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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** Some additional variant attributes */
@org.apache.avro.specific.AvroGenerated
public class VariantAttributes 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\":\"VariantAttributes\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"Some additional variant attributes\",\"fields\":[{\"name\":\"genomicChanges\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"gDNA change, HGVS nomenclature (e.g.: g.476A>T)\"},{\"name\":\"cdnaChanges\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"cDNA change, HGVS nomenclature (e.g.: c.76A>T)\"},{\"name\":\"proteinChanges\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Protein change, HGVS nomenclature (e.g.: p.Lys76Asn)\"},{\"name\":\"additionalTextualVariantAnnotations\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Any additional information in a free text field. For example a quote from a paper\"},{\"name\":\"references\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Additional references for ths variant. For example HGMD ID or Pubmed Id\"},{\"name\":\"variantIdentifiers\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantIdentifiers\",\"fields\":[{\"name\":\"dbSnpId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Variant identifier in dbSNP\"},{\"name\":\"cosmicIds\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Variant identifier in Cosmic\"},{\"name\":\"clinVarIds\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Variant identifier in ClinVar\"},{\"name\":\"otherIds\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Identifier\",\"fields\":[{\"name\":\"source\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Source i.e, esenmbl\"},{\"name\":\"identifier\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"identifier\"}]}}]}]}]},{\"name\":\"alleleFrequencies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AlleleFrequency\",\"doc\":\"The population allele frequency of a given variant in a given study and optionally population\",\"fields\":[{\"name\":\"study\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The study from where this data comes from\"},{\"name\":\"population\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The specific population where this allele frequency belongs\"},{\"name\":\"alternateFrequency\",\"type\":\"float\",\"doc\":\"The frequency of the alternate allele\"}]}}],\"doc\":\"A list of population allele frequencies\"},{\"name\":\"additionalNumericVariantAnnotations\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"float\",\"avro.java.string\":\"String\"}],\"doc\":\"Additional numeric variant annotations for this variant. For Example (Allele Frequency, sift, polyphen,\\n mutationTaster, CADD. ..)\"},{\"name\":\"comments\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Comments\"},{\"name\":\"alleleOrigins\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"enum\",\"name\":\"AlleleOrigin\",\"doc\":\"Allele origin.\\n\\n* `SO_0001781`: de novo variant. http://purl.obolibrary.org/obo/SO_0001781\\n* `SO_0001778`: germline variant. http://purl.obolibrary.org/obo/SO_0001778\\n* `SO_0001775`: maternal variant. http://purl.obolibrary.org/obo/SO_0001775\\n* `SO_0001776`: paternal variant. http://purl.obolibrary.org/obo/SO_0001776\\n* `SO_0001779`: pedigree specific variant. http://purl.obolibrary.org/obo/SO_0001779\\n* `SO_0001780`: population specific variant. http://purl.obolibrary.org/obo/SO_0001780\\n* `SO_0001777`: somatic variant. http://purl.obolibrary.org/obo/SO_0001777\",\"symbols\":[\"de_novo_variant\",\"germline_variant\",\"maternal_variant\",\"paternal_variant\",\"pedigree_specific_variant\",\"population_specific_variant\",\"somatic_variant\"]}}],\"doc\":\"List of allele origins for this variant in this report\"},{\"name\":\"ihp\",\"type\":[\"null\",\"int\"],\"doc\":\"Largest reference interrupted homopolymer length intersecting with the indel\"},{\"name\":\"recurrentlyReported\",\"type\":[\"null\",\"boolean\"],\"doc\":\"Flag indicating if the variant is recurrently reported\"},{\"name\":\"fdp50\",\"type\":[\"null\",\"float\"],\"doc\":\"Average tier1 number of basecalls filtered from original read depth within 50 bases\"},{\"name\":\"others\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Map of other attributes where keys are the attribute names and values are the attributes\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** gDNA change, HGVS nomenclature (e.g.: g.476A>T) */
private java.util.List genomicChanges;
/** cDNA change, HGVS nomenclature (e.g.: c.76A>T) */
private java.util.List cdnaChanges;
/** Protein change, HGVS nomenclature (e.g.: p.Lys76Asn) */
private java.util.List proteinChanges;
/** Any additional information in a free text field. For example a quote from a paper */
private java.util.Map additionalTextualVariantAnnotations;
/** Additional references for ths variant. For example HGMD ID or Pubmed Id */
private java.util.Map references;
private org.gel.models.report.avro.VariantIdentifiers variantIdentifiers;
/** A list of population allele frequencies */
private java.util.List alleleFrequencies;
/** Additional numeric variant annotations for this variant. For Example (Allele Frequency, sift, polyphen,
mutationTaster, CADD. ..) */
private java.util.Map additionalNumericVariantAnnotations;
/** Comments */
private java.util.List comments;
/** List of allele origins for this variant in this report */
private java.util.List alleleOrigins;
/** Largest reference interrupted homopolymer length intersecting with the indel */
private java.lang.Integer ihp;
/** Flag indicating if the variant is recurrently reported */
private java.lang.Boolean recurrentlyReported;
/** Average tier1 number of basecalls filtered from original read depth within 50 bases */
private java.lang.Float fdp50;
/** Map of other attributes where keys are the attribute names and values are the attributes */
private java.util.Map others;
/**
* 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 VariantAttributes() {}
/**
* All-args constructor.
*/
public VariantAttributes(java.util.List genomicChanges, java.util.List cdnaChanges, java.util.List proteinChanges, java.util.Map additionalTextualVariantAnnotations, java.util.Map references, org.gel.models.report.avro.VariantIdentifiers variantIdentifiers, java.util.List alleleFrequencies, java.util.Map additionalNumericVariantAnnotations, java.util.List comments, java.util.List alleleOrigins, java.lang.Integer ihp, java.lang.Boolean recurrentlyReported, java.lang.Float fdp50, java.util.Map others) {
this.genomicChanges = genomicChanges;
this.cdnaChanges = cdnaChanges;
this.proteinChanges = proteinChanges;
this.additionalTextualVariantAnnotations = additionalTextualVariantAnnotations;
this.references = references;
this.variantIdentifiers = variantIdentifiers;
this.alleleFrequencies = alleleFrequencies;
this.additionalNumericVariantAnnotations = additionalNumericVariantAnnotations;
this.comments = comments;
this.alleleOrigins = alleleOrigins;
this.ihp = ihp;
this.recurrentlyReported = recurrentlyReported;
this.fdp50 = fdp50;
this.others = others;
}
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 genomicChanges;
case 1: return cdnaChanges;
case 2: return proteinChanges;
case 3: return additionalTextualVariantAnnotations;
case 4: return references;
case 5: return variantIdentifiers;
case 6: return alleleFrequencies;
case 7: return additionalNumericVariantAnnotations;
case 8: return comments;
case 9: return alleleOrigins;
case 10: return ihp;
case 11: return recurrentlyReported;
case 12: return fdp50;
case 13: return others;
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$) {
case 0: genomicChanges = (java.util.List)value$; break;
case 1: cdnaChanges = (java.util.List)value$; break;
case 2: proteinChanges = (java.util.List)value$; break;
case 3: additionalTextualVariantAnnotations = (java.util.Map)value$; break;
case 4: references = (java.util.Map)value$; break;
case 5: variantIdentifiers = (org.gel.models.report.avro.VariantIdentifiers)value$; break;
case 6: alleleFrequencies = (java.util.List)value$; break;
case 7: additionalNumericVariantAnnotations = (java.util.Map)value$; break;
case 8: comments = (java.util.List)value$; break;
case 9: alleleOrigins = (java.util.List)value$; break;
case 10: ihp = (java.lang.Integer)value$; break;
case 11: recurrentlyReported = (java.lang.Boolean)value$; break;
case 12: fdp50 = (java.lang.Float)value$; break;
case 13: others = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'genomicChanges' field.
* gDNA change, HGVS nomenclature (e.g.: g.476A>T) */
public java.util.List getGenomicChanges() {
return genomicChanges;
}
/**
* Sets the value of the 'genomicChanges' field.
* gDNA change, HGVS nomenclature (e.g.: g.476A>T) * @param value the value to set.
*/
public void setGenomicChanges(java.util.List value) {
this.genomicChanges = value;
}
/**
* Gets the value of the 'cdnaChanges' field.
* cDNA change, HGVS nomenclature (e.g.: c.76A>T) */
public java.util.List getCdnaChanges() {
return cdnaChanges;
}
/**
* Sets the value of the 'cdnaChanges' field.
* cDNA change, HGVS nomenclature (e.g.: c.76A>T) * @param value the value to set.
*/
public void setCdnaChanges(java.util.List value) {
this.cdnaChanges = value;
}
/**
* Gets the value of the 'proteinChanges' field.
* Protein change, HGVS nomenclature (e.g.: p.Lys76Asn) */
public java.util.List getProteinChanges() {
return proteinChanges;
}
/**
* Sets the value of the 'proteinChanges' field.
* Protein change, HGVS nomenclature (e.g.: p.Lys76Asn) * @param value the value to set.
*/
public void setProteinChanges(java.util.List value) {
this.proteinChanges = value;
}
/**
* Gets the value of the 'additionalTextualVariantAnnotations' field.
* Any additional information in a free text field. For example a quote from a paper */
public java.util.Map getAdditionalTextualVariantAnnotations() {
return additionalTextualVariantAnnotations;
}
/**
* Sets the value of the 'additionalTextualVariantAnnotations' field.
* Any additional information in a free text field. For example a quote from a paper * @param value the value to set.
*/
public void setAdditionalTextualVariantAnnotations(java.util.Map value) {
this.additionalTextualVariantAnnotations = value;
}
/**
* Gets the value of the 'references' field.
* Additional references for ths variant. For example HGMD ID or Pubmed Id */
public java.util.Map getReferences() {
return references;
}
/**
* Sets the value of the 'references' field.
* Additional references for ths variant. For example HGMD ID or Pubmed Id * @param value the value to set.
*/
public void setReferences(java.util.Map value) {
this.references = value;
}
/**
* Gets the value of the 'variantIdentifiers' field.
*/
public org.gel.models.report.avro.VariantIdentifiers getVariantIdentifiers() {
return variantIdentifiers;
}
/**
* Sets the value of the 'variantIdentifiers' field.
* @param value the value to set.
*/
public void setVariantIdentifiers(org.gel.models.report.avro.VariantIdentifiers value) {
this.variantIdentifiers = value;
}
/**
* Gets the value of the 'alleleFrequencies' field.
* A list of population allele frequencies */
public java.util.List getAlleleFrequencies() {
return alleleFrequencies;
}
/**
* Sets the value of the 'alleleFrequencies' field.
* A list of population allele frequencies * @param value the value to set.
*/
public void setAlleleFrequencies(java.util.List value) {
this.alleleFrequencies = value;
}
/**
* Gets the value of the 'additionalNumericVariantAnnotations' field.
* Additional numeric variant annotations for this variant. For Example (Allele Frequency, sift, polyphen,
mutationTaster, CADD. ..) */
public java.util.Map getAdditionalNumericVariantAnnotations() {
return additionalNumericVariantAnnotations;
}
/**
* Sets the value of the 'additionalNumericVariantAnnotations' field.
* Additional numeric variant annotations for this variant. For Example (Allele Frequency, sift, polyphen,
mutationTaster, CADD. ..) * @param value the value to set.
*/
public void setAdditionalNumericVariantAnnotations(java.util.Map value) {
this.additionalNumericVariantAnnotations = value;
}
/**
* Gets the value of the 'comments' field.
* Comments */
public java.util.List getComments() {
return comments;
}
/**
* Sets the value of the 'comments' field.
* Comments * @param value the value to set.
*/
public void setComments(java.util.List value) {
this.comments = value;
}
/**
* Gets the value of the 'alleleOrigins' field.
* List of allele origins for this variant in this report */
public java.util.List getAlleleOrigins() {
return alleleOrigins;
}
/**
* Sets the value of the 'alleleOrigins' field.
* List of allele origins for this variant in this report * @param value the value to set.
*/
public void setAlleleOrigins(java.util.List value) {
this.alleleOrigins = value;
}
/**
* Gets the value of the 'ihp' field.
* Largest reference interrupted homopolymer length intersecting with the indel */
public java.lang.Integer getIhp() {
return ihp;
}
/**
* Sets the value of the 'ihp' field.
* Largest reference interrupted homopolymer length intersecting with the indel * @param value the value to set.
*/
public void setIhp(java.lang.Integer value) {
this.ihp = value;
}
/**
* Gets the value of the 'recurrentlyReported' field.
* Flag indicating if the variant is recurrently reported */
public java.lang.Boolean getRecurrentlyReported() {
return recurrentlyReported;
}
/**
* Sets the value of the 'recurrentlyReported' field.
* Flag indicating if the variant is recurrently reported * @param value the value to set.
*/
public void setRecurrentlyReported(java.lang.Boolean value) {
this.recurrentlyReported = value;
}
/**
* Gets the value of the 'fdp50' field.
* Average tier1 number of basecalls filtered from original read depth within 50 bases */
public java.lang.Float getFdp50() {
return fdp50;
}
/**
* Sets the value of the 'fdp50' field.
* Average tier1 number of basecalls filtered from original read depth within 50 bases * @param value the value to set.
*/
public void setFdp50(java.lang.Float value) {
this.fdp50 = value;
}
/**
* Gets the value of the 'others' field.
* Map of other attributes where keys are the attribute names and values are the attributes */
public java.util.Map getOthers() {
return others;
}
/**
* Sets the value of the 'others' field.
* Map of other attributes where keys are the attribute names and values are the attributes * @param value the value to set.
*/
public void setOthers(java.util.Map value) {
this.others = value;
}
/** Creates a new VariantAttributes RecordBuilder */
public static org.gel.models.report.avro.VariantAttributes.Builder newBuilder() {
return new org.gel.models.report.avro.VariantAttributes.Builder();
}
/** Creates a new VariantAttributes RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.VariantAttributes.Builder newBuilder(org.gel.models.report.avro.VariantAttributes.Builder other) {
return new org.gel.models.report.avro.VariantAttributes.Builder(other);
}
/** Creates a new VariantAttributes RecordBuilder by copying an existing VariantAttributes instance */
public static org.gel.models.report.avro.VariantAttributes.Builder newBuilder(org.gel.models.report.avro.VariantAttributes other) {
return new org.gel.models.report.avro.VariantAttributes.Builder(other);
}
/**
* RecordBuilder for VariantAttributes instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.util.List genomicChanges;
private java.util.List cdnaChanges;
private java.util.List proteinChanges;
private java.util.Map additionalTextualVariantAnnotations;
private java.util.Map references;
private org.gel.models.report.avro.VariantIdentifiers variantIdentifiers;
private java.util.List alleleFrequencies;
private java.util.Map additionalNumericVariantAnnotations;
private java.util.List comments;
private java.util.List alleleOrigins;
private java.lang.Integer ihp;
private java.lang.Boolean recurrentlyReported;
private java.lang.Float fdp50;
private java.util.Map others;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.VariantAttributes.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.VariantAttributes.Builder other) {
super(other);
if (isValidValue(fields()[0], other.genomicChanges)) {
this.genomicChanges = data().deepCopy(fields()[0].schema(), other.genomicChanges);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.cdnaChanges)) {
this.cdnaChanges = data().deepCopy(fields()[1].schema(), other.cdnaChanges);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.proteinChanges)) {
this.proteinChanges = data().deepCopy(fields()[2].schema(), other.proteinChanges);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.additionalTextualVariantAnnotations)) {
this.additionalTextualVariantAnnotations = data().deepCopy(fields()[3].schema(), other.additionalTextualVariantAnnotations);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.references)) {
this.references = data().deepCopy(fields()[4].schema(), other.references);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.variantIdentifiers)) {
this.variantIdentifiers = data().deepCopy(fields()[5].schema(), other.variantIdentifiers);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.alleleFrequencies)) {
this.alleleFrequencies = data().deepCopy(fields()[6].schema(), other.alleleFrequencies);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.additionalNumericVariantAnnotations)) {
this.additionalNumericVariantAnnotations = data().deepCopy(fields()[7].schema(), other.additionalNumericVariantAnnotations);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.comments)) {
this.comments = data().deepCopy(fields()[8].schema(), other.comments);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.alleleOrigins)) {
this.alleleOrigins = data().deepCopy(fields()[9].schema(), other.alleleOrigins);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.ihp)) {
this.ihp = data().deepCopy(fields()[10].schema(), other.ihp);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.recurrentlyReported)) {
this.recurrentlyReported = data().deepCopy(fields()[11].schema(), other.recurrentlyReported);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.fdp50)) {
this.fdp50 = data().deepCopy(fields()[12].schema(), other.fdp50);
fieldSetFlags()[12] = true;
}
if (isValidValue(fields()[13], other.others)) {
this.others = data().deepCopy(fields()[13].schema(), other.others);
fieldSetFlags()[13] = true;
}
}
/** Creates a Builder by copying an existing VariantAttributes instance */
private Builder(org.gel.models.report.avro.VariantAttributes other) {
super(org.gel.models.report.avro.VariantAttributes.SCHEMA$);
if (isValidValue(fields()[0], other.genomicChanges)) {
this.genomicChanges = data().deepCopy(fields()[0].schema(), other.genomicChanges);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.cdnaChanges)) {
this.cdnaChanges = data().deepCopy(fields()[1].schema(), other.cdnaChanges);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.proteinChanges)) {
this.proteinChanges = data().deepCopy(fields()[2].schema(), other.proteinChanges);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.additionalTextualVariantAnnotations)) {
this.additionalTextualVariantAnnotations = data().deepCopy(fields()[3].schema(), other.additionalTextualVariantAnnotations);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.references)) {
this.references = data().deepCopy(fields()[4].schema(), other.references);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.variantIdentifiers)) {
this.variantIdentifiers = data().deepCopy(fields()[5].schema(), other.variantIdentifiers);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.alleleFrequencies)) {
this.alleleFrequencies = data().deepCopy(fields()[6].schema(), other.alleleFrequencies);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.additionalNumericVariantAnnotations)) {
this.additionalNumericVariantAnnotations = data().deepCopy(fields()[7].schema(), other.additionalNumericVariantAnnotations);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.comments)) {
this.comments = data().deepCopy(fields()[8].schema(), other.comments);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.alleleOrigins)) {
this.alleleOrigins = data().deepCopy(fields()[9].schema(), other.alleleOrigins);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.ihp)) {
this.ihp = data().deepCopy(fields()[10].schema(), other.ihp);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.recurrentlyReported)) {
this.recurrentlyReported = data().deepCopy(fields()[11].schema(), other.recurrentlyReported);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.fdp50)) {
this.fdp50 = data().deepCopy(fields()[12].schema(), other.fdp50);
fieldSetFlags()[12] = true;
}
if (isValidValue(fields()[13], other.others)) {
this.others = data().deepCopy(fields()[13].schema(), other.others);
fieldSetFlags()[13] = true;
}
}
/** Gets the value of the 'genomicChanges' field */
public java.util.List getGenomicChanges() {
return genomicChanges;
}
/** Sets the value of the 'genomicChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder setGenomicChanges(java.util.List value) {
validate(fields()[0], value);
this.genomicChanges = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'genomicChanges' field has been set */
public boolean hasGenomicChanges() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'genomicChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearGenomicChanges() {
genomicChanges = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'cdnaChanges' field */
public java.util.List getCdnaChanges() {
return cdnaChanges;
}
/** Sets the value of the 'cdnaChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder setCdnaChanges(java.util.List value) {
validate(fields()[1], value);
this.cdnaChanges = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'cdnaChanges' field has been set */
public boolean hasCdnaChanges() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'cdnaChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearCdnaChanges() {
cdnaChanges = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'proteinChanges' field */
public java.util.List getProteinChanges() {
return proteinChanges;
}
/** Sets the value of the 'proteinChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder setProteinChanges(java.util.List value) {
validate(fields()[2], value);
this.proteinChanges = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'proteinChanges' field has been set */
public boolean hasProteinChanges() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'proteinChanges' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearProteinChanges() {
proteinChanges = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'additionalTextualVariantAnnotations' field */
public java.util.Map getAdditionalTextualVariantAnnotations() {
return additionalTextualVariantAnnotations;
}
/** Sets the value of the 'additionalTextualVariantAnnotations' field */
public org.gel.models.report.avro.VariantAttributes.Builder setAdditionalTextualVariantAnnotations(java.util.Map value) {
validate(fields()[3], value);
this.additionalTextualVariantAnnotations = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'additionalTextualVariantAnnotations' field has been set */
public boolean hasAdditionalTextualVariantAnnotations() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'additionalTextualVariantAnnotations' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearAdditionalTextualVariantAnnotations() {
additionalTextualVariantAnnotations = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'references' field */
public java.util.Map getReferences() {
return references;
}
/** Sets the value of the 'references' field */
public org.gel.models.report.avro.VariantAttributes.Builder setReferences(java.util.Map value) {
validate(fields()[4], value);
this.references = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'references' field has been set */
public boolean hasReferences() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'references' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearReferences() {
references = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'variantIdentifiers' field */
public org.gel.models.report.avro.VariantIdentifiers getVariantIdentifiers() {
return variantIdentifiers;
}
/** Sets the value of the 'variantIdentifiers' field */
public org.gel.models.report.avro.VariantAttributes.Builder setVariantIdentifiers(org.gel.models.report.avro.VariantIdentifiers value) {
validate(fields()[5], value);
this.variantIdentifiers = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'variantIdentifiers' field has been set */
public boolean hasVariantIdentifiers() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'variantIdentifiers' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearVariantIdentifiers() {
variantIdentifiers = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'alleleFrequencies' field */
public java.util.List getAlleleFrequencies() {
return alleleFrequencies;
}
/** Sets the value of the 'alleleFrequencies' field */
public org.gel.models.report.avro.VariantAttributes.Builder setAlleleFrequencies(java.util.List value) {
validate(fields()[6], value);
this.alleleFrequencies = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'alleleFrequencies' field has been set */
public boolean hasAlleleFrequencies() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'alleleFrequencies' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearAlleleFrequencies() {
alleleFrequencies = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'additionalNumericVariantAnnotations' field */
public java.util.Map getAdditionalNumericVariantAnnotations() {
return additionalNumericVariantAnnotations;
}
/** Sets the value of the 'additionalNumericVariantAnnotations' field */
public org.gel.models.report.avro.VariantAttributes.Builder setAdditionalNumericVariantAnnotations(java.util.Map value) {
validate(fields()[7], value);
this.additionalNumericVariantAnnotations = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'additionalNumericVariantAnnotations' field has been set */
public boolean hasAdditionalNumericVariantAnnotations() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'additionalNumericVariantAnnotations' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearAdditionalNumericVariantAnnotations() {
additionalNumericVariantAnnotations = null;
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'comments' field */
public java.util.List getComments() {
return comments;
}
/** Sets the value of the 'comments' field */
public org.gel.models.report.avro.VariantAttributes.Builder setComments(java.util.List value) {
validate(fields()[8], value);
this.comments = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'comments' field has been set */
public boolean hasComments() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'comments' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearComments() {
comments = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'alleleOrigins' field */
public java.util.List getAlleleOrigins() {
return alleleOrigins;
}
/** Sets the value of the 'alleleOrigins' field */
public org.gel.models.report.avro.VariantAttributes.Builder setAlleleOrigins(java.util.List value) {
validate(fields()[9], value);
this.alleleOrigins = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'alleleOrigins' field has been set */
public boolean hasAlleleOrigins() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'alleleOrigins' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearAlleleOrigins() {
alleleOrigins = null;
fieldSetFlags()[9] = false;
return this;
}
/** Gets the value of the 'ihp' field */
public java.lang.Integer getIhp() {
return ihp;
}
/** Sets the value of the 'ihp' field */
public org.gel.models.report.avro.VariantAttributes.Builder setIhp(java.lang.Integer value) {
validate(fields()[10], value);
this.ihp = value;
fieldSetFlags()[10] = true;
return this;
}
/** Checks whether the 'ihp' field has been set */
public boolean hasIhp() {
return fieldSetFlags()[10];
}
/** Clears the value of the 'ihp' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearIhp() {
ihp = null;
fieldSetFlags()[10] = false;
return this;
}
/** Gets the value of the 'recurrentlyReported' field */
public java.lang.Boolean getRecurrentlyReported() {
return recurrentlyReported;
}
/** Sets the value of the 'recurrentlyReported' field */
public org.gel.models.report.avro.VariantAttributes.Builder setRecurrentlyReported(java.lang.Boolean value) {
validate(fields()[11], value);
this.recurrentlyReported = value;
fieldSetFlags()[11] = true;
return this;
}
/** Checks whether the 'recurrentlyReported' field has been set */
public boolean hasRecurrentlyReported() {
return fieldSetFlags()[11];
}
/** Clears the value of the 'recurrentlyReported' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearRecurrentlyReported() {
recurrentlyReported = null;
fieldSetFlags()[11] = false;
return this;
}
/** Gets the value of the 'fdp50' field */
public java.lang.Float getFdp50() {
return fdp50;
}
/** Sets the value of the 'fdp50' field */
public org.gel.models.report.avro.VariantAttributes.Builder setFdp50(java.lang.Float value) {
validate(fields()[12], value);
this.fdp50 = value;
fieldSetFlags()[12] = true;
return this;
}
/** Checks whether the 'fdp50' field has been set */
public boolean hasFdp50() {
return fieldSetFlags()[12];
}
/** Clears the value of the 'fdp50' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearFdp50() {
fdp50 = null;
fieldSetFlags()[12] = false;
return this;
}
/** Gets the value of the 'others' field */
public java.util.Map getOthers() {
return others;
}
/** Sets the value of the 'others' field */
public org.gel.models.report.avro.VariantAttributes.Builder setOthers(java.util.Map value) {
validate(fields()[13], value);
this.others = value;
fieldSetFlags()[13] = true;
return this;
}
/** Checks whether the 'others' field has been set */
public boolean hasOthers() {
return fieldSetFlags()[13];
}
/** Clears the value of the 'others' field */
public org.gel.models.report.avro.VariantAttributes.Builder clearOthers() {
others = null;
fieldSetFlags()[13] = false;
return this;
}
@Override
public VariantAttributes build() {
try {
VariantAttributes record = new VariantAttributes();
record.genomicChanges = fieldSetFlags()[0] ? this.genomicChanges : (java.util.List) defaultValue(fields()[0]);
record.cdnaChanges = fieldSetFlags()[1] ? this.cdnaChanges : (java.util.List) defaultValue(fields()[1]);
record.proteinChanges = fieldSetFlags()[2] ? this.proteinChanges : (java.util.List) defaultValue(fields()[2]);
record.additionalTextualVariantAnnotations = fieldSetFlags()[3] ? this.additionalTextualVariantAnnotations : (java.util.Map) defaultValue(fields()[3]);
record.references = fieldSetFlags()[4] ? this.references : (java.util.Map) defaultValue(fields()[4]);
record.variantIdentifiers = fieldSetFlags()[5] ? this.variantIdentifiers : (org.gel.models.report.avro.VariantIdentifiers) defaultValue(fields()[5]);
record.alleleFrequencies = fieldSetFlags()[6] ? this.alleleFrequencies : (java.util.List) defaultValue(fields()[6]);
record.additionalNumericVariantAnnotations = fieldSetFlags()[7] ? this.additionalNumericVariantAnnotations : (java.util.Map) defaultValue(fields()[7]);
record.comments = fieldSetFlags()[8] ? this.comments : (java.util.List) defaultValue(fields()[8]);
record.alleleOrigins = fieldSetFlags()[9] ? this.alleleOrigins : (java.util.List) defaultValue(fields()[9]);
record.ihp = fieldSetFlags()[10] ? this.ihp : (java.lang.Integer) defaultValue(fields()[10]);
record.recurrentlyReported = fieldSetFlags()[11] ? this.recurrentlyReported : (java.lang.Boolean) defaultValue(fields()[11]);
record.fdp50 = fieldSetFlags()[12] ? this.fdp50 : (java.lang.Float) defaultValue(fields()[12]);
record.others = fieldSetFlags()[13] ? this.others : (java.util.Map) defaultValue(fields()[13]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
