org.gel.models.report.avro.VariantInterpretationLog Maven / Gradle / Ivy
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class VariantInterpretationLog 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\":\"VariantInterpretationLog\",\"namespace\":\"org.gel.models.report.avro\",\"fields\":[{\"name\":\"variantCoordinates\",\"type\":{\"type\":\"record\",\"name\":\"VariantCoordinates\",\"doc\":\"The variant coordinates representing uniquely a small variant.\\n No multi-allelic variant supported, alternate only represents one alternate allele.\",\"fields\":[{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"position\",\"type\":\"int\",\"doc\":\"Genomic position\"},{\"name\":\"reference\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The reference bases.\"},{\"name\":\"alternate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The alternate bases\"},{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"doc\":\"The assembly to which this variant corresponds\"}]},\"doc\":\"Variant coordinates\"},{\"name\":\"user\",\"type\":{\"type\":\"record\",\"name\":\"User\",\"fields\":[{\"name\":\"userid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Azure Active Directory immutable user OID\"},{\"name\":\"email\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"User email address\"},{\"name\":\"username\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Username\"},{\"name\":\"role\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"groups\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}]},\"doc\":\"User who set classification\"},{\"name\":\"timestamp\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Date of classification. Format YYYY-MM-DD (e.g. 2020-01-31)\"},{\"name\":\"groupId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"GeL group ID. For GMS cases this will be the referral ID. For 100k rare disease cases this will be the family ID. For 100k cancer cases this will be the participant ID.\"},{\"name\":\"caseId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Interpretation request ID including CIP prefix and version suffix (e.g. SAP-1234-1)\"},{\"name\":\"variantValidation\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantValidation\",\"fields\":[{\"name\":\"validationTechnology\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Technology used to perform secondary confirmation of this variant (e.g. Sanger)\"},{\"name\":\"validationResult\",\"type\":{\"type\":\"enum\",\"name\":\"ValidationResult\",\"symbols\":[\"NotPerformed\",\"Confirmed\",\"NotConfirmed\",\"Pending\"]},\"doc\":\"Status/outcome of validation\"}]}],\"doc\":\"Independent validation of variant\"},{\"name\":\"comments\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"UserComment\",\"fields\":[{\"name\":\"comment\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Comment text\"},{\"name\":\"user\",\"type\":[\"null\",\"User\"],\"doc\":\"User who created comment\"},{\"name\":\"timestamp\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Date and time comment was created (ISO 8601 datetime with seconds and timezone e.g. 2020-11-23T15:52:36+00:00)\"}]}}],\"doc\":\"User comments attached to this variant in this case\"},{\"name\":\"variantClassification\",\"type\":{\"type\":\"record\",\"name\":\"GuidelineBasedVariantClassification\",\"doc\":\"Variant classification based on guidlines, AMP and ACMG are supported\",\"fields\":[{\"name\":\"acmgVariantClassification\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"AcmgVariantClassification\",\"doc\":\"Full record for the ACMG variant clasiffication, including all selectedd evidences and the final classification.\",\"fields\":[{\"name\":\"acmgEvidences\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AcmgEvidence\",\"doc\":\"AcmgEvidence. This should be buit for each one of the evidences assing to a variants following the ACMG guidelines.\\n An AcmgEvidence, should map with one of the criteria defined, i.e, PVS1, BA1, PM1...\",\"fields\":[{\"name\":\"category\",\"type\":{\"type\":\"enum\",\"name\":\"AcmgEvidenceCategory\",\"doc\":\"Each ACMG criterion is classified in one of these categories\",\"symbols\":[\"population_data\",\"computational_and_predictive_data\",\"functional_data\",\"segregation_data\",\"de_novo_data\",\"allelic_data\",\"other_database\",\"other_data\"]},\"doc\":\"Evidence category as defined in ACMG guidelines\"},{\"name\":\"type\",\"type\":{\"type\":\"enum\",\"name\":\"AcmgEvidenceType\",\"doc\":\"Each ACMG cirterion will be classifed as benign or pathogenic\",\"symbols\":[\"benign\",\"pathogenic\"]},\"doc\":\"Evidence type: benign or pathogenic\"},{\"name\":\"weight\",\"type\":{\"type\":\"enum\",\"name\":\"AcmgEvidenceWeight\",\"doc\":\"Each ACMG criterion is weighted using the following terms:\\n\\n* `stand_alone`: `A`, stand-alone applied for benign variant critieria `(BA1)`\\n* `supporting`: `P`, supporting applied for benign variant critieria `(BP1-6)` and pathogenic variant criteria `(PP1-5)`\\n* `moderate`: `M`, moderate applied for pathogenic variant critieria (PM1-6)\\n* `strong`: `S`, strong applied for pathogenic variant critieria (PS1-4)\\n* `very_strong`: `S`, Very Stong applied for pathogenic variant critieria (PVS1)\",\"symbols\":[\"stand_alone\",\"supporting\",\"moderate\",\"strong\",\"very_strong\"]},\"doc\":\"Default strength for criterion as defined in Table 3 of ACMG guidelines (Richards et al 2015). e.g. PM2 would be \\\"moderate\\\"\"},{\"name\":\"modifier\",\"type\":\"int\",\"doc\":\"The number suffix at the end of the ACMG criteria code e.g PM2 would be 2\"},{\"name\":\"activationStrength\",\"type\":{\"type\":\"enum\",\"name\":\"ActivationStrength\",\"doc\":\"Activation Strength enumeration:\\n* `strong`\\n* `moderate`\\n* `supporting`\\n* `very_strong`\\n* `stand_alone`\",\"symbols\":[\"strong\",\"moderate\",\"supporting\",\"very_strong\",\"stand_alone\"]},\"doc\":\"The strength this criterion has been used at in this interpretation. e.g. if PM2 was only used at \\\"supporting\\\" rather than \\\"moderate\\\", the activation strength would be \\\"supporting\\\"\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The description of the evidence as described in ACMG guidelines e.g. for PM2 the description would be \\\"Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium\\\"\"},{\"name\":\"comments\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"UserComment\"}],\"doc\":\"User comments attached to this ACMG criteria in this case\"}]}},\"doc\":\"Details of ACMG criteria used to score this variant\"},{\"name\":\"clinicalSignificance\",\"type\":{\"type\":\"enum\",\"name\":\"ClinicalSignificance\",\"symbols\":[\"benign\",\"likely_benign\",\"likely_pathogenic\",\"pathogenic\",\"uncertain_significance\",\"excluded\"]},\"doc\":\"Final classification selected by user\"},{\"name\":\"calculatedClinicalSignificance\",\"type\":[\"null\",\"ClinicalSignificance\"],\"doc\":\"Classification computed from ACMG scores\"},{\"name\":\"assessment\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"noAcmgEvidence\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"AcmgEvidenceCategory\"}],\"doc\":\"ACMG evidence categories for which the user has indicated there is no evidence available\"}]}],\"doc\":\"Variant classification using ACMG framework\"},{\"name\":\"ampVariantClassification\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"AmpVariantClassification\",\"doc\":\"Full Variant classification acording to AMP guideline, including all supporting evidences and the final\\n assessment\",\"fields\":[{\"name\":\"ampEvidences\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AmpEvidence\",\"doc\":\"Evidences as defined in AMP guidelines, they are composed by a evidence type (first column in the evidence table of\\n the guidlines) and a assessment of the evicence, this last one will define the streght of the evidence, supporting\\n the variant to be classified as TierI-IV\",\"fields\":[{\"name\":\"type\",\"type\":{\"type\":\"enum\",\"name\":\"AmpEvidenceType\",\"doc\":\"Type of evidence in the AMP guideline\",\"symbols\":[\"mutation_type\",\"therapies\",\"variant_frequencies\",\"potential_germline\",\"population_database_presence\",\"germline_database_presence\",\"somatic_database_presence\",\"impact_predictive_software\",\"pathway_involvement\",\"publications\"]},\"doc\":\"AMP evidence type according to Guidlines, i.e germline_database_presence\"},{\"name\":\"evidenceAssessment\",\"type\":{\"type\":\"st","ring\",\"avro.java.string\":\"String\"},\"doc\":\"Assessment for AMP evidence, i.e Present in ClinVar\"}]}},\"doc\":\"List of AMP evidences\"},{\"name\":\"ampTier\",\"type\":{\"type\":\"enum\",\"name\":\"AmpTier\",\"doc\":\"AMP tier:\\n* `TierI`: Variants of Strong Clinical Significance\\n* `TierII`: Variants of Potential Clinical Significance\\n* `TierIII`: Variants of Unknown Clinical Significance\\n* `TierIV`: Benign or Likely Benign Variants\",\"symbols\":[\"tierI\",\"tierII\",\"tierIII\",\"tierIV\"]},\"doc\":\"Final Clasification taken in account the evidences\"},{\"name\":\"ampClincialOrExperimentalEvidence\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AmpClincialOrExperimentalEvidence\",\"doc\":\"Amp Clinical or Experimental Evidence, the level will define the overal clasification of the variant together with\\n the tiering.\",\"fields\":[{\"name\":\"category\",\"type\":{\"type\":\"enum\",\"name\":\"AmpClinicalOrExperimentalEvidenceCategory\",\"doc\":\"Categories of Clinical and/or Experimental Evidence as defined in AMP guidelines\",\"symbols\":[\"therapeutic\",\"diagnosis\",\"prognosis\"]},\"doc\":\"As denined in AMP guidelines: therapeutic, diagnosis or prognosis\"},{\"name\":\"level\",\"type\":{\"type\":\"enum\",\"name\":\"AmpClinicalOrExperimentalEvidenceLevel\",\"doc\":\"Levels for categories of Clinical and/or Experimental Evidence as defined in AMP guidelines\",\"symbols\":[\"levelA\",\"levelB\",\"levelC\",\"levelD\"]},\"doc\":\"As denined in AMP guidelines: levelA, levelB, levelC, levelD\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Description of the evidence\"}]}}],\"doc\":\"Clinical or Experimental evicence\"},{\"name\":\"assessment\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Final Assessment\"}]}],\"doc\":\"Variant classification using AMP framework\"}]},\"doc\":\"Guideline-based variant classification\"},{\"name\":\"Artifact\",\"type\":[\"null\",\"boolean\"],\"doc\":\"User has marked the variant as an artefact\"},{\"name\":\"decisionSupportSystemFilters\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Filter settings applied at time variant was classified\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Variant coordinates */
private org.gel.models.report.avro.VariantCoordinates variantCoordinates;
/** User who set classification */
private org.gel.models.report.avro.User user;
/** Date of classification. Format YYYY-MM-DD (e.g. 2020-01-31) */
private java.lang.String timestamp;
/** GeL group ID. For GMS cases this will be the referral ID. For 100k rare disease cases this will be the family ID. For 100k cancer cases this will be the participant ID. */
private java.lang.String groupId;
/** Interpretation request ID including CIP prefix and version suffix (e.g. SAP-1234-1) */
private java.lang.String caseId;
/** Independent validation of variant */
private org.gel.models.report.avro.VariantValidation variantValidation;
/** User comments attached to this variant in this case */
private java.util.List comments;
/** Guideline-based variant classification */
private org.gel.models.report.avro.GuidelineBasedVariantClassification variantClassification;
/** User has marked the variant as an artefact */
private java.lang.Boolean Artifact;
/** Filter settings applied at time variant was classified */
private java.util.Map decisionSupportSystemFilters;
/**
* 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 VariantInterpretationLog() {}
/**
* All-args constructor.
*/
public VariantInterpretationLog(org.gel.models.report.avro.VariantCoordinates variantCoordinates, org.gel.models.report.avro.User user, java.lang.String timestamp, java.lang.String groupId, java.lang.String caseId, org.gel.models.report.avro.VariantValidation variantValidation, java.util.List comments, org.gel.models.report.avro.GuidelineBasedVariantClassification variantClassification, java.lang.Boolean Artifact, java.util.Map decisionSupportSystemFilters) {
this.variantCoordinates = variantCoordinates;
this.user = user;
this.timestamp = timestamp;
this.groupId = groupId;
this.caseId = caseId;
this.variantValidation = variantValidation;
this.comments = comments;
this.variantClassification = variantClassification;
this.Artifact = Artifact;
this.decisionSupportSystemFilters = decisionSupportSystemFilters;
}
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 variantCoordinates;
case 1: return user;
case 2: return timestamp;
case 3: return groupId;
case 4: return caseId;
case 5: return variantValidation;
case 6: return comments;
case 7: return variantClassification;
case 8: return Artifact;
case 9: return decisionSupportSystemFilters;
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$) {
case 0: variantCoordinates = (org.gel.models.report.avro.VariantCoordinates)value$; break;
case 1: user = (org.gel.models.report.avro.User)value$; break;
case 2: timestamp = (java.lang.String)value$; break;
case 3: groupId = (java.lang.String)value$; break;
case 4: caseId = (java.lang.String)value$; break;
case 5: variantValidation = (org.gel.models.report.avro.VariantValidation)value$; break;
case 6: comments = (java.util.List)value$; break;
case 7: variantClassification = (org.gel.models.report.avro.GuidelineBasedVariantClassification)value$; break;
case 8: Artifact = (java.lang.Boolean)value$; break;
case 9: decisionSupportSystemFilters = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'variantCoordinates' field.
* Variant coordinates */
public org.gel.models.report.avro.VariantCoordinates getVariantCoordinates() {
return variantCoordinates;
}
/**
* Sets the value of the 'variantCoordinates' field.
* Variant coordinates * @param value the value to set.
*/
public void setVariantCoordinates(org.gel.models.report.avro.VariantCoordinates value) {
this.variantCoordinates = value;
}
/**
* Gets the value of the 'user' field.
* User who set classification */
public org.gel.models.report.avro.User getUser() {
return user;
}
/**
* Sets the value of the 'user' field.
* User who set classification * @param value the value to set.
*/
public void setUser(org.gel.models.report.avro.User value) {
this.user = value;
}
/**
* Gets the value of the 'timestamp' field.
* Date of classification. Format YYYY-MM-DD (e.g. 2020-01-31) */
public java.lang.String getTimestamp() {
return timestamp;
}
/**
* Sets the value of the 'timestamp' field.
* Date of classification. Format YYYY-MM-DD (e.g. 2020-01-31) * @param value the value to set.
*/
public void setTimestamp(java.lang.String value) {
this.timestamp = value;
}
/**
* Gets the value of the 'groupId' field.
* GeL group ID. For GMS cases this will be the referral ID. For 100k rare disease cases this will be the family ID. For 100k cancer cases this will be the participant ID. */
public java.lang.String getGroupId() {
return groupId;
}
/**
* Sets the value of the 'groupId' field.
* GeL group ID. For GMS cases this will be the referral ID. For 100k rare disease cases this will be the family ID. For 100k cancer cases this will be the participant ID. * @param value the value to set.
*/
public void setGroupId(java.lang.String value) {
this.groupId = value;
}
/**
* Gets the value of the 'caseId' field.
* Interpretation request ID including CIP prefix and version suffix (e.g. SAP-1234-1) */
public java.lang.String getCaseId() {
return caseId;
}
/**
* Sets the value of the 'caseId' field.
* Interpretation request ID including CIP prefix and version suffix (e.g. SAP-1234-1) * @param value the value to set.
*/
public void setCaseId(java.lang.String value) {
this.caseId = value;
}
/**
* Gets the value of the 'variantValidation' field.
* Independent validation of variant */
public org.gel.models.report.avro.VariantValidation getVariantValidation() {
return variantValidation;
}
/**
* Sets the value of the 'variantValidation' field.
* Independent validation of variant * @param value the value to set.
*/
public void setVariantValidation(org.gel.models.report.avro.VariantValidation value) {
this.variantValidation = value;
}
/**
* Gets the value of the 'comments' field.
* User comments attached to this variant in this case */
public java.util.List getComments() {
return comments;
}
/**
* Sets the value of the 'comments' field.
* User comments attached to this variant in this case * @param value the value to set.
*/
public void setComments(java.util.List value) {
this.comments = value;
}
/**
* Gets the value of the 'variantClassification' field.
* Guideline-based variant classification */
public org.gel.models.report.avro.GuidelineBasedVariantClassification getVariantClassification() {
return variantClassification;
}
/**
* Sets the value of the 'variantClassification' field.
* Guideline-based variant classification * @param value the value to set.
*/
public void setVariantClassification(org.gel.models.report.avro.GuidelineBasedVariantClassification value) {
this.variantClassification = value;
}
/**
* Gets the value of the 'Artifact' field.
* User has marked the variant as an artefact */
public java.lang.Boolean getArtifact() {
return Artifact;
}
/**
* Sets the value of the 'Artifact' field.
* User has marked the variant as an artefact * @param value the value to set.
*/
public void setArtifact(java.lang.Boolean value) {
this.Artifact = value;
}
/**
* Gets the value of the 'decisionSupportSystemFilters' field.
* Filter settings applied at time variant was classified */
public java.util.Map getDecisionSupportSystemFilters() {
return decisionSupportSystemFilters;
}
/**
* Sets the value of the 'decisionSupportSystemFilters' field.
* Filter settings applied at time variant was classified * @param value the value to set.
*/
public void setDecisionSupportSystemFilters(java.util.Map value) {
this.decisionSupportSystemFilters = value;
}
/** Creates a new VariantInterpretationLog RecordBuilder */
public static org.gel.models.report.avro.VariantInterpretationLog.Builder newBuilder() {
return new org.gel.models.report.avro.VariantInterpretationLog.Builder();
}
/** Creates a new VariantInterpretationLog RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.VariantInterpretationLog.Builder newBuilder(org.gel.models.report.avro.VariantInterpretationLog.Builder other) {
return new org.gel.models.report.avro.VariantInterpretationLog.Builder(other);
}
/** Creates a new VariantInterpretationLog RecordBuilder by copying an existing VariantInterpretationLog instance */
public static org.gel.models.report.avro.VariantInterpretationLog.Builder newBuilder(org.gel.models.report.avro.VariantInterpretationLog other) {
return new org.gel.models.report.avro.VariantInterpretationLog.Builder(other);
}
/**
* RecordBuilder for VariantInterpretationLog instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.gel.models.report.avro.VariantCoordinates variantCoordinates;
private org.gel.models.report.avro.User user;
private java.lang.String timestamp;
private java.lang.String groupId;
private java.lang.String caseId;
private org.gel.models.report.avro.VariantValidation variantValidation;
private java.util.List comments;
private org.gel.models.report.avro.GuidelineBasedVariantClassification variantClassification;
private java.lang.Boolean Artifact;
private java.util.Map decisionSupportSystemFilters;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.VariantInterpretationLog.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.VariantInterpretationLog.Builder other) {
super(other);
if (isValidValue(fields()[0], other.variantCoordinates)) {
this.variantCoordinates = data().deepCopy(fields()[0].schema(), other.variantCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.user)) {
this.user = data().deepCopy(fields()[1].schema(), other.user);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.timestamp)) {
this.timestamp = data().deepCopy(fields()[2].schema(), other.timestamp);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.groupId)) {
this.groupId = data().deepCopy(fields()[3].schema(), other.groupId);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.caseId)) {
this.caseId = data().deepCopy(fields()[4].schema(), other.caseId);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.variantValidation)) {
this.variantValidation = data().deepCopy(fields()[5].schema(), other.variantValidation);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.comments)) {
this.comments = data().deepCopy(fields()[6].schema(), other.comments);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.variantClassification)) {
this.variantClassification = data().deepCopy(fields()[7].schema(), other.variantClassification);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.Artifact)) {
this.Artifact = data().deepCopy(fields()[8].schema(), other.Artifact);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.decisionSupportSystemFilters)) {
this.decisionSupportSystemFilters = data().deepCopy(fields()[9].schema(), other.decisionSupportSystemFilters);
fieldSetFlags()[9] = true;
}
}
/** Creates a Builder by copying an existing VariantInterpretationLog instance */
private Builder(org.gel.models.report.avro.VariantInterpretationLog other) {
super(org.gel.models.report.avro.VariantInterpretationLog.SCHEMA$);
if (isValidValue(fields()[0], other.variantCoordinates)) {
this.variantCoordinates = data().deepCopy(fields()[0].schema(), other.variantCoordinates);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.user)) {
this.user = data().deepCopy(fields()[1].schema(), other.user);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.timestamp)) {
this.timestamp = data().deepCopy(fields()[2].schema(), other.timestamp);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.groupId)) {
this.groupId = data().deepCopy(fields()[3].schema(), other.groupId);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.caseId)) {
this.caseId = data().deepCopy(fields()[4].schema(), other.caseId);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.variantValidation)) {
this.variantValidation = data().deepCopy(fields()[5].schema(), other.variantValidation);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.comments)) {
this.comments = data().deepCopy(fields()[6].schema(), other.comments);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.variantClassification)) {
this.variantClassification = data().deepCopy(fields()[7].schema(), other.variantClassification);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.Artifact)) {
this.Artifact = data().deepCopy(fields()[8].schema(), other.Artifact);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.decisionSupportSystemFilters)) {
this.decisionSupportSystemFilters = data().deepCopy(fields()[9].schema(), other.decisionSupportSystemFilters);
fieldSetFlags()[9] = true;
}
}
/** Gets the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantCoordinates getVariantCoordinates() {
return variantCoordinates;
}
/** Sets the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setVariantCoordinates(org.gel.models.report.avro.VariantCoordinates value) {
validate(fields()[0], value);
this.variantCoordinates = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'variantCoordinates' field has been set */
public boolean hasVariantCoordinates() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'variantCoordinates' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearVariantCoordinates() {
variantCoordinates = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'user' field */
public org.gel.models.report.avro.User getUser() {
return user;
}
/** Sets the value of the 'user' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setUser(org.gel.models.report.avro.User value) {
validate(fields()[1], value);
this.user = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'user' field has been set */
public boolean hasUser() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'user' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearUser() {
user = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'timestamp' field */
public java.lang.String getTimestamp() {
return timestamp;
}
/** Sets the value of the 'timestamp' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setTimestamp(java.lang.String value) {
validate(fields()[2], value);
this.timestamp = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'timestamp' field has been set */
public boolean hasTimestamp() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'timestamp' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearTimestamp() {
timestamp = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'groupId' field */
public java.lang.String getGroupId() {
return groupId;
}
/** Sets the value of the 'groupId' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setGroupId(java.lang.String value) {
validate(fields()[3], value);
this.groupId = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'groupId' field has been set */
public boolean hasGroupId() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'groupId' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearGroupId() {
groupId = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'caseId' field */
public java.lang.String getCaseId() {
return caseId;
}
/** Sets the value of the 'caseId' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setCaseId(java.lang.String value) {
validate(fields()[4], value);
this.caseId = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'caseId' field has been set */
public boolean hasCaseId() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'caseId' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearCaseId() {
caseId = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'variantValidation' field */
public org.gel.models.report.avro.VariantValidation getVariantValidation() {
return variantValidation;
}
/** Sets the value of the 'variantValidation' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setVariantValidation(org.gel.models.report.avro.VariantValidation value) {
validate(fields()[5], value);
this.variantValidation = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'variantValidation' field has been set */
public boolean hasVariantValidation() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'variantValidation' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearVariantValidation() {
variantValidation = null;
fieldSetFlags()[5] = 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.VariantInterpretationLog.Builder setComments(java.util.List value) {
validate(fields()[6], value);
this.comments = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'comments' field has been set */
public boolean hasComments() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'comments' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearComments() {
comments = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'variantClassification' field */
public org.gel.models.report.avro.GuidelineBasedVariantClassification getVariantClassification() {
return variantClassification;
}
/** Sets the value of the 'variantClassification' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setVariantClassification(org.gel.models.report.avro.GuidelineBasedVariantClassification value) {
validate(fields()[7], value);
this.variantClassification = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'variantClassification' field has been set */
public boolean hasVariantClassification() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'variantClassification' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearVariantClassification() {
variantClassification = null;
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'Artifact' field */
public java.lang.Boolean getArtifact() {
return Artifact;
}
/** Sets the value of the 'Artifact' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setArtifact(java.lang.Boolean value) {
validate(fields()[8], value);
this.Artifact = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'Artifact' field has been set */
public boolean hasArtifact() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'Artifact' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearArtifact() {
Artifact = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'decisionSupportSystemFilters' field */
public java.util.Map getDecisionSupportSystemFilters() {
return decisionSupportSystemFilters;
}
/** Sets the value of the 'decisionSupportSystemFilters' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder setDecisionSupportSystemFilters(java.util.Map value) {
validate(fields()[9], value);
this.decisionSupportSystemFilters = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'decisionSupportSystemFilters' field has been set */
public boolean hasDecisionSupportSystemFilters() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'decisionSupportSystemFilters' field */
public org.gel.models.report.avro.VariantInterpretationLog.Builder clearDecisionSupportSystemFilters() {
decisionSupportSystemFilters = null;
fieldSetFlags()[9] = false;
return this;
}
@Override
public VariantInterpretationLog build() {
try {
VariantInterpretationLog record = new VariantInterpretationLog();
record.variantCoordinates = fieldSetFlags()[0] ? this.variantCoordinates : (org.gel.models.report.avro.VariantCoordinates) defaultValue(fields()[0]);
record.user = fieldSetFlags()[1] ? this.user : (org.gel.models.report.avro.User) defaultValue(fields()[1]);
record.timestamp = fieldSetFlags()[2] ? this.timestamp : (java.lang.String) defaultValue(fields()[2]);
record.groupId = fieldSetFlags()[3] ? this.groupId : (java.lang.String) defaultValue(fields()[3]);
record.caseId = fieldSetFlags()[4] ? this.caseId : (java.lang.String) defaultValue(fields()[4]);
record.variantValidation = fieldSetFlags()[5] ? this.variantValidation : (org.gel.models.report.avro.VariantValidation) defaultValue(fields()[5]);
record.comments = fieldSetFlags()[6] ? this.comments : (java.util.List) defaultValue(fields()[6]);
record.variantClassification = fieldSetFlags()[7] ? this.variantClassification : (org.gel.models.report.avro.GuidelineBasedVariantClassification) defaultValue(fields()[7]);
record.Artifact = fieldSetFlags()[8] ? this.Artifact : (java.lang.Boolean) defaultValue(fields()[8]);
record.decisionSupportSystemFilters = fieldSetFlags()[9] ? this.decisionSupportSystemFilters : (java.util.Map) defaultValue(fields()[9]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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