalledVariant().getGenotype(sample.getIndex());
                if (output1.isQualifiedGeno(geno1)) {
                    output1.calculateLooFreq(sample);
                    if (output1.isMaxLooMafValid()) {
                        if (isOutputValid(output1, geno1, sample, summary)) {
                            continue;
                        }
                        for (int j = i + 1; j < outputSize; j++) {
                            output2 = geneOutputList.get(j);
                            checkOutputValid(output1, output2, sample, summary);
                        }
                    }
                }
            }
        }
        variantIdSet.clear();
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}

Example 24 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class CollapsingSummary method countSample.

public void countSample() {
    for (Sample sample : SampleManager.getList()) {
        if (sample.isCase()) {
            if (variantNumBySample[sample.getIndex()] > 0) {
                qualifiedCase++;
            }
        } else {
            if (variantNumBySample[sample.getIndex()] > 0) {
                qualifiedCtrl++;
            }
        }
    }
    unqualifiedCase = totalCase - qualifiedCase;
    unqualifiedCtrl = totalCtrl - qualifiedCtrl;
    qualifiedCaseFreq = MathManager.devide(qualifiedCase, totalCase);
    qualifiedCtrlFreq = MathManager.devide(qualifiedCtrl, totalCtrl);
    if (qualifiedCaseFreq == 0 && qualifiedCtrlFreq == 0) {
        enrichedDirection = "NA";
    } else if (qualifiedCaseFreq == qualifiedCtrlFreq) {
        enrichedDirection = "none";
    } else if (qualifiedCaseFreq < qualifiedCtrlFreq) {
        enrichedDirection = "ctrl";
    } else if (qualifiedCaseFreq > qualifiedCtrlFreq) {
        enrichedDirection = "case";
    }
}

Example 25 with Sample

use of function.genotype.base.Sample in project atav by igm-team.

the class FamilyOutput method calculateFamilyNum.

public void calculateFamilyNum(String familyId) {
    int geno, pheno, type;
    for (Sample sample : SampleManager.getList()) {
        if (familyId.equals(sample.getFamilyId())) {
            geno = calledVar.getGenotype(sample.getIndex());
            pheno = (int) sample.getPheno();
            type = getGenoType(geno, sample);
            countFamilySample(type, pheno);
        }
    }
}