org.opencb.biodata.models.variant.metadata.SampleVariantStats Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.metadata;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class SampleVariantStats 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\":\"SampleVariantStats\",\"namespace\":\"org.opencb.biodata.models.variant.metadata\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample identifier *\"},{\"name\":\"variantCount\",\"type\":\"int\",\"doc\":\"Number of variants where the sample has the main allele (i.e. 0/1, 1/1, ./1, 1/2, ...)\"},{\"name\":\"chromosomeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"Number of variants per chromosome *\",\"default\":{}},{\"name\":\"typeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ...\",\"default\":{}},{\"name\":\"genotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"Number of variants per genotype. Only counts genotypes with the main allele. Phase is ignored. *\",\"default\":{}},{\"name\":\"indelLengthCount\",\"type\":{\"type\":\"record\",\"name\":\"IndelLength\",\"fields\":[{\"name\":\"lt5\",\"type\":\"int\"},{\"name\":\"lt10\",\"type\":\"int\"},{\"name\":\"lt15\",\"type\":\"int\"},{\"name\":\"lt20\",\"type\":\"int\"},{\"name\":\"gte20\",\"type\":\"int\"}]},\"doc\":\"Indel length grouped in ranges *\"},{\"name\":\"filterCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"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\":\"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\":\"heterozygosityRate\",\"type\":\"float\",\"doc\":\"* Heterozygosity rate as defined by PLINK: (N–O)/N\\n *\\n * N is the number of non-missing genotypes\\n * O is the observed number of homozygous genotypes for a given individual\\n *\"},{\"name\":\"mendelianErrorCount\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"Number of mendelian errors grouped by PLINK error codes grouped by Chromosome. *\",\"default\":{}},{\"name\":\"depthCount\",\"type\":{\"type\":\"record\",\"name\":\"DepthCount\",\"fields\":[{\"name\":\"na\",\"type\":\"int\"},{\"name\":\"lt5\",\"type\":\"int\"},{\"name\":\"lt10\",\"type\":\"int\"},{\"name\":\"lt15\",\"type\":\"int\"},{\"name\":\"lt20\",\"type\":\"int\"},{\"name\":\"gte20\",\"type\":\"int\"}]}},{\"name\":\"consequenceTypeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"* Variants count group by consequence type. e.g. missense_variant, synonymous_variant, stop_lost, ...\\n * Each counter is increased at most one per variant. If multiple overlapping transcripts have the same consequence type, it will count as one.\",\"default\":{}},{\"name\":\"biotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"* Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ...\\n * Each counter is increased at most one per variant. If multiple overlapping genes have the same biotypes, it will count as one.\",\"default\":{}},{\"name\":\"clinicalSignificanceCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"* Variants count group by clinical significance. e.g. benign, likely_benign, likely_pathogenic, pathogenic, uncertain_significance ...\\n * Each counter is increased at most one per variant. If multiple variant traits have the same clinical significance, it will count as one.\",\"default\":{}}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Sample identifier * */
private java.lang.String id;
/** Number of variants where the sample has the main allele (i.e. 0/1, 1/1, ./1, 1/2, ...) */
private int variantCount;
/** Number of variants per chromosome * */
private java.util.Map chromosomeCount;
/** Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ... */
private java.util.Map typeCount;
/** Number of variants per genotype. Only counts genotypes with the main allele. Phase is ignored. * */
private java.util.Map genotypeCount;
/** Indel length grouped in ranges * */
private org.opencb.biodata.models.variant.metadata.IndelLength indelLengthCount;
/** * 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;
/** 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;
/** * Heterozygosity rate as defined by PLINK: (N–O)/N
*
* N is the number of non-missing genotypes
* O is the observed number of homozygous genotypes for a given individual
* */
private float heterozygosityRate;
/** Number of mendelian errors grouped by PLINK error codes grouped by Chromosome. * */
private java.util.Map> mendelianErrorCount;
private org.opencb.biodata.models.variant.metadata.DepthCount depthCount;
/** * Variants count group by consequence type. e.g. missense_variant, synonymous_variant, stop_lost, ...
* Each counter is increased at most one per variant. If multiple overlapping transcripts have the same consequence type, it will count as one. */
private java.util.Map consequenceTypeCount;
/** * Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ...
* Each counter is increased at most one per variant. If multiple overlapping genes have the same biotypes, it will count as one. */
private java.util.Map biotypeCount;
/** * Variants count group by clinical significance. e.g. benign, likely_benign, likely_pathogenic, pathogenic, uncertain_significance ...
* Each counter is increased at most one per variant. If multiple variant traits have the same clinical significance, it will count as one. */
private java.util.Map clinicalSignificanceCount;
/**
* 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 SampleVariantStats() {}
/**
* All-args constructor.
*/
public SampleVariantStats(java.lang.String id, java.lang.Integer variantCount, java.util.Map chromosomeCount, java.util.Map typeCount, java.util.Map genotypeCount, org.opencb.biodata.models.variant.metadata.IndelLength indelLengthCount, java.util.Map filterCount, java.lang.Float tiTvRatio, java.lang.Float qualityAvg, java.lang.Float qualityStdDev, java.lang.Float heterozygosityRate, java.util.Map> mendelianErrorCount, org.opencb.biodata.models.variant.metadata.DepthCount depthCount, java.util.Map consequenceTypeCount, java.util.Map biotypeCount, java.util.Map clinicalSignificanceCount) {
this.id = id;
this.variantCount = variantCount;
this.chromosomeCount = chromosomeCount;
this.typeCount = typeCount;
this.genotypeCount = genotypeCount;
this.indelLengthCount = indelLengthCount;
this.filterCount = filterCount;
this.tiTvRatio = tiTvRatio;
this.qualityAvg = qualityAvg;
this.qualityStdDev = qualityStdDev;
this.heterozygosityRate = heterozygosityRate;
this.mendelianErrorCount = mendelianErrorCount;
this.depthCount = depthCount;
this.consequenceTypeCount = consequenceTypeCount;
this.biotypeCount = biotypeCount;
this.clinicalSignificanceCount = clinicalSignificanceCount;
}
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 id;
case 1: return variantCount;
case 2: return chromosomeCount;
case 3: return typeCount;
case 4: return genotypeCount;
case 5: return indelLengthCount;
case 6: return filterCount;
case 7: return tiTvRatio;
case 8: return qualityAvg;
case 9: return qualityStdDev;
case 10: return heterozygosityRate;
case 11: return mendelianErrorCount;
case 12: return depthCount;
case 13: return consequenceTypeCount;
case 14: return biotypeCount;
case 15: return clinicalSignificanceCount;
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$) {
case 0: id = (java.lang.String)value$; break;
case 1: variantCount = (java.lang.Integer)value$; break;
case 2: chromosomeCount = (java.util.Map)value$; break;
case 3: typeCount = (java.util.Map)value$; break;
case 4: genotypeCount = (java.util.Map)value$; break;
case 5: indelLengthCount = (org.opencb.biodata.models.variant.metadata.IndelLength)value$; break;
case 6: filterCount = (java.util.Map)value$; break;
case 7: tiTvRatio = (java.lang.Float)value$; break;
case 8: qualityAvg = (java.lang.Float)value$; break;
case 9: qualityStdDev = (java.lang.Float)value$; break;
case 10: heterozygosityRate = (java.lang.Float)value$; break;
case 11: mendelianErrorCount = (java.util.Map>)value$; break;
case 12: depthCount = (org.opencb.biodata.models.variant.metadata.DepthCount)value$; break;
case 13: consequenceTypeCount = (java.util.Map)value$; break;
case 14: biotypeCount = (java.util.Map)value$; break;
case 15: clinicalSignificanceCount = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'id' field.
* Sample identifier * */
public java.lang.String getId() {
return id;
}
/**
* Sets the value of the 'id' field.
* Sample identifier * * @param value the value to set.
*/
public void setId(java.lang.String value) {
this.id = value;
}
/**
* Gets the value of the 'variantCount' field.
* Number of variants where the sample has the main allele (i.e. 0/1, 1/1, ./1, 1/2, ...) */
public java.lang.Integer getVariantCount() {
return variantCount;
}
/**
* Sets the value of the 'variantCount' field.
* Number of variants where the sample has the main allele (i.e. 0/1, 1/1, ./1, 1/2, ...) * @param value the value to set.
*/
public void setVariantCount(java.lang.Integer value) {
this.variantCount = 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 '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 'genotypeCount' field.
* Number of variants per genotype. Only counts genotypes with the main allele. Phase is ignored. * */
public java.util.Map getGenotypeCount() {
return genotypeCount;
}
/**
* Sets the value of the 'genotypeCount' field.
* Number of variants per genotype. Only counts genotypes with the main allele. Phase is ignored. * * @param value the value to set.
*/
public void setGenotypeCount(java.util.Map value) {
this.genotypeCount = value;
}
/**
* Gets the value of the 'indelLengthCount' field.
* Indel length grouped in ranges * */
public org.opencb.biodata.models.variant.metadata.IndelLength getIndelLengthCount() {
return indelLengthCount;
}
/**
* Sets the value of the 'indelLengthCount' field.
* Indel length grouped in ranges * * @param value the value to set.
*/
public void setIndelLengthCount(org.opencb.biodata.models.variant.metadata.IndelLength value) {
this.indelLengthCount = 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 '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 'heterozygosityRate' field.
* * Heterozygosity rate as defined by PLINK: (N–O)/N
*
* N is the number of non-missing genotypes
* O is the observed number of homozygous genotypes for a given individual
* */
public java.lang.Float getHeterozygosityRate() {
return heterozygosityRate;
}
/**
* Sets the value of the 'heterozygosityRate' field.
* * Heterozygosity rate as defined by PLINK: (N–O)/N
*
* N is the number of non-missing genotypes
* O is the observed number of homozygous genotypes for a given individual
* * @param value the value to set.
*/
public void setHeterozygosityRate(java.lang.Float value) {
this.heterozygosityRate = value;
}
/**
* Gets the value of the 'mendelianErrorCount' field.
* Number of mendelian errors grouped by PLINK error codes grouped by Chromosome. * */
public java.util.Map> getMendelianErrorCount() {
return mendelianErrorCount;
}
/**
* Sets the value of the 'mendelianErrorCount' field.
* Number of mendelian errors grouped by PLINK error codes grouped by Chromosome. * * @param value the value to set.
*/
public void setMendelianErrorCount(java.util.Map> value) {
this.mendelianErrorCount = value;
}
/**
* Gets the value of the 'depthCount' field.
*/
public org.opencb.biodata.models.variant.metadata.DepthCount getDepthCount() {
return depthCount;
}
/**
* Sets the value of the 'depthCount' field.
* @param value the value to set.
*/
public void setDepthCount(org.opencb.biodata.models.variant.metadata.DepthCount value) {
this.depthCount = value;
}
/**
* Gets the value of the 'consequenceTypeCount' field.
* * Variants count group by consequence type. e.g. missense_variant, synonymous_variant, stop_lost, ...
* Each counter is increased at most one per variant. If multiple overlapping transcripts have the same consequence type, it will count as one. */
public java.util.Map getConsequenceTypeCount() {
return consequenceTypeCount;
}
/**
* Sets the value of the 'consequenceTypeCount' field.
* * Variants count group by consequence type. e.g. missense_variant, synonymous_variant, stop_lost, ...
* Each counter is increased at most one per variant. If multiple overlapping transcripts have the same consequence type, it will count as one. * @param value the value to set.
*/
public void setConsequenceTypeCount(java.util.Map value) {
this.consequenceTypeCount = value;
}
/**
* Gets the value of the 'biotypeCount' field.
* * Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ...
* Each counter is increased at most one per variant. If multiple overlapping genes have the same biotypes, it will count as one. */
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, ...
* Each counter is increased at most one per variant. If multiple overlapping genes have the same biotypes, it will count as one. * @param value the value to set.
*/
public void setBiotypeCount(java.util.Map value) {
this.biotypeCount = value;
}
/**
* Gets the value of the 'clinicalSignificanceCount' field.
* * Variants count group by clinical significance. e.g. benign, likely_benign, likely_pathogenic, pathogenic, uncertain_significance ...
* Each counter is increased at most one per variant. If multiple variant traits have the same clinical significance, it will count as one. */
public java.util.Map getClinicalSignificanceCount() {
return clinicalSignificanceCount;
}
/**
* Sets the value of the 'clinicalSignificanceCount' field.
* * Variants count group by clinical significance. e.g. benign, likely_benign, likely_pathogenic, pathogenic, uncertain_significance ...
* Each counter is increased at most one per variant. If multiple variant traits have the same clinical significance, it will count as one. * @param value the value to set.
*/
public void setClinicalSignificanceCount(java.util.Map value) {
this.clinicalSignificanceCount = value;
}
/** Creates a new SampleVariantStats RecordBuilder */
public static org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder newBuilder() {
return new org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder();
}
/** Creates a new SampleVariantStats RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder newBuilder(org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder other) {
return new org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder(other);
}
/** Creates a new SampleVariantStats RecordBuilder by copying an existing SampleVariantStats instance */
public static org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder newBuilder(org.opencb.biodata.models.variant.metadata.SampleVariantStats other) {
return new org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder(other);
}
/**
* RecordBuilder for SampleVariantStats instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String id;
private int variantCount;
private java.util.Map chromosomeCount;
private java.util.Map typeCount;
private java.util.Map genotypeCount;
private org.opencb.biodata.models.variant.metadata.IndelLength indelLengthCount;
private java.util.Map filterCount;
private float tiTvRatio;
private float qualityAvg;
private float qualityStdDev;
private float heterozygosityRate;
private java.util.Map> mendelianErrorCount;
private org.opencb.biodata.models.variant.metadata.DepthCount depthCount;
private java.util.Map consequenceTypeCount;
private java.util.Map biotypeCount;
private java.util.Map clinicalSignificanceCount;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.metadata.SampleVariantStats.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder other) {
super(other);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.variantCount)) {
this.variantCount = data().deepCopy(fields()[1].schema(), other.variantCount);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosomeCount)) {
this.chromosomeCount = data().deepCopy(fields()[2].schema(), other.chromosomeCount);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.typeCount)) {
this.typeCount = data().deepCopy(fields()[3].schema(), other.typeCount);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.genotypeCount)) {
this.genotypeCount = data().deepCopy(fields()[4].schema(), other.genotypeCount);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.indelLengthCount)) {
this.indelLengthCount = data().deepCopy(fields()[5].schema(), other.indelLengthCount);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.filterCount)) {
this.filterCount = data().deepCopy(fields()[6].schema(), other.filterCount);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.tiTvRatio)) {
this.tiTvRatio = data().deepCopy(fields()[7].schema(), other.tiTvRatio);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.qualityAvg)) {
this.qualityAvg = data().deepCopy(fields()[8].schema(), other.qualityAvg);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.qualityStdDev)) {
this.qualityStdDev = data().deepCopy(fields()[9].schema(), other.qualityStdDev);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.heterozygosityRate)) {
this.heterozygosityRate = data().deepCopy(fields()[10].schema(), other.heterozygosityRate);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.mendelianErrorCount)) {
this.mendelianErrorCount = data().deepCopy(fields()[11].schema(), other.mendelianErrorCount);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.depthCount)) {
this.depthCount = data().deepCopy(fields()[12].schema(), other.depthCount);
fieldSetFlags()[12] = true;
}
if (isValidValue(fields()[13], other.consequenceTypeCount)) {
this.consequenceTypeCount = data().deepCopy(fields()[13].schema(), other.consequenceTypeCount);
fieldSetFlags()[13] = true;
}
if (isValidValue(fields()[14], other.biotypeCount)) {
this.biotypeCount = data().deepCopy(fields()[14].schema(), other.biotypeCount);
fieldSetFlags()[14] = true;
}
if (isValidValue(fields()[15], other.clinicalSignificanceCount)) {
this.clinicalSignificanceCount = data().deepCopy(fields()[15].schema(), other.clinicalSignificanceCount);
fieldSetFlags()[15] = true;
}
}
/** Creates a Builder by copying an existing SampleVariantStats instance */
private Builder(org.opencb.biodata.models.variant.metadata.SampleVariantStats other) {
super(org.opencb.biodata.models.variant.metadata.SampleVariantStats.SCHEMA$);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.variantCount)) {
this.variantCount = data().deepCopy(fields()[1].schema(), other.variantCount);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosomeCount)) {
this.chromosomeCount = data().deepCopy(fields()[2].schema(), other.chromosomeCount);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.typeCount)) {
this.typeCount = data().deepCopy(fields()[3].schema(), other.typeCount);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.genotypeCount)) {
this.genotypeCount = data().deepCopy(fields()[4].schema(), other.genotypeCount);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.indelLengthCount)) {
this.indelLengthCount = data().deepCopy(fields()[5].schema(), other.indelLengthCount);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.filterCount)) {
this.filterCount = data().deepCopy(fields()[6].schema(), other.filterCount);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.tiTvRatio)) {
this.tiTvRatio = data().deepCopy(fields()[7].schema(), other.tiTvRatio);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.qualityAvg)) {
this.qualityAvg = data().deepCopy(fields()[8].schema(), other.qualityAvg);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.qualityStdDev)) {
this.qualityStdDev = data().deepCopy(fields()[9].schema(), other.qualityStdDev);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.heterozygosityRate)) {
this.heterozygosityRate = data().deepCopy(fields()[10].schema(), other.heterozygosityRate);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.mendelianErrorCount)) {
this.mendelianErrorCount = data().deepCopy(fields()[11].schema(), other.mendelianErrorCount);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.depthCount)) {
this.depthCount = data().deepCopy(fields()[12].schema(), other.depthCount);
fieldSetFlags()[12] = true;
}
if (isValidValue(fields()[13], other.consequenceTypeCount)) {
this.consequenceTypeCount = data().deepCopy(fields()[13].schema(), other.consequenceTypeCount);
fieldSetFlags()[13] = true;
}
if (isValidValue(fields()[14], other.biotypeCount)) {
this.biotypeCount = data().deepCopy(fields()[14].schema(), other.biotypeCount);
fieldSetFlags()[14] = true;
}
if (isValidValue(fields()[15], other.clinicalSignificanceCount)) {
this.clinicalSignificanceCount = data().deepCopy(fields()[15].schema(), other.clinicalSignificanceCount);
fieldSetFlags()[15] = true;
}
}
/** Gets the value of the 'id' field */
public java.lang.String getId() {
return id;
}
/** Sets the value of the 'id' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setId(java.lang.String value) {
validate(fields()[0], value);
this.id = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'id' field has been set */
public boolean hasId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'id' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearId() {
id = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'variantCount' field */
public java.lang.Integer getVariantCount() {
return variantCount;
}
/** Sets the value of the 'variantCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setVariantCount(int value) {
validate(fields()[1], value);
this.variantCount = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'variantCount' field has been set */
public boolean hasVariantCount() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'variantCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearVariantCount() {
fieldSetFlags()[1] = 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.SampleVariantStats.Builder setChromosomeCount(java.util.Map value) {
validate(fields()[2], value);
this.chromosomeCount = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'chromosomeCount' field has been set */
public boolean hasChromosomeCount() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'chromosomeCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearChromosomeCount() {
chromosomeCount = null;
fieldSetFlags()[2] = 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.SampleVariantStats.Builder setTypeCount(java.util.Map value) {
validate(fields()[3], value);
this.typeCount = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'typeCount' field has been set */
public boolean hasTypeCount() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'typeCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearTypeCount() {
typeCount = null;
fieldSetFlags()[3] = 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.SampleVariantStats.Builder setGenotypeCount(java.util.Map value) {
validate(fields()[4], value);
this.genotypeCount = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'genotypeCount' field has been set */
public boolean hasGenotypeCount() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'genotypeCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearGenotypeCount() {
genotypeCount = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'indelLengthCount' field */
public org.opencb.biodata.models.variant.metadata.IndelLength getIndelLengthCount() {
return indelLengthCount;
}
/** Sets the value of the 'indelLengthCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setIndelLengthCount(org.opencb.biodata.models.variant.metadata.IndelLength value) {
validate(fields()[5], value);
this.indelLengthCount = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'indelLengthCount' field has been set */
public boolean hasIndelLengthCount() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'indelLengthCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearIndelLengthCount() {
indelLengthCount = null;
fieldSetFlags()[5] = 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.SampleVariantStats.Builder setFilterCount(java.util.Map value) {
validate(fields()[6], value);
this.filterCount = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'filterCount' field has been set */
public boolean hasFilterCount() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'filterCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearFilterCount() {
filterCount = null;
fieldSetFlags()[6] = 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.SampleVariantStats.Builder setTiTvRatio(float value) {
validate(fields()[7], value);
this.tiTvRatio = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'tiTvRatio' field has been set */
public boolean hasTiTvRatio() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'tiTvRatio' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearTiTvRatio() {
fieldSetFlags()[7] = 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.SampleVariantStats.Builder setQualityAvg(float value) {
validate(fields()[8], value);
this.qualityAvg = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'qualityAvg' field has been set */
public boolean hasQualityAvg() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'qualityAvg' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearQualityAvg() {
fieldSetFlags()[8] = 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.SampleVariantStats.Builder setQualityStdDev(float value) {
validate(fields()[9], value);
this.qualityStdDev = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'qualityStdDev' field has been set */
public boolean hasQualityStdDev() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'qualityStdDev' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearQualityStdDev() {
fieldSetFlags()[9] = false;
return this;
}
/** Gets the value of the 'heterozygosityRate' field */
public java.lang.Float getHeterozygosityRate() {
return heterozygosityRate;
}
/** Sets the value of the 'heterozygosityRate' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setHeterozygosityRate(float value) {
validate(fields()[10], value);
this.heterozygosityRate = value;
fieldSetFlags()[10] = true;
return this;
}
/** Checks whether the 'heterozygosityRate' field has been set */
public boolean hasHeterozygosityRate() {
return fieldSetFlags()[10];
}
/** Clears the value of the 'heterozygosityRate' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearHeterozygosityRate() {
fieldSetFlags()[10] = false;
return this;
}
/** Gets the value of the 'mendelianErrorCount' field */
public java.util.Map> getMendelianErrorCount() {
return mendelianErrorCount;
}
/** Sets the value of the 'mendelianErrorCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setMendelianErrorCount(java.util.Map> value) {
validate(fields()[11], value);
this.mendelianErrorCount = value;
fieldSetFlags()[11] = true;
return this;
}
/** Checks whether the 'mendelianErrorCount' field has been set */
public boolean hasMendelianErrorCount() {
return fieldSetFlags()[11];
}
/** Clears the value of the 'mendelianErrorCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearMendelianErrorCount() {
mendelianErrorCount = null;
fieldSetFlags()[11] = false;
return this;
}
/** Gets the value of the 'depthCount' field */
public org.opencb.biodata.models.variant.metadata.DepthCount getDepthCount() {
return depthCount;
}
/** Sets the value of the 'depthCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setDepthCount(org.opencb.biodata.models.variant.metadata.DepthCount value) {
validate(fields()[12], value);
this.depthCount = value;
fieldSetFlags()[12] = true;
return this;
}
/** Checks whether the 'depthCount' field has been set */
public boolean hasDepthCount() {
return fieldSetFlags()[12];
}
/** Clears the value of the 'depthCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearDepthCount() {
depthCount = null;
fieldSetFlags()[12] = 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.SampleVariantStats.Builder setConsequenceTypeCount(java.util.Map value) {
validate(fields()[13], value);
this.consequenceTypeCount = value;
fieldSetFlags()[13] = true;
return this;
}
/** Checks whether the 'consequenceTypeCount' field has been set */
public boolean hasConsequenceTypeCount() {
return fieldSetFlags()[13];
}
/** Clears the value of the 'consequenceTypeCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearConsequenceTypeCount() {
consequenceTypeCount = null;
fieldSetFlags()[13] = 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.SampleVariantStats.Builder setBiotypeCount(java.util.Map value) {
validate(fields()[14], value);
this.biotypeCount = value;
fieldSetFlags()[14] = true;
return this;
}
/** Checks whether the 'biotypeCount' field has been set */
public boolean hasBiotypeCount() {
return fieldSetFlags()[14];
}
/** Clears the value of the 'biotypeCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearBiotypeCount() {
biotypeCount = null;
fieldSetFlags()[14] = false;
return this;
}
/** Gets the value of the 'clinicalSignificanceCount' field */
public java.util.Map getClinicalSignificanceCount() {
return clinicalSignificanceCount;
}
/** Sets the value of the 'clinicalSignificanceCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder setClinicalSignificanceCount(java.util.Map value) {
validate(fields()[15], value);
this.clinicalSignificanceCount = value;
fieldSetFlags()[15] = true;
return this;
}
/** Checks whether the 'clinicalSignificanceCount' field has been set */
public boolean hasClinicalSignificanceCount() {
return fieldSetFlags()[15];
}
/** Clears the value of the 'clinicalSignificanceCount' field */
public org.opencb.biodata.models.variant.metadata.SampleVariantStats.Builder clearClinicalSignificanceCount() {
clinicalSignificanceCount = null;
fieldSetFlags()[15] = false;
return this;
}
@Override
public SampleVariantStats build() {
try {
SampleVariantStats record = new SampleVariantStats();
record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]);
record.variantCount = fieldSetFlags()[1] ? this.variantCount : (java.lang.Integer) defaultValue(fields()[1]);
record.chromosomeCount = fieldSetFlags()[2] ? this.chromosomeCount : (java.util.Map) defaultValue(fields()[2]);
record.typeCount = fieldSetFlags()[3] ? this.typeCount : (java.util.Map) defaultValue(fields()[3]);
record.genotypeCount = fieldSetFlags()[4] ? this.genotypeCount : (java.util.Map) defaultValue(fields()[4]);
record.indelLengthCount = fieldSetFlags()[5] ? this.indelLengthCount : (org.opencb.biodata.models.variant.metadata.IndelLength) defaultValue(fields()[5]);
record.filterCount = fieldSetFlags()[6] ? this.filterCount : (java.util.Map) defaultValue(fields()[6]);
record.tiTvRatio = fieldSetFlags()[7] ? this.tiTvRatio : (java.lang.Float) defaultValue(fields()[7]);
record.qualityAvg = fieldSetFlags()[8] ? this.qualityAvg : (java.lang.Float) defaultValue(fields()[8]);
record.qualityStdDev = fieldSetFlags()[9] ? this.qualityStdDev : (java.lang.Float) defaultValue(fields()[9]);
record.heterozygosityRate = fieldSetFlags()[10] ? this.heterozygosityRate : (java.lang.Float) defaultValue(fields()[10]);
record.mendelianErrorCount = fieldSetFlags()[11] ? this.mendelianErrorCount : (java.util.Map>) defaultValue(fields()[11]);
record.depthCount = fieldSetFlags()[12] ? this.depthCount : (org.opencb.biodata.models.variant.metadata.DepthCount) defaultValue(fields()[12]);
record.consequenceTypeCount = fieldSetFlags()[13] ? this.consequenceTypeCount : (java.util.Map) defaultValue(fields()[13]);
record.biotypeCount = fieldSetFlags()[14] ? this.biotypeCount : (java.util.Map) defaultValue(fields()[14]);
record.clinicalSignificanceCount = fieldSetFlags()[15] ? this.clinicalSignificanceCount : (java.util.Map) defaultValue(fields()[15]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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