public VariantSetStats convertStats(org.opencb.biodata.models.variant.avro.legacy.VariantGlobalStats legacyStats) { return new VariantSetStats(org.opencb.biodata.models.variant.metadata.VariantSetStats.newBuilder() .setNumVariants(legacyStats.getNumRecords()) .setMeanQuality(legacyStats.getMeanQuality().floatValue()) .setNumPass(legacyStats.getPassCount()) .setNumSamples(legacyStats.getSamplesCount()) .setTiTvRatio(legacyStats.getTransitionsCount() / (float) legacyStats.getTransversionsCount()) .setVariantTypeCounts(legacyStats.getVariantTypeCounts()) .setConsequenceTypesCounts(legacyStats.getConsequenceTypesCount()) .setStdDevQuality(0) .setChromosomeStats(legacyStats.getChromosomeCounts().entrySet().stream() .collect(Collectors.toMap(Map.Entry::getKey, entry -> new ChromosomeStats(entry.getValue(), 0F)))).build()); }
if (isValidValue(fields()[0], other.numVariants)) { this.numVariants = data().deepCopy(fields()[0].schema(), other.numVariants); fieldSetFlags()[0] = true; if (isValidValue(fields()[1], other.numSamples)) { this.numSamples = data().deepCopy(fields()[1].schema(), other.numSamples); fieldSetFlags()[1] = true; if (isValidValue(fields()[2], other.numPass)) { this.numPass = data().deepCopy(fields()[2].schema(), other.numPass); fieldSetFlags()[2] = true; if (isValidValue(fields()[3], other.tiTvRatio)) { this.tiTvRatio = data().deepCopy(fields()[3].schema(), other.tiTvRatio); fieldSetFlags()[3] = true; if (isValidValue(fields()[4], other.meanQuality)) { this.meanQuality = data().deepCopy(fields()[4].schema(), other.meanQuality); fieldSetFlags()[4] = true; if (isValidValue(fields()[5], other.stdDevQuality)) { this.stdDevQuality = data().deepCopy(fields()[5].schema(), other.stdDevQuality); fieldSetFlags()[5] = true; if (isValidValue(fields()[6], other.numRareVariants)) { this.numRareVariants = data().deepCopy(fields()[6].schema(), other.numRareVariants); fieldSetFlags()[6] = true; if (isValidValue(fields()[7], other.variantTypeCounts)) {
@Override public VariantSetStats build() { try { VariantSetStats record = new VariantSetStats(); record.numVariants = fieldSetFlags()[0] ? this.numVariants : (java.lang.Integer) defaultValue(fields()[0]); record.numSamples = fieldSetFlags()[1] ? this.numSamples : (java.lang.Integer) defaultValue(fields()[1]); record.numPass = fieldSetFlags()[2] ? this.numPass : (java.lang.Integer) defaultValue(fields()[2]); record.tiTvRatio = fieldSetFlags()[3] ? this.tiTvRatio : (java.lang.Float) defaultValue(fields()[3]); record.meanQuality = fieldSetFlags()[4] ? this.meanQuality : (java.lang.Float) defaultValue(fields()[4]); record.stdDevQuality = fieldSetFlags()[5] ? this.stdDevQuality : (java.lang.Float) defaultValue(fields()[5]); record.numRareVariants = fieldSetFlags()[6] ? this.numRareVariants : (java.util.List<org.opencb.biodata.models.variant.metadata.VariantsByFrequency>) defaultValue(fields()[6]); record.variantTypeCounts = fieldSetFlags()[7] ? this.variantTypeCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[7]); record.variantBiotypeCounts = fieldSetFlags()[8] ? this.variantBiotypeCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[8]); record.consequenceTypesCounts = fieldSetFlags()[9] ? this.consequenceTypesCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[9]); record.chromosomeStats = fieldSetFlags()[10] ? this.chromosomeStats : (java.util.Map<java.lang.String,org.opencb.biodata.models.variant.metadata.ChromosomeStats>) defaultValue(fields()[10]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
if (isValidValue(fields()[0], other.numVariants)) { this.numVariants = data().deepCopy(fields()[0].schema(), other.numVariants); fieldSetFlags()[0] = true; if (isValidValue(fields()[1], other.numSamples)) { this.numSamples = data().deepCopy(fields()[1].schema(), other.numSamples); fieldSetFlags()[1] = true; if (isValidValue(fields()[2], other.numPass)) { this.numPass = data().deepCopy(fields()[2].schema(), other.numPass); fieldSetFlags()[2] = true; if (isValidValue(fields()[3], other.tiTvRatio)) { this.tiTvRatio = data().deepCopy(fields()[3].schema(), other.tiTvRatio); fieldSetFlags()[3] = true; if (isValidValue(fields()[4], other.meanQuality)) { this.meanQuality = data().deepCopy(fields()[4].schema(), other.meanQuality); fieldSetFlags()[4] = true; if (isValidValue(fields()[5], other.stdDevQuality)) { this.stdDevQuality = data().deepCopy(fields()[5].schema(), other.stdDevQuality); fieldSetFlags()[5] = true; if (isValidValue(fields()[6], other.numRareVariants)) { this.numRareVariants = data().deepCopy(fields()[6].schema(), other.numRareVariants); fieldSetFlags()[6] = true; if (isValidValue(fields()[7], other.variantTypeCounts)) {
/** Checks whether the 'chromosomeStats' field has been set */ public boolean hasChromosomeStats() { return fieldSetFlags()[10]; }
/** Checks whether the 'numPass' field has been set */ public boolean hasNumPass() { return fieldSetFlags()[2]; }
/** Checks whether the 'numVariants' field has been set */ public boolean hasNumVariants() { return fieldSetFlags()[0]; }
/** Checks whether the 'variantBiotypeCounts' field has been set */ public boolean hasVariantBiotypeCounts() { return fieldSetFlags()[8]; }
/** Checks whether the 'stdDevQuality' field has been set */ public boolean hasStdDevQuality() { return fieldSetFlags()[5]; }
/** Checks whether the 'meanQuality' field has been set */ public boolean hasMeanQuality() { return fieldSetFlags()[4]; }
/** Checks whether the 'tiTvRatio' field has been set */ public boolean hasTiTvRatio() { return fieldSetFlags()[3]; }
/** Checks whether the 'numSamples' field has been set */ public boolean hasNumSamples() { return fieldSetFlags()[1]; }
/** Checks whether the 'consequenceTypesCounts' field has been set */ public boolean hasConsequenceTypesCounts() { return fieldSetFlags()[9]; }
/** Checks whether the 'numRareVariants' field has been set */ public boolean hasNumRareVariants() { return fieldSetFlags()[6]; }
/** Creates a new VariantSetStats RecordBuilder */ public static org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder newBuilder() { return new org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder(); }
/** Clears the value of the 'numRareVariants' field */ public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearNumRareVariants() { numRareVariants = null; fieldSetFlags()[6] = false; return this; }
/** Clears the value of the 'tiTvRatio' field */ public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearTiTvRatio() { fieldSetFlags()[3] = false; return this; }
/** Clears the value of the 'numPass' field */ public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearNumPass() { fieldSetFlags()[2] = false; return this; }
/** Sets the value of the 'chromosomeStats' field */ public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setChromosomeStats(java.util.Map<java.lang.String,org.opencb.biodata.models.variant.metadata.ChromosomeStats> value) { validate(fields()[10], value); this.chromosomeStats = value; fieldSetFlags()[10] = true; return this; }
/** Sets the value of the 'consequenceTypesCounts' field */ public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setConsequenceTypesCounts(java.util.Map<java.lang.String,java.lang.Integer> value) { validate(fields()[9], value); this.consequenceTypesCounts = value; fieldSetFlags()[9] = true; return this; }