Java Genotype.hasAnyAttribute方法代码示例

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
 * Create the contingency table by retrieving the per-sample strand bias annotation and adding them together
 *
 * @param genotypes the genotypes from which to pull out the per-sample strand bias annotation
 * @param minCount  minimum threshold for the sample strand bias counts for each ref and alt.
 *                  If both ref and alt counts are above minCount the whole sample strand bias is added to the resulting table
 * @return the table used for several strand bias tests, will be null if none of the genotypes contain the per-sample SB annotation
 */
protected int[][] getTableFromSamples(final GenotypesContext genotypes, final int minCount) {
    if (genotypes == null) {
        throw new IllegalArgumentException("Genotypes cannot be null.");
    }

    final int[] sbArray = {0, 0, 0, 0}; // reference-forward-reverse -by- alternate-forward-reverse
    boolean foundData = false;

    for (final Genotype g : genotypes) {
        if (g.isNoCall() || !g.hasAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME))
            continue;

        foundData = true;
        final ArrayList<Integer> sbbsString = (ArrayList<Integer>) g.getAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME);
        final int[] data = Utils.list2Array(sbbsString);
        if (passesMinimumThreshold(data, minCount)) {
            for (int index = 0; index < sbArray.length; index++) {
                sbArray[index] += data[index];
            }
        }
    }

    return (foundData ? decodeSBBS(sbArray) : null);
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
@Override
public Map<String, Object> annotate(RefMetaDataTracker tracker, ChromosomeInformationShare ref, VariantContext vc) {

	// do not process if not a variant
	if (!vc.isVariant())
		return null;

	// if the genotype and strand bias are provided, calculate the
	// annotation from the Genotype (GT) field
	if (vc.hasGenotypes()) {
		for (final Genotype g : vc.getGenotypes()) {
			if (g.hasAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY)) {
				return calculateAnnotationFromGTfield(vc.getGenotypes());
			}
		}
	}

	return null;
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
@Override
//template method for calculating strand bias annotations using the three different methods
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
                                    final AnnotatorCompatible walker,
                                    final ReferenceContext ref,
                                    final Map<String, AlignmentContext> stratifiedContexts,
                                    final VariantContext vc,
                                    final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
    if (!vc.isVariant())
        return null;

    if (vc.hasGenotypes()) {
        boolean hasSB = false;
        for (final Genotype g : vc.getGenotypes()) {
            if (g.hasAnyAttribute(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME)) {
                hasSB = true;
                break;
            }
        }
        if (hasSB)
            return calculateAnnotationFromGTfield(vc.getGenotypes());
    }

    //stratifiedContexts can come come from VariantAnnotator, but will be size 0 if no reads were provided
    if (vc.isSNP() && stratifiedContexts != null && stratifiedContexts.size() > 0) {
        return calculateAnnotationFromStratifiedContexts(stratifiedContexts, vc);
    }

    //stratifiedPerReadAllelelikelihoodMap can come from HaplotypeCaller call to VariantAnnotatorEngine
    else if (stratifiedPerReadAlleleLikelihoodMap != null) {
        return calculateAnnotationFromLikelihoodMap(stratifiedPerReadAlleleLikelihoodMap, vc);
    } else
        // for non-snp variants, we  need per-read likelihoods.
        // for snps, we can get same result from simple pileup
        return null;
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
/**
 */
protected int[][] getTableFromSamples(final GenotypesContext genotypes, final int minCount) {
	if (genotypes == null) {
		if (!getTableFromSamplesWarningLogged) {
			getTableFromSamplesWarningLogged = true;
		}
		return null;
	}

	final int[] sbArray = { 0, 0, 0, 0 }; // reference-forward-reverse -by-
											// alternate-forward-reverse
	boolean foundData = false;

	for (final Genotype g : genotypes) {
		if (g.isNoCall() || !g.hasAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY))
			continue;

		foundData = true;
		int[] data;
		if (g.getAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass().equals(String.class)) {
			final String sbbsString = (String) g.getAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY);
			data = encodeSBBS(sbbsString);
		} else if (g.getAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY).getClass()
				.equals(ArrayList.class)) {
			ArrayList sbbsList = (ArrayList) g.getAnyAttribute(GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY);
			data = encodeSBBS(sbbsList);
		} else
			throw new IllegalArgumentException(
					"Unexpected " + GaeaVCFConstants.STRAND_BIAS_BY_SAMPLE_KEY + " type");

		if (passesMinimumThreshold(data, minCount)) {
			for (int index = 0; index < sbArray.length; index++) {
				sbArray[index] += data[index];
			}
		}
	}

	return (foundData ? decodeSBBS(sbArray) : null);
}
 

import htsjdk.variant.variantcontext.Genotype; //导入方法依赖的package包/类
private static boolean parseOtherGenotypeFields(String field, VariantContext vc,
    ListValue.Builder lvBuilder, Genotype g, VCFHeader header) {

  if (!g.hasAnyAttribute(field)) {
    return false;
  }

  final VCFFormatHeaderLine metaData = header.getFormatHeaderLine(field);
  if (metaData == null) {
    logger.log(Level.WARNING, String.format("Could not find matching VCF header field for "
        + "genotype field %s", field));
    return false;
  }

  VCFHeaderLineType type = metaData.getType();
  Object value = g.getExtendedAttribute(field);
  final int fieldCount = metaData.getCount(vc);
  if (fieldCount == 1) {
    lvBuilder.addValues(createTypedValue(type, value));
    return true;
  }

  if (!(value instanceof String)) {
    throw new IllegalStateException("received non-Flag genotype field as non-String type");
  }
  String[] valueArray = ((String) value).split(",");
  if (valueArray.length == 1) {
    throw new IllegalStateException(String.format("header indicating a count greater than 1 "
        + "with non-List type found for field %s",
        field));
  }

  boolean allFalse = true;
  for (int i = 0; i < valueArray.length; i++) {
    VCFHeaderLineType thisType = VCFHeaderLineType.String;
    if (!valueArray[i].equals(VCFConstants.MISSING_VALUE_v4)) {
      thisType = type;
      allFalse = false;
    }

    lvBuilder.addValues(createTypedValue(thisType, valueArray[i]));
  }
  // We only add the lvBuilder if there is at least one non-missing value
  return !allFalse;
}