Java Code Examples for htsjdk.variant.variantcontext.Genotype#getExtendedAttribute()

public void add(@NotNull final VariantContext context) {
    final VariantHotspot hotspot = hotspot(context);
    final Counter counter = map.computeIfAbsent(hotspot, Counter::new);
    final Genotype genotype = context.getGenotype(0);
    if (!hotspot.ref().contains("N") && genotype.hasExtendedAttribute(SageVCF.RAW_ALLELIC_DEPTH)) {
        String rawDepth = (String) genotype.getExtendedAttribute(SageVCF.RAW_ALLELIC_DEPTH);
        int allelicDepth = Integer.parseInt(rawDepth.split(",")[1]);
        if (allelicDepth >= MIN_INPUT_ALLELIC_DEPTH) {
            counter.increment(allelicDepth);
        }
    }
}
 

/**
 * Returns an attribute as a string.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 */
public static String getAttributeAsString(final Genotype genotype, final String key, final String defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        return String.valueOf(value);
    }
}
 

/**
 * Returns an attribute as an integer.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 * @throws NumberFormatException if the annotation exists, and its string transformation cannot be convert into an integer.
 */
public static int getAttributeAsInt(final Genotype genotype, final String key, final int defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        try {
            return Integer.parseInt(String.valueOf(value));
        } catch (final NumberFormatException ex) {
            throw new NumberFormatException(String.format("attribute '%s' does not have a valid integer value: '%s'", key, String.valueOf(value)));
        }
    }
}
 

/**
 * Returns an attribute as a double.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 * @throws NumberFormatException if the annotation exists, and its string transformation cannot be convert into a double.
 */
public static double getAttributeAsDouble(final Genotype genotype, final String key, final double defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        try {
            return Double.parseDouble(String.valueOf(value));
        } catch (final NumberFormatException ex) {
            throw new NumberFormatException(String.format("attribute '%s' does not have a valid double value: '%s'", key, String.valueOf(value)));
        }
    }
}
 

/**
 * Gets an attribute value by transforming the string its string representation using an translation function.
 * @param g the source genotype.
 * @param key the attribute key.
 * @param translate the function to translate from an string to the return class of interest.
 * @param defaultValue the default value to return in case the attribute is not defined or is declared as missing.
 * @param <T> the return object type.
 * @return {@code null} or an instance of the class {@link T}
 */
public static <T> T getAttributeAsObject(final Genotype g, final String key, final Function<String, T> translate,
                                                                          final T defaultValue) {
    Utils.nonNull(g);
    Utils.nonNull(key);
    final Object value = g.getExtendedAttribute(key);
    if (value == null || VCFConstants.MISSING_VALUE_v4.equals(value)) {
        return defaultValue;
    } else {
        return translate.apply(String.valueOf(value));
    }
}
 

static private String anchorFromVc(final VariantContext vc) {
    final Genotype genotype = vc.getGenotype(0);

    if (genotype == null || !genotype.hasExtendedAttribute(VCFConstants.PHASE_SET_KEY)) {
        return SYNTHETIC_PHASESET_PREFIX + "_" + vc.getContig() + "_" + vc.getStart();
    } else {
        return PHASESET_PREFIX + "_" + vc.getContig() + "_" + genotype.getExtendedAttribute(VCFConstants.PHASE_SET_KEY);
    }
}
 

/**
 * Returns an attribute as an integer.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 * @throws NumberFormatException if the annotation exists, and its string transformation cannot be convert into an integer.
 */
public static int getAttributeAsInt(final Genotype genotype, final String key, final int defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        try {
            return Integer.parseInt(String.valueOf(value));
        } catch (final NumberFormatException ex) {
            throw new NumberFormatException(String.format("attribute '%s' does not have a valid integer value: '%s'", key, String.valueOf(value)));
        }
    }
}
 

/**
 * Returns an attribute as a double.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 * @throws NumberFormatException if the annotation exists, and its string transformation cannot be convert into a double.
 */
public static double getAttributeAsDouble(final Genotype genotype, final String key, final double defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        try {
            return Double.parseDouble(String.valueOf(value));
        } catch (final NumberFormatException ex) {
            throw new NumberFormatException(String.format("attribute '%s' does not have a valid double value: '%s'", key, String.valueOf(value)));
        }
    }
}
 

/**
 * Returns an attribute as a string.
 * @param genotype the source genotype.
 * @param key the attribute key.
 * @param defaultValue default value to return in case the attribute does not have a value defined.
 * @return the string version of the attribute value.
 * @throws IllegalArgumentException if {@code genotype} or {@code key} is {@code null}.
 */
public static String getAttributeAsString(final Genotype genotype, final String key, final String defaultValue) {
    Utils.nonNull(genotype);
    Utils.nonNull(key);
    final Object value = genotype.getExtendedAttribute(key);
    if (value == null) {
        return defaultValue;
    } else {
        return String.valueOf(value);
    }
}
 

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;
}
 

private void updateDetailMetric(final CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics metric,
                                final Genotype genotype,
                                final VariantContext vc,
                                final boolean hasSingletonSample) {
    metric.NUM_ASSAYS++;
    if (!vc.isFiltered() || vc.getCommonInfo().getFilters().contains(InfiniumVcfFields.DUPE)) {
        metric.NUM_NON_FILTERED_ASSAYS++;
        if (genotype.isCalled()) {
            metric.NUM_CALLS++;
            String gtA = (String) genotype.getExtendedAttribute(InfiniumVcfFields.GTA, genotype.getGenotypeString());
            if (!gtA.equals(VCFConstants.EMPTY_GENOTYPE)) {
                metric.NUM_AUTOCALL_CALLS++;
            }
        } else {
            metric.NUM_NO_CALLS++;
        }

        if (vc.isSNP()) {
            // Biallelic SNPs
            final boolean isInDbSnp = dbsnp.snps.isDbSnpSite(vc.getContig(), vc.getStart());

            metric.NUM_SNPS++;

            if (isInDbSnp) {
                metric.NUM_IN_DB_SNP++;
            }
        } else if (vc.isIndel()) {
            metric.NUM_INDELS++;
        }

        if (hasSingletonSample) {
            metric.NUM_SINGLETONS++;
        }

        if (genotype.isHet()) {
            metric.numHets++;
        } else if (genotype.isHomVar()) {
            metric.numHomVar++;
        }
    } else {
        metric.NUM_FILTERED_ASSAYS++;
        if (vc.getCommonInfo().getFilters().contains(InfiniumVcfFields.ZEROED_OUT_ASSAY)) {
            // A "zeroed-out SNP".  Marked as unusable/uncallable
            metric.NUM_ZEROED_OUT_ASSAYS++;
        }
    }
}
 

private static Optional<String> makePhasingString(final Genotype genotype) {
    final String pgt = (String) genotype.getExtendedAttribute(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_GT_KEY, null);
    final String pid = (String) genotype.getExtendedAttribute(GATKVCFConstants.HAPLOTYPE_CALLER_PHASING_ID_KEY, null);
    return (pgt == null || pid == null) ? Optional.empty() : Optional.of(pgt + pid);
}
 

/**
 *  Get field value as a string.  This method can be slow.  If the field value is empty or the field does not exist,
 *   returns {@link VCFConstants#MISSING_VALUE_v4}.
 *
 * @param g genotype Never {@code null}
 * @param fieldName Name of the field (format field).
 * @return field value or {@link VCFConstants#MISSING_VALUE_v4}
 */
public static String getGenotypeString(final Genotype g, final String fieldName) {
    Utils.nonNull(g);
    final Object genotypeExtendedAttribute = g.getExtendedAttribute(fieldName, VCFConstants.MISSING_VALUE_v4);
    return String.valueOf(genotypeExtendedAttribute);
}