Java GenotypeType.NO_CALL属性代码示例

private boolean[] basicStatics(Genotype gt, IntArray array, Allele Ref,GenotypeType type) {
	boolean[] conf = new boolean[4];
	Arrays.fill(conf, false);

	List<Allele> alts = gt.getAlleles();
	if(type == GenotypeType.NO_CALL || type == GenotypeType.HOM_REF)
		return conf;
	boolean isBiallelic = determinePolymorphicType(Ref, alts, conf);
	if(!isBiallelic)
		return new boolean[]{false,false,false,false};
	
	array.incr(VariantEnum.VARIANTS);
	if (conf[0])
		array.incr(VariantEnum.SNPS);
	if (conf[1])
		array.incr(VariantEnum.MNPS);
	if (conf[2]) {
		array.incr(VariantEnum.INSERTIONS);
	}
	if (conf[3]) {
		array.incr(VariantEnum.DELETIONS);
	}

	if (conf[2] || conf[3])
		array.incr(VariantEnum.INDELS);

	if (conf[0] && isBiallelic && isTransition(alts.get(0),alts.get(1))) {
		array.incr(VariantEnum.TRANSITIONS);
	} else if (conf[0] && isBiallelic)
		array.incr(VariantEnum.TRANSVERSIONS);

	return conf;
}
 

private GenotypeType determineType(final List<Allele> alleles) {
    if ( alleles.isEmpty() )
        return GenotypeType.UNAVAILABLE;

    boolean sawNoCall = false, sawMultipleAlleles = false;
    Allele observedAllele = null;

    for ( final Allele allele : alleles ) {
        if ( allele.isNoCall() )
            sawNoCall = true;
        else if ( observedAllele == null )
            observedAllele = allele;
        else if ( !allele.equals(observedAllele) )
            sawMultipleAlleles = true;
    }

    if ( sawNoCall ) {
        if ( observedAllele == null )
            return GenotypeType.NO_CALL;
        return GenotypeType.MIXED;
    }

    if ( observedAllele == null )
        throw new IllegalStateException("BUG: there are no alleles present in this genotype but the alleles list is not null");

    return sawMultipleAlleles ? GenotypeType.HET : observedAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR;
}
 

private void initGenotypeTypeField(VariantContext variant) {
    String mutationString = null;
    GenotypeType gtt = GenotypeType.NO_CALL;
    String prefSampleName = VariantReviewPlugin.getPreferentialSampleName();

    //If there is only one sample, or we find the preferential sample,
    //use that data.
    for (String sampleName : variant.getSampleNamesOrderedByName()) {
        boolean isPref = sampleName.equalsIgnoreCase(prefSampleName);
        if (isPref || mutationString == null) {
            if(!variantContext.isBiallelic())
                sampleVC = variantContext.subContextFromSamples(Collections.singleton(sampleName), true);
            else
                sampleVC = variantContext;

            mutationString = ParsingUtils.join(",", ParsingUtils.sortList(sampleVC.getAlleles()));
            Genotype genotype = sampleVC.getGenotype(sampleName);
            gtt = genotype.getType();
            if (isPref) break;
        } else {
            //If we have several samples with different mutations, don't know which
            //to pick. Make that obvious to the user
            if (gtt != sampleVC.getGenotype(sampleName).getType()) {
                mutationString = "./.";
                gtt = GenotypeType.UNAVAILABLE;
            }
        }
    }

    genotypeTypeField.setSelectedItem(gtt);
    mutField.setText(mutationString);
    mutField.setToolTipText(mutationString);
}
 

private void genotype(Genotype gt, String contig, IntArray statics, boolean[] conf,GenotypeType type) {
	if(type == GenotypeType.NO_CALL)
		return;
	boolean snp = conf[0], mnp = conf[1], insertion = conf[2], deletion = conf[3];
	contig = contig.toUpperCase();
	
	if (type ==  GenotypeType.HOM_VAR || type == GenotypeType.HOM_REF) {
		statics.incr(VariantEnum.HOM);
		if (snp)
			statics.incr(VariantEnum.SNP_HOM);
		if (mnp)
			statics.incr(VariantEnum.MNP_HOM);
		if (insertion) {
			statics.incr(VariantEnum.INSERTION_HOM);
		}
		if (deletion) {
			statics.incr(VariantEnum.DELETION_HOM);
		}

		if (insertion || deletion)
			statics.incr(VariantEnum.INDEL_HOM);

		if (contig.equals("CHRX") || contig.equals("X")) {
			statics.incr(VariantEnum.CHROM_X_HOM);
		}

		if (type == GenotypeType.HOM_REF)
			statics.incr(VariantEnum.HOM_RR);
		else
			statics.incr(VariantEnum.HOM_AA);
	}else{
		statics.incr(VariantEnum.HET);
		if (snp)
			statics.incr(VariantEnum.SNP_HET);
		if (mnp)
			statics.incr(VariantEnum.MNP_HET);
		if (insertion) {
			statics.incr(VariantEnum.INSERTION_HET);
		}
		if (deletion) {
			statics.incr(VariantEnum.DELETION_HET);
		}

		if (insertion || deletion)
			statics.incr(VariantEnum.INDEL_HET);

		if (contig.equals("CHRX") || contig.equals("X")) {
			statics.incr(VariantEnum.CHROM_X_HET);
		}

		if (gt.getAllele(0).isNonReference() && gt.getAllele(1).isNonReference())
			statics.incr(VariantEnum.HET_AA);
		else
			statics.incr(VariantEnum.HET_RA);
	}
}