Java GenotypesContext.get方法代码示例

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Fix the AD for the GenotypesContext of a VariantContext that has been subset
 *
 * @param originalGs       the original GenotypesContext
 * @param originalVC       the original VariantContext
 * @param allelesToUse     the new (sub)set of alleles to use
 * @return a new non-null GenotypesContext
 */
static private GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {

    // the bitset representing the allele indexes we want to keep
    final boolean[] alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

    // the samples
    final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

    // create the new genotypes
    for ( int k = 0; k < originalGs.size(); k++ ) {
        final Genotype g = originalGs.get(sampleIndices.get(k));
        newGTs.add(fixAD(g, alleleIndexesToUse, allelesToUse.size()));
    }

    return newGTs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Returns a AF calculator capable to handle a particular variant-context.
 * @param variantContext the target context build.
 * @param defaultPloidy the assumed ploidy in case that there is no a GT call present to determine it.
 * @return never {@code null}
 */
public AFCalculator getInstance(final VariantContext variantContext, final int defaultPloidy, final int maximumAltAlleles) {
    if (variantContext == null)
        throw new IllegalArgumentException("variant context cannot be null");

    final int sampleCount = variantContext.getNSamples();
    if  (sampleCount == 0)
        return getInstance(defaultPloidy,maximumAltAlleles);

    final GenotypesContext genotypes = variantContext.getGenotypes();

    final Genotype firstGenotype = genotypes.get(0);
    int ploidy = firstGenotype.getPloidy();
    if (ploidy <= 0) ploidy = defaultPloidy;
    for (int i = 1 ; i < sampleCount; i++) {
        final Genotype genotype = genotypes.get(i);
        final int declaredPloidy = genotype.getPloidy();
        final int actualPloidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if (actualPloidy != ploidy) {
            ploidy = AFCalculatorImplementation.UNBOUND_PLOIDY;
            break;
        }
    }
    return getInstance(ploidy,Math.min(variantContext.getNAlleles() - 1, maximumAltAlleles));
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Fix the AD for the GenotypesContext of a VariantContext that has been
 * subset
 *
 * @param originalGs
 *            the original GenotypesContext
 * @param originalVC
 *            the original VariantContext
 * @param allelesToUse
 *            the new (sub)set of alleles to use
 * @return a new non-null GenotypesContext
 */
public static GenotypesContext fixADFromSubsettedAlleles(final GenotypesContext originalGs,
		final VariantContext originalVC, final List<Allele> allelesToUse) {
	if (originalGs == null)
		throw new IllegalArgumentException("the original Gs cannot be null");
	if (originalVC == null)
		throw new IllegalArgumentException("the original VC cannot be null");
	if (allelesToUse == null)
		throw new IllegalArgumentException("the alleles to use list cannot be null");

	// the bitset representing the allele indexes we want to keep
	final BitSet alleleIndexesToUse = getAlleleIndexBitset(originalVC, allelesToUse);

	// the new genotypes to create
	final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

	// the samples
	final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

	// create the new genotypes
	for (int k = 0; k < originalGs.size(); k++) {
		final Genotype g = originalGs.get(sampleIndices.get(k));
		newGTs.add(fixAD(g, alleleIndexesToUse));
	}

	return newGTs;
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Returns a AF calculator capable to handle a particular variant-context.
 * @param variantContext the target context build.
 * @param defaultPloidy the assumed ploidy in case that there is no a GT call present to determine it.
 * @return never {@code null}
 */
public AFCalculator getInstance(final VariantContext variantContext, final int defaultPloidy, final int maximumAltAlleles) {
    Utils.nonNull(variantContext, "variant context cannot be null");

    final int sampleCount = variantContext.getNSamples();
    if  (sampleCount == 0) {
        return getInstance(defaultPloidy, maximumAltAlleles);
    }

    final GenotypesContext genotypes = variantContext.getGenotypes();

    final Genotype firstGenotype = genotypes.get(0);
    int ploidy = firstGenotype.getPloidy();
    if (ploidy <= 0) {
        ploidy = defaultPloidy;
    }
    for (int i = 1 ; i < sampleCount; i++) {
        final Genotype genotype = genotypes.get(i);
        final int declaredPloidy = genotype.getPloidy();
        final int actualPloidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if (actualPloidy != ploidy) {
            ploidy = AFCalculatorImplementation.UNBOUND_PLOIDY;
            break;
        }
    }
    return getInstance(ploidy, Math.min(variantContext.getNAlleles() - 1, maximumAltAlleles));
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * Create the new GenotypesContext with the subsetted PLs and ADs
 *
 * @param originalGs               the original GenotypesContext
 * @param vc                       the original VariantContext
 * @param allelesToUse             the actual alleles to use with the new Genotypes
 * @param likelihoodIndexesToUse   the indexes in the PL to use given the allelesToUse (@see #determineLikelihoodIndexesToUse())
 * @param assignGenotypes          assignment strategy for the (subsetted) PLs
 * @return a new non-null GenotypesContext
 */
private static GenotypesContext createGenotypesWithSubsettedLikelihoods(final GenotypesContext originalGs,
                                                                        final VariantContext vc,
                                                                        final List<Allele> allelesToUse,
                                                                        final List<Integer> likelihoodIndexesToUse,
                                                                        final GenotypeAssignmentMethod assignGenotypes) {
    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create(originalGs.size());

    // make sure we are seeing the expected number of likelihoods per sample
    final int expectedNumLikelihoods = GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), 2);

    // the samples
    final List<String> sampleIndices = originalGs.getSampleNamesOrderedByName();

    // create the new genotypes
    for ( int k = 0; k < originalGs.size(); k++ ) {
        final Genotype g = originalGs.get(sampleIndices.get(k));
        final GenotypeBuilder gb = new GenotypeBuilder(g);

        // create the new likelihoods array from the alleles we are allowed to use
        double[] newLikelihoods;
        if ( !g.hasLikelihoods() ) {
            // we don't have any likelihoods, so we null out PLs and make G ./.
            newLikelihoods = null;
            gb.noPL();
        } else {
            final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
            if ( likelihoodIndexesToUse == null ) {
                newLikelihoods = originalLikelihoods;
            } else if ( originalLikelihoods.length != expectedNumLikelihoods ) {
                newLikelihoods = null;
            } else {
                newLikelihoods = new double[likelihoodIndexesToUse.size()];
                int newIndex = 0;
                for ( final int oldIndex : likelihoodIndexesToUse )
                    newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];

                // might need to re-normalize
                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
            }

            if ( newLikelihoods == null || likelihoodsAreUninformative(newLikelihoods) )
                gb.noPL();
            else
                gb.PL(newLikelihoods);
        }

        updateGenotypeAfterSubsetting(g.getAlleles(), gb, assignGenotypes, newLikelihoods, allelesToUse);
        newGTs.add(gb.make());
    }

    return fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
/**
 * From a given variant context, extract a given subset of alleles, and update genotype context accordingly,
 * including updating the PL's, and assign genotypes accordingly
 *
 * @param vc              variant context with alleles and genotype likelihoods
 * @param defaultPloidy   ploidy to assume in case that {@code vc} does not contain that information
 *                        for a sample.
 * @param allelesToUse    alleles to subset
 * @param assignGenotypes true: assign hard genotypes, false: leave as no-call
 * @return GenotypesContext with new PLs
 */
public GenotypesContext subsetAlleles(final VariantContext vc, final int defaultPloidy,
                                      final List<Allele> allelesToUse,
                                      final boolean assignGenotypes) {
    // the genotypes with PLs
    final GenotypesContext oldGTs = vc.getGenotypes();

    // samples
    final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create();

    // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
    final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
    final int numNewAltAlleles = allelesToUse.size() - 1;


    // create the new genotypes
    for (int k = 0; k < oldGTs.size(); k++) {
        final Genotype g = oldGTs.get(sampleIndices.get(k));
        final int declaredPloidy = g.getPloidy();
        final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if (!g.hasLikelihoods()) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
            continue;
        }

        // create the new likelihoods array from the alleles we are allowed to use
        final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
        double[] newLikelihoods;

        // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
        // and subsetting
        if (numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
            newLikelihoods = originalLikelihoods;
        } else {
            newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);

            // might need to re-normalize
            newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
        }

        // if there is no mass on the (new) likelihoods, then just no-call the sample
        if (MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GATKVariantContextUtils.noCallAlleles(ploidy)));
        } else {
            final GenotypeBuilder gb = new GenotypeBuilder(g);

            if (numNewAltAlleles == 0)
                gb.noPL();
            else
                gb.PL(newLikelihoods);

            // if we weren't asked to assign a genotype, then just no-call the sample
            if (!assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL)
                gb.alleles(GATKVariantContextUtils.noCallAlleles(ploidy));
            else
                assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);
            newGTs.add(gb.make());
        }
    }

    return newGTs;

}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
@Override
@Requires("vc != null && allelesToUse != null")
public GenotypesContext subsetAlleles(VariantContext vc, int defaultPloidy, List<Allele> allelesToUse, boolean assignGenotypes) {
    // the genotypes with PLs
    final GenotypesContext oldGTs = vc.getGenotypes();

    // samples
    final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();

    // the new genotypes to create
    final GenotypesContext newGTs = GenotypesContext.create();

    // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
    final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
    final int numNewAltAlleles = allelesToUse.size() - 1;


    // create the new genotypes
    for ( int k = 0; k < oldGTs.size(); k++ ) {
        final Genotype g = oldGTs.get(sampleIndices.get(k));
        final int declaredPloidy = g.getPloidy();
        final int ploidy = declaredPloidy <= 0 ? defaultPloidy : declaredPloidy;
        if ( !g.hasLikelihoods() ) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(),GaeaGvcfVariantContextUtils.noCallAlleles(ploidy)));
            continue;
        }

        // create the new likelihoods array from the alleles we are allowed to use
        final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
        double[] newLikelihoods;

        // Optimization: if # of new alt alleles = 0 (pure ref call), keep original likelihoods so we skip normalization
        // and subsetting
        if ( numOriginalAltAlleles == numNewAltAlleles || numNewAltAlleles == 0) {
            newLikelihoods = originalLikelihoods;
        } else {
            newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);

            // might need to re-normalize
            newLikelihoods = GvcfMathUtils.normalizeFromLog10(newLikelihoods, false, true);
        }

        // if there is no mass on the (new) likelihoods, then just no-call the sample
        if ( GvcfMathUtils.sum(newLikelihoods) > GaeaGvcfVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
            newGTs.add(GenotypeBuilder.create(g.getSampleName(), GaeaGvcfVariantContextUtils.noCallAlleles(ploidy)));
        } else {
            final GenotypeBuilder gb = new GenotypeBuilder(g);
            final String sampleName = g.getSampleName();

            if ( numNewAltAlleles == 0 )
                gb.noPL();
            else
                gb.PL(newLikelihoods);

            // if we weren't asked to assign a genotype, then just no-call the sample
            if ( !assignGenotypes || GvcfMathUtils.sum(newLikelihoods) > GaeaGvcfVariantContextUtils.SUM_GL_THRESH_NOCALL )
                gb.alleles(GaeaGvcfVariantContextUtils.noCallAlleles(ploidy));
            else
                assignGenotype(gb, vc, sampleName, newLikelihoods, allelesToUse, ploidy);
            newGTs.add(gb.make());
        }
    }

    return GaeaGvcfVariantContextUtils.fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
private void report(
	final File f,
	final VCFHeader header,
	final VariantContext ctx,
	final Mutation mpos
	)
{

final GenotypesContext genotypes=ctx.getGenotypes();
if(genotypes==null || genotypes.isEmpty())
	{
	reportPos(f,header,ctx);
	out.println();
	}
else
	{
	VCFFormatHeaderLine DP4header = header.getFormatHeaderLine("DP4");
	if(DP4header!=null &&
		!( DP4header.getType().equals(VCFHeaderLineType.Integer) &&
			DP4header.getCount()==4))
		{
		DP4header=null;
		}
	for(int i=0;i< genotypes.size();++i)
		{
		Genotype g=genotypes.get(i);
		if(!g.isCalled() && this.hideNoCall) continue;
		if(g.isHomRef() && this.hideHomRef) continue;
		reportPos(f,header,ctx);
		out.print('\t');
		out.print(g.getSampleName());
		out.print('\t');
		out.print(g.getType());
		out.print('\t');
		List<Allele> alleles=g.getAlleles();
		for(int na=0;na<alleles.size();++na)
			{
			if(na>0) out.print(" ");
			out.print(alleles.get(na).getDisplayString());
			}
		if(DP4header!=null)
			{
			final  Object dp4=g.getExtendedAttribute("DP4");
			if(dp4!=null )
				{
				out.print('\t');
				out.print(String.valueOf(dp4));//it's a String not an int[] ??
				}
			}
		out.println();
		}
	}
}
 

import htsjdk.variant.variantcontext.GenotypesContext; //导入方法依赖的package包/类
@Override
public int doWork(final List<String> args)
	{
	PrintStream out = null;
	VcfIterator in = null;
	try
		{
		in = super.openVcfIterator(oneAndOnlyOneFile(args));
	
		out = openFileOrStdoutAsPrintStream(outputFile);
		
		
		out.println("CHR\tPOS\tID\tREF\tALT\tTOTAL_CNT\tALT_CNT\tFRQ");
		while(in.hasNext() && !out.checkError())
			{
			
			final VariantContext ctx=in.next();
			final Allele ref=ctx.getReference();
			if(ref==null) continue;
			if(ctx.getNSamples()==0 || ctx.getAlternateAlleles().isEmpty()) continue;
			final Allele alt=ctx.getAltAlleleWithHighestAlleleCount();
			if(alt==null) continue;
			
			GenotypesContext genotypes=ctx.getGenotypes();
			if(genotypes==null) continue;
			int total_ctn=0;
			int alt_ctn=0;
			for(int i=0;i< genotypes.size();++i)
				{
				Genotype g=genotypes.get(i);
				for(final Allele allele: g.getAlleles())
					{
					if(allele.equals(ref))
						{
						total_ctn++;
						}
					else if (allele.equals(alt))
						{
						total_ctn++;
						alt_ctn++;
						}
					}
				
				}
			
			
			out.print(ctx.getContig());
			out.print("\t");
			out.print(ctx.getStart());
			out.print("\t");
			out.print(ctx.hasID()?ctx.getID():".");
			out.print("\t");
			out.print(ref.getBaseString());
			out.print("\t");
			out.print(alt.getBaseString());
			out.print("\t");
			out.print(total_ctn);
			out.print("\t");
			out.print(alt_ctn);
			out.print("\t");
			out.print(alt_ctn/(float)total_ctn);
			out.println();
			}
		out.flush();
		
		
	return RETURN_OK;
	}
catch(Exception err)
	{
	LOG.error(err);
	return -1;
	}
finally
	{
	CloserUtil.close(out);
	CloserUtil.close(in);
	}
}