org.opencb.biodata.models.variant.metadata.VariantSetStats Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.metadata;
@SuppressWarnings("all")
/** Variant statistics for a set of variants.
The variants set can be contain a whole study, a cohort, a sample, a region, ... */
@org.apache.avro.specific.AvroGenerated
public class VariantSetStats extends org.apache.avro.specific.SpecificRecordBase implements org.apache.avro.specific.SpecificRecord {
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"record\",\"name\":\"VariantSetStats\",\"namespace\":\"org.opencb.biodata.models.variant.metadata\",\"doc\":\"Variant statistics for a set of variants.\\n The variants set can be contain a whole study, a cohort, a sample, a region, ...\",\"fields\":[{\"name\":\"variantCount\",\"type\":\"long\",\"doc\":\"Number of variants in the variant set\"},{\"name\":\"sampleCount\",\"type\":\"long\",\"doc\":\"Number of samples in the variant set\"},{\"name\":\"filterCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"* The number of occurrences for each FILTER value in files from this set.\\n * Each file can contain more than one filter value (usually separated by ';').\\n *\"},{\"name\":\"genotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Number of genotypes found for all samples in variants set\",\"default\":{}},{\"name\":\"filesCount\",\"type\":\"long\",\"doc\":\"Number of files in the variant set\"},{\"name\":\"tiTvRatio\",\"type\":\"float\",\"doc\":\"TiTvRatio = num. transitions / num. transversions\"},{\"name\":\"qualityAvg\",\"type\":\"float\",\"doc\":\"Mean Quality for all the variants with quality\"},{\"name\":\"qualityStdDev\",\"type\":\"float\",\"doc\":\"Standard Deviation of the quality\"},{\"name\":\"typeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ...\",\"default\":{}},{\"name\":\"biotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ...\",\"default\":{}},{\"name\":\"consequenceTypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ...\",\"default\":{}},{\"name\":\"chromosomeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Number of variants per chromosome\",\"default\":{}},{\"name\":\"chromosomeDensity\",\"type\":{\"type\":\"map\",\"values\":\"float\",\"avro.java.string\":\"String\"},\"doc\":\"Total density of variants within the chromosome. counts / chromosome.length\",\"default\":{}}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Number of variants in the variant set */
private long variantCount;
/** Number of samples in the variant set */
private long sampleCount;
/** * The number of occurrences for each FILTER value in files from this set.
* Each file can contain more than one filter value (usually separated by ';').
* */
private java.util.Map filterCount;
/** Number of genotypes found for all samples in variants set */
private java.util.Map genotypeCount;
/** Number of files in the variant set */
private long filesCount;
/** TiTvRatio = num. transitions / num. transversions */
private float tiTvRatio;
/** Mean Quality for all the variants with quality */
private float qualityAvg;
/** Standard Deviation of the quality */
private float qualityStdDev;
/** Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ... */
private java.util.Map typeCount;
/** Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ... */
private java.util.Map biotypeCount;
/** Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ... */
private java.util.Map consequenceTypeCount;
/** Number of variants per chromosome */
private java.util.Map chromosomeCount;
/** Total density of variants within the chromosome. counts / chromosome.length */
private java.util.Map chromosomeDensity;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public VariantSetStats() {}
/**
* All-args constructor.
*/
public VariantSetStats(java.lang.Long variantCount, java.lang.Long sampleCount, java.util.Map filterCount, java.util.Map genotypeCount, java.lang.Long filesCount, java.lang.Float tiTvRatio, java.lang.Float qualityAvg, java.lang.Float qualityStdDev, java.util.Map typeCount, java.util.Map biotypeCount, java.util.Map consequenceTypeCount, java.util.Map chromosomeCount, java.util.Map chromosomeDensity) {
this.variantCount = variantCount;
this.sampleCount = sampleCount;
this.filterCount = filterCount;
this.genotypeCount = genotypeCount;
this.filesCount = filesCount;
this.tiTvRatio = tiTvRatio;
this.qualityAvg = qualityAvg;
this.qualityStdDev = qualityStdDev;
this.typeCount = typeCount;
this.biotypeCount = biotypeCount;
this.consequenceTypeCount = consequenceTypeCount;
this.chromosomeCount = chromosomeCount;
this.chromosomeDensity = chromosomeDensity;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return variantCount;
case 1: return sampleCount;
case 2: return filterCount;
case 3: return genotypeCount;
case 4: return filesCount;
case 5: return tiTvRatio;
case 6: return qualityAvg;
case 7: return qualityStdDev;
case 8: return typeCount;
case 9: return biotypeCount;
case 10: return consequenceTypeCount;
case 11: return chromosomeCount;
case 12: return chromosomeDensity;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: variantCount = (java.lang.Long)value$; break;
case 1: sampleCount = (java.lang.Long)value$; break;
case 2: filterCount = (java.util.Map)value$; break;
case 3: genotypeCount = (java.util.Map)value$; break;
case 4: filesCount = (java.lang.Long)value$; break;
case 5: tiTvRatio = (java.lang.Float)value$; break;
case 6: qualityAvg = (java.lang.Float)value$; break;
case 7: qualityStdDev = (java.lang.Float)value$; break;
case 8: typeCount = (java.util.Map)value$; break;
case 9: biotypeCount = (java.util.Map)value$; break;
case 10: consequenceTypeCount = (java.util.Map)value$; break;
case 11: chromosomeCount = (java.util.Map)value$; break;
case 12: chromosomeDensity = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantCount' field.
* Number of variants in the variant set */
public java.lang.Long getVariantCount() {
return variantCount;
}
/**
* Sets the value of the 'variantCount' field.
* Number of variants in the variant set * @param value the value to set.
*/
public void setVariantCount(java.lang.Long value) {
this.variantCount = value;
}
/**
* Gets the value of the 'sampleCount' field.
* Number of samples in the variant set */
public java.lang.Long getSampleCount() {
return sampleCount;
}
/**
* Sets the value of the 'sampleCount' field.
* Number of samples in the variant set * @param value the value to set.
*/
public void setSampleCount(java.lang.Long value) {
this.sampleCount = value;
}
/**
* Gets the value of the 'filterCount' field.
* * The number of occurrences for each FILTER value in files from this set.
* Each file can contain more than one filter value (usually separated by ';').
* */
public java.util.Map getFilterCount() {
return filterCount;
}
/**
* Sets the value of the 'filterCount' field.
* * The number of occurrences for each FILTER value in files from this set.
* Each file can contain more than one filter value (usually separated by ';').
* * @param value the value to set.
*/
public void setFilterCount(java.util.Map value) {
this.filterCount = value;
}
/**
* Gets the value of the 'genotypeCount' field.
* Number of genotypes found for all samples in variants set */
public java.util.Map getGenotypeCount() {
return genotypeCount;
}
/**
* Sets the value of the 'genotypeCount' field.
* Number of genotypes found for all samples in variants set * @param value the value to set.
*/
public void setGenotypeCount(java.util.Map value) {
this.genotypeCount = value;
}
/**
* Gets the value of the 'filesCount' field.
* Number of files in the variant set */
public java.lang.Long getFilesCount() {
return filesCount;
}
/**
* Sets the value of the 'filesCount' field.
* Number of files in the variant set * @param value the value to set.
*/
public void setFilesCount(java.lang.Long value) {
this.filesCount = value;
}
/**
* Gets the value of the 'tiTvRatio' field.
* TiTvRatio = num. transitions / num. transversions */
public java.lang.Float getTiTvRatio() {
return tiTvRatio;
}
/**
* Sets the value of the 'tiTvRatio' field.
* TiTvRatio = num. transitions / num. transversions * @param value the value to set.
*/
public void setTiTvRatio(java.lang.Float value) {
this.tiTvRatio = value;
}
/**
* Gets the value of the 'qualityAvg' field.
* Mean Quality for all the variants with quality */
public java.lang.Float getQualityAvg() {
return qualityAvg;
}
/**
* Sets the value of the 'qualityAvg' field.
* Mean Quality for all the variants with quality * @param value the value to set.
*/
public void setQualityAvg(java.lang.Float value) {
this.qualityAvg = value;
}
/**
* Gets the value of the 'qualityStdDev' field.
* Standard Deviation of the quality */
public java.lang.Float getQualityStdDev() {
return qualityStdDev;
}
/**
* Sets the value of the 'qualityStdDev' field.
* Standard Deviation of the quality * @param value the value to set.
*/
public void setQualityStdDev(java.lang.Float value) {
this.qualityStdDev = value;
}
/**
* Gets the value of the 'typeCount' field.
* Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ... */
public java.util.Map getTypeCount() {
return typeCount;
}
/**
* Sets the value of the 'typeCount' field.
* Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ... * @param value the value to set.
*/
public void setTypeCount(java.util.Map value) {
this.typeCount = value;
}
/**
* Gets the value of the 'biotypeCount' field.
* Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ... */
public java.util.Map getBiotypeCount() {
return biotypeCount;
}
/**
* Sets the value of the 'biotypeCount' field.
* Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ... * @param value the value to set.
*/
public void setBiotypeCount(java.util.Map value) {
this.biotypeCount = value;
}
/**
* Gets the value of the 'consequenceTypeCount' field.
* Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ... */
public java.util.Map getConsequenceTypeCount() {
return consequenceTypeCount;
}
/**
* Sets the value of the 'consequenceTypeCount' field.
* Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ... * @param value the value to set.
*/
public void setConsequenceTypeCount(java.util.Map value) {
this.consequenceTypeCount = value;
}
/**
* Gets the value of the 'chromosomeCount' field.
* Number of variants per chromosome */
public java.util.Map getChromosomeCount() {
return chromosomeCount;
}
/**
* Sets the value of the 'chromosomeCount' field.
* Number of variants per chromosome * @param value the value to set.
*/
public void setChromosomeCount(java.util.Map value) {
this.chromosomeCount = value;
}
/**
* Gets the value of the 'chromosomeDensity' field.
* Total density of variants within the chromosome. counts / chromosome.length */
public java.util.Map getChromosomeDensity() {
return chromosomeDensity;
}
/**
* Sets the value of the 'chromosomeDensity' field.
* Total density of variants within the chromosome. counts / chromosome.length * @param value the value to set.
*/
public void setChromosomeDensity(java.util.Map value) {
this.chromosomeDensity = value;
}
/** 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();
}
/** Creates a new VariantSetStats RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder other) {
return new org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder(other);
}
/** Creates a new VariantSetStats RecordBuilder by copying an existing VariantSetStats instance */
public static org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantSetStats other) {
return new org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder(other);
}
/**
* RecordBuilder for VariantSetStats instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private long variantCount;
private long sampleCount;
private java.util.Map filterCount;
private java.util.Map genotypeCount;
private long filesCount;
private float tiTvRatio;
private float qualityAvg;
private float qualityStdDev;
private java.util.Map typeCount;
private java.util.Map biotypeCount;
private java.util.Map consequenceTypeCount;
private java.util.Map chromosomeCount;
private java.util.Map chromosomeDensity;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.metadata.VariantSetStats.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantCount)) {
this.variantCount = data().deepCopy(fields()[0].schema(), other.variantCount);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.sampleCount)) {
this.sampleCount = data().deepCopy(fields()[1].schema(), other.sampleCount);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.filterCount)) {
this.filterCount = data().deepCopy(fields()[2].schema(), other.filterCount);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.genotypeCount)) {
this.genotypeCount = data().deepCopy(fields()[3].schema(), other.genotypeCount);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.filesCount)) {
this.filesCount = data().deepCopy(fields()[4].schema(), other.filesCount);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.tiTvRatio)) {
this.tiTvRatio = data().deepCopy(fields()[5].schema(), other.tiTvRatio);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.qualityAvg)) {
this.qualityAvg = data().deepCopy(fields()[6].schema(), other.qualityAvg);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.qualityStdDev)) {
this.qualityStdDev = data().deepCopy(fields()[7].schema(), other.qualityStdDev);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.typeCount)) {
this.typeCount = data().deepCopy(fields()[8].schema(), other.typeCount);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.biotypeCount)) {
this.biotypeCount = data().deepCopy(fields()[9].schema(), other.biotypeCount);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.consequenceTypeCount)) {
this.consequenceTypeCount = data().deepCopy(fields()[10].schema(), other.consequenceTypeCount);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.chromosomeCount)) {
this.chromosomeCount = data().deepCopy(fields()[11].schema(), other.chromosomeCount);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.chromosomeDensity)) {
this.chromosomeDensity = data().deepCopy(fields()[12].schema(), other.chromosomeDensity);
fieldSetFlags()[12] = true;
}
}
/** Creates a Builder by copying an existing VariantSetStats instance */
private Builder(org.opencb.biodata.models.variant.metadata.VariantSetStats other) {
super(org.opencb.biodata.models.variant.metadata.VariantSetStats.SCHEMA$);
if (isValidValue(fields()[0], other.variantCount)) {
this.variantCount = data().deepCopy(fields()[0].schema(), other.variantCount);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.sampleCount)) {
this.sampleCount = data().deepCopy(fields()[1].schema(), other.sampleCount);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.filterCount)) {
this.filterCount = data().deepCopy(fields()[2].schema(), other.filterCount);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.genotypeCount)) {
this.genotypeCount = data().deepCopy(fields()[3].schema(), other.genotypeCount);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.filesCount)) {
this.filesCount = data().deepCopy(fields()[4].schema(), other.filesCount);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.tiTvRatio)) {
this.tiTvRatio = data().deepCopy(fields()[5].schema(), other.tiTvRatio);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.qualityAvg)) {
this.qualityAvg = data().deepCopy(fields()[6].schema(), other.qualityAvg);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.qualityStdDev)) {
this.qualityStdDev = data().deepCopy(fields()[7].schema(), other.qualityStdDev);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.typeCount)) {
this.typeCount = data().deepCopy(fields()[8].schema(), other.typeCount);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.biotypeCount)) {
this.biotypeCount = data().deepCopy(fields()[9].schema(), other.biotypeCount);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.consequenceTypeCount)) {
this.consequenceTypeCount = data().deepCopy(fields()[10].schema(), other.consequenceTypeCount);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.chromosomeCount)) {
this.chromosomeCount = data().deepCopy(fields()[11].schema(), other.chromosomeCount);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.chromosomeDensity)) {
this.chromosomeDensity = data().deepCopy(fields()[12].schema(), other.chromosomeDensity);
fieldSetFlags()[12] = true;
}
}
/** Gets the value of the 'variantCount' field */
public java.lang.Long getVariantCount() {
return variantCount;
}
/** Sets the value of the 'variantCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setVariantCount(long value) {
validate(fields()[0], value);
this.variantCount = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantCount' field has been set */
public boolean hasVariantCount() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearVariantCount() {
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'sampleCount' field */
public java.lang.Long getSampleCount() {
return sampleCount;
}
/** Sets the value of the 'sampleCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setSampleCount(long value) {
validate(fields()[1], value);
this.sampleCount = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'sampleCount' field has been set */
public boolean hasSampleCount() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'sampleCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearSampleCount() {
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'filterCount' field */
public java.util.Map getFilterCount() {
return filterCount;
}
/** Sets the value of the 'filterCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setFilterCount(java.util.Map value) {
validate(fields()[2], value);
this.filterCount = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'filterCount' field has been set */
public boolean hasFilterCount() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'filterCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearFilterCount() {
filterCount = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'genotypeCount' field */
public java.util.Map getGenotypeCount() {
return genotypeCount;
}
/** Sets the value of the 'genotypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setGenotypeCount(java.util.Map value) {
validate(fields()[3], value);
this.genotypeCount = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'genotypeCount' field has been set */
public boolean hasGenotypeCount() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'genotypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearGenotypeCount() {
genotypeCount = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'filesCount' field */
public java.lang.Long getFilesCount() {
return filesCount;
}
/** Sets the value of the 'filesCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setFilesCount(long value) {
validate(fields()[4], value);
this.filesCount = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'filesCount' field has been set */
public boolean hasFilesCount() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'filesCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearFilesCount() {
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'tiTvRatio' field */
public java.lang.Float getTiTvRatio() {
return tiTvRatio;
}
/** Sets the value of the 'tiTvRatio' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setTiTvRatio(float value) {
validate(fields()[5], value);
this.tiTvRatio = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'tiTvRatio' field has been set */
public boolean hasTiTvRatio() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'tiTvRatio' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearTiTvRatio() {
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'qualityAvg' field */
public java.lang.Float getQualityAvg() {
return qualityAvg;
}
/** Sets the value of the 'qualityAvg' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setQualityAvg(float value) {
validate(fields()[6], value);
this.qualityAvg = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'qualityAvg' field has been set */
public boolean hasQualityAvg() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'qualityAvg' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearQualityAvg() {
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'qualityStdDev' field */
public java.lang.Float getQualityStdDev() {
return qualityStdDev;
}
/** Sets the value of the 'qualityStdDev' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setQualityStdDev(float value) {
validate(fields()[7], value);
this.qualityStdDev = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'qualityStdDev' field has been set */
public boolean hasQualityStdDev() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'qualityStdDev' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearQualityStdDev() {
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'typeCount' field */
public java.util.Map getTypeCount() {
return typeCount;
}
/** Sets the value of the 'typeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setTypeCount(java.util.Map value) {
validate(fields()[8], value);
this.typeCount = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'typeCount' field has been set */
public boolean hasTypeCount() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'typeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearTypeCount() {
typeCount = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'biotypeCount' field */
public java.util.Map getBiotypeCount() {
return biotypeCount;
}
/** Sets the value of the 'biotypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setBiotypeCount(java.util.Map value) {
validate(fields()[9], value);
this.biotypeCount = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'biotypeCount' field has been set */
public boolean hasBiotypeCount() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'biotypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearBiotypeCount() {
biotypeCount = null;
fieldSetFlags()[9] = false;
return this;
}
/** Gets the value of the 'consequenceTypeCount' field */
public java.util.Map getConsequenceTypeCount() {
return consequenceTypeCount;
}
/** Sets the value of the 'consequenceTypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setConsequenceTypeCount(java.util.Map value) {
validate(fields()[10], value);
this.consequenceTypeCount = value;
fieldSetFlags()[10] = true;
return this;
}
/** Checks whether the 'consequenceTypeCount' field has been set */
public boolean hasConsequenceTypeCount() {
return fieldSetFlags()[10];
}
/** Clears the value of the 'consequenceTypeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearConsequenceTypeCount() {
consequenceTypeCount = null;
fieldSetFlags()[10] = false;
return this;
}
/** Gets the value of the 'chromosomeCount' field */
public java.util.Map getChromosomeCount() {
return chromosomeCount;
}
/** Sets the value of the 'chromosomeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setChromosomeCount(java.util.Map value) {
validate(fields()[11], value);
this.chromosomeCount = value;
fieldSetFlags()[11] = true;
return this;
}
/** Checks whether the 'chromosomeCount' field has been set */
public boolean hasChromosomeCount() {
return fieldSetFlags()[11];
}
/** Clears the value of the 'chromosomeCount' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearChromosomeCount() {
chromosomeCount = null;
fieldSetFlags()[11] = false;
return this;
}
/** Gets the value of the 'chromosomeDensity' field */
public java.util.Map getChromosomeDensity() {
return chromosomeDensity;
}
/** Sets the value of the 'chromosomeDensity' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder setChromosomeDensity(java.util.Map value) {
validate(fields()[12], value);
this.chromosomeDensity = value;
fieldSetFlags()[12] = true;
return this;
}
/** Checks whether the 'chromosomeDensity' field has been set */
public boolean hasChromosomeDensity() {
return fieldSetFlags()[12];
}
/** Clears the value of the 'chromosomeDensity' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats.Builder clearChromosomeDensity() {
chromosomeDensity = null;
fieldSetFlags()[12] = false;
return this;
}
@Override
public VariantSetStats build() {
try {
VariantSetStats record = new VariantSetStats();
record.variantCount = fieldSetFlags()[0] ? this.variantCount : (java.lang.Long) defaultValue(fields()[0]);
record.sampleCount = fieldSetFlags()[1] ? this.sampleCount : (java.lang.Long) defaultValue(fields()[1]);
record.filterCount = fieldSetFlags()[2] ? this.filterCount : (java.util.Map) defaultValue(fields()[2]);
record.genotypeCount = fieldSetFlags()[3] ? this.genotypeCount : (java.util.Map) defaultValue(fields()[3]);
record.filesCount = fieldSetFlags()[4] ? this.filesCount : (java.lang.Long) defaultValue(fields()[4]);
record.tiTvRatio = fieldSetFlags()[5] ? this.tiTvRatio : (java.lang.Float) defaultValue(fields()[5]);
record.qualityAvg = fieldSetFlags()[6] ? this.qualityAvg : (java.lang.Float) defaultValue(fields()[6]);
record.qualityStdDev = fieldSetFlags()[7] ? this.qualityStdDev : (java.lang.Float) defaultValue(fields()[7]);
record.typeCount = fieldSetFlags()[8] ? this.typeCount : (java.util.Map) defaultValue(fields()[8]);
record.biotypeCount = fieldSetFlags()[9] ? this.biotypeCount : (java.util.Map) defaultValue(fields()[9]);
record.consequenceTypeCount = fieldSetFlags()[10] ? this.consequenceTypeCount : (java.util.Map) defaultValue(fields()[10]);
record.chromosomeCount = fieldSetFlags()[11] ? this.chromosomeCount : (java.util.Map) defaultValue(fields()[11]);
record.chromosomeDensity = fieldSetFlags()[12] ? this.chromosomeDensity : (java.util.Map) defaultValue(fields()[12]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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