static analyzeVariant()

in client/client/dataServices/vcf/vcf-analyzer.js [18:165]
140 lines of code
39 McCabe index (conditional complexity)

    static analyzeVariant(variant, currentChromosome, sample){
        if (variant.analyzed) {
            return variant;
        }
        let zygosity = 0; // unknown

        let organismType;

        if (variant.genotypeData && variant.genotypeData.organismType) {
            organismType = variant.genotypeData.organismType;
        } else if (sample && variant.genotypeData[sample]) {
            organismType = variant.genotypeData[sample].organismType;
        } else if (variant.genotypeData) {
            const [firstSample] = Object.values(variant.genotypeData || {});
            if (firstSample && firstSample.organismType) {
                organismType = firstSample.organismType;
            }
        }
        switch ((organismType || '').toLowerCase()){
            case 'homozygous': zygosity = 1; break;
            case 'heterozygous': zygosity = 2; break;
        }
        const result = {
            analyzed: true,
            alternativeAllelesInfo: [],
            symbol: null,
            name: null,
            length: variant.endIndex - variant.startIndex + 1,
            interChromosome: false,
            isDefaultPositioning: true,
            startIndexCorrected: variant.startIndex + VcfAnalyzer.getVariantTranslation(variant),
            serverStartIndex: variant.startIndex,
            positioningInfos:[{
                startIndex: variant.startIndex + VcfAnalyzer.getVariantTranslation(variant),
                endIndex: variant.endIndex,
                length: variant.endIndex - variant.startIndex + 1
            }],
            zygosity
        };
        variant = Object.assign(variant, result);
        if (variant.type !== undefined && variant.type !== null && variant.type.toLowerCase() === 'statistic') {
            return variant;
        }
        if (variant.type.toLowerCase() === 'ins') {
            variant.endIndex = variant.startIndex;
        }
        const alternativeAllelesInfo = VcfAnalyzer.analyzeAlternativeAlleles(variant);
        let name = null;
        let symbol = null;
        let structuralSymbol = null;
        if (variant.type === null || variant.type === undefined){
            for (let i = 0; i < alternativeAllelesInfo.length; i++){
                if (alternativeAllelesInfo[i].info && alternativeAllelesInfo[i].info.type){
                    variant.type = alternativeAllelesInfo[i].info.type;
                    break;
                }
            }
        }
        if (variant.type === null || variant.type === undefined){
            variant.type = '';
        }
        switch (variant.type.toLowerCase()){
            case 'ins':
                {
                    symbol = structuralSymbol = name = '+';
                }
                break;
            case 'del':
                {
                    symbol = structuralSymbol = name = '\u2014';
                }
                break;
            case 'snv':
                {
                    symbol = structuralSymbol = name = '\u2192';
                }
                break;
        }
        if (name === null){
            symbol = structuralSymbol = name = variant.type;
        }
        if (variant.structural) {
            symbol = '';
        }
        let isInterChromosome = false;
        let currentChromosomeWithPrefix = currentChromosome;
        const currentChromosomeWithBrackets = `<${  currentChromosome  }>`;
        if (currentChromosomeWithPrefix.toLowerCase().indexOf('chr') === -1){
            currentChromosomeWithPrefix = `chr${  currentChromosomeWithPrefix}`;
        }
        alternativeAllelesInfo.forEach(alt => {
            if (alt.mate){
                alt.mate.intraChromosome = VcfAnalyzer.isCurrentChromosome(
                    {
                        chromosome: currentChromosome,
                        chromosomeWithPrefix: currentChromosomeWithPrefix,
                        chromosomeWithBrackets: currentChromosomeWithBrackets
                    }, alt.mate.chromosome);
                if (alt.mate.intraChromosome && alt.mate.position !== null && alt.mate.position !== undefined){
                    alt.mate.boundaries = {
                        startIndex: Math.min(variant.startIndex, alt.mate.position),
                        endIndex: Math.max(variant.startIndex, alt.mate.position)
                    };
                }
                isInterChromosome = isInterChromosome || !alt.mate.intraChromosome;
            }

        });

        const variantPositioningInfos = [];
        for (let i = 0; i < alternativeAllelesInfo.length; i++){
            const alt = alternativeAllelesInfo[i];
            if (alt.mate && alt.mate.boundaries){
                alt.positioningInfoIndex = variantPositioningInfos.length;
                variantPositioningInfos.push({
                    startIndex: alt.mate.boundaries.startIndex + VcfAnalyzer.getVariantTranslation(variant),
                    endIndex: alt.mate.boundaries.endIndex,
                    length: alt.mate.boundaries.endIndex - alt.mate.boundaries.startIndex + 1
                });
            }
        }

        if (variantPositioningInfos.length === 0){
            variant.isDefaultPositioning = true;
            variantPositioningInfos.push({
                startIndex: variant.startIndex + VcfAnalyzer.getVariantTranslation(variant),
                endIndex: variant.endIndex,
                length: variant.endIndex - variant.startIndex + 1
            });
        }
        else {
            variant.isDefaultPositioning = false;
        }
        const buildDisplayTextFn = function(alternativeAlleleInfo) {
            VcfAnalyzer.buildAlternativeAlleleDisplayText(variant, alternativeAlleleInfo);
        };
        alternativeAllelesInfo.forEach(buildDisplayTextFn);
        variant.analyzed = true;
        variant.alternativeAllelesInfo = alternativeAllelesInfo;
        variant.positioningInfos = variantPositioningInfos;
        variant.symbol = symbol;
        variant.name = name;
        variant.structuralSymbol = structuralSymbol;
        variant.length = variant.endIndex - variant.startIndex + 1;
        variant.interChromosome = isInterChromosome;
        variant.zygosity = zygosity;
        return variant;
    }