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

Example 11 with Sample

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

the class CoverageAnalysisBase method outputSampleGeneSummary.

private void outputSampleGeneSummary(Gene gene) {
    try {
        StringBuilder sb = new StringBuilder();
        for (Sample sample : SampleManager.getList()) {
            sb.append(sample.getName()).append(",");
            sb.append(gene.getName()).append(",");
            sb.append(gene.getChr()).append(",");
            sb.append(gene.getLength()).append(",");
            sb.append(geneSampleCoverage[gene.getIndex()][sample.getIndex()]).append(",");
            double ratio = MathManager.devide(geneSampleCoverage[gene.getIndex()][sample.getIndex()], gene.getLength());
            sb.append(FormatManager.getSixDegitDouble(ratio)).append(",");
            int pass = ratio >= CoverageCommand.minPercentRegionCovered ? 1 : 0;
            sb.append(pass);
            writeToFile(sb.toString(), bwCoverageDetails);
            sb.setLength(0);
            // count region per sample
            sampleCoverageCount[sample.getIndex()] += pass;
        }
    } catch (Exception ex) {
        ErrorManager.send(ex);
    }
}

Example 12 with Sample

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

the class CoverageSummary method outputCoverageDetailsByExon.

private void outputCoverageDetailsByExon(HashMap<Integer, Integer> sampleCoveredLengthMap, Gene gene, Exon exon) {
    try {
        StringBuilder sb = new StringBuilder();
        for (Sample sample : SampleManager.getList()) {
            sb.append(sample.getName()).append(",");
            sb.append(gene.getName()).append(",");
            sb.append(exon.getChrStr()).append(",");
            sb.append(exon.getIdStr()).append(",");
            sb.append(exon.getStartPosition()).append(",");
            sb.append(exon.getEndPosition()).append(",");
            sb.append(exon.getLength()).append(",");
            Integer coveredLength = sampleCoveredLengthMap.get(sample.getId());
            if (coveredLength == null) {
                coveredLength = 0;
            }
            sb.append(coveredLength).append(",");
            double ratio = MathManager.devide(coveredLength, exon.getLength());
            sb.append(FormatManager.getSixDegitDouble(ratio)).append(",");
            sb.append(ratio >= CoverageCommand.minPercentRegionCovered ? 1 : 0);
            writeToFile(sb.toString(), bwCoverageDetailsByExon);
            sb.setLength(0);
        }
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}

Example 13 with Sample

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

the class FamilyManager method initList.

private static void initList() {
    HashMap<String, Family> familyMap = new HashMap<>();
    for (Sample sample : SampleManager.getList()) {
        if (!sample.getPaternalId().equals("0") || !sample.getMaternalId().equals("0")) {
            if (familyMap.containsKey(sample.getFamilyId())) {
                Family family = familyMap.get(sample.getFamilyId());
                family.addChild(sample);
            } else {
                Family family = new Family(sample);
                familyMap.put(sample.getFamilyId(), family);
            }
        }
    }
    for (Family family : familyMap.values()) {
        familyList.add(family);
    }
    if (familyList.isEmpty()) {
        ErrorManager.print("Missing family in sample file", ErrorManager.INPUT_PARSING);
    } else {
        LogManager.writeAndPrint("Total families: " + familyList.size());
    }
}

Example 14 with Sample

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

the class ParentalMosaic method processVariant.

@Override
public void processVariant(CalledVariant calledVar) {
    try {
        ParentalOutput output = new ParentalOutput(calledVar);
        output.countSampleGeno();
        output.calculate();
        if (output.isValid()) {
            for (Family family : FamilyManager.getList()) {
                for (Sample child : family.getChildList()) {
                    if (output.isChildValid(child)) {
                        for (Sample parent : family.getParentList()) {
                            if (output.isParentValid(parent)) {
                                doOutput(output.getString());
                            }
                        }
                    }
                }
            }
        }
    } catch (Exception e) {
        ErrorManager.send(e);
    }
}

Example 15 with Sample

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

the class FamilyManager method initList.

private static void initList() {
    HashMap<String, Family> familyMap = new HashMap<String, Family>();
    for (Sample sample : SampleManager.getList()) {
        if (sample.isCase() && !sample.getPaternalId().equals("0") && !sample.getMaternalId().equals("0")) {
            if (familyMap.containsKey(sample.getFamilyId())) {
                Family sibling = familyMap.get(sample.getFamilyId());
                sibling.addChild(sample);
            } else {
                Family sibling = new Family(sample);
                familyMap.put(sample.getFamilyId(), sibling);
            }
        }
    }
    for (Family family : familyMap.values()) {
        familyList.add(family);
    }
    if (familyList.isEmpty()) {
        ErrorManager.print("Missing sibling in sample file", ErrorManager.INPUT_PARSING);
    } else {
        LogManager.writeAndPrint("Total siblings: " + familyList.size());
    }
}