org.opencb.biodata.models.variant.avro.StudyEntry Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class StudyEntry 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\":\"StudyEntry\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"fields\":[{\"name\":\"studyId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Unique identifier of the study.\"},{\"name\":\"files\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"FileEntry\",\"fields\":[{\"name\":\"fileId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Unique identifier of the source file.\"},{\"name\":\"call\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"OriginalCall\",\"fields\":[{\"name\":\"variantId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Original variant ID before normalization including all secondary alternates.\"},{\"name\":\"alleleIndex\",\"type\":[\"null\",\"int\"],\"doc\":\"* Alternate allele index of the original multi-allellic variant call in which was decomposed.\"}]}],\"doc\":\"* Original call position for the variant, if the file was normalized.\\n *\\n * {position}:{reference}:{alternate}(,{other_alternate})*:{allele_index}\"},{\"name\":\"data\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"* Optional data that probably depend on the format of the file the\\n * variant was initially read from.\"}]}},\"doc\":\"* List of files from the study where the variant was present.\",\"default\":[]},{\"name\":\"secondaryAlternates\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AlternateCoordinate\",\"fields\":[{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"start\",\"type\":[\"null\",\"int\"],\"doc\":\"* First position 1-based of the alternate. If null, the start is the same of the variant.\"},{\"name\":\"end\",\"type\":[\"null\",\"int\"],\"doc\":\"* End position 1-based of the alternate. If null, the end is the same of the variant.\"},{\"name\":\"reference\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Reference allele. If null, the reference is the same of the variant.\"},{\"name\":\"alternate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Alternate allele.\"},{\"name\":\"type\",\"type\":{\"type\":\"enum\",\"name\":\"VariantType\",\"doc\":\"* Type of variation, which depends mostly on its length.\\n * \\n * - SNVs involve a single nucleotide, without changes in length
\\n * - MNVs involve multiple nucleotides, without changes in length
\\n * - Indels are insertions or deletions of less than SV_THRESHOLD (50) nucleotides
\\n * - Structural variations are large changes of more than SV_THRESHOLD nucleotides
\\n * - Copy-number variations alter the number of copies of a region
\\n *
\",\"symbols\":[\"SNV\",\"MNV\",\"INDEL\",\"SV\",\"INSERTION\",\"DELETION\",\"TRANSLOCATION\",\"INVERSION\",\"COPY_NUMBER\",\"COPY_NUMBER_GAIN\",\"COPY_NUMBER_LOSS\",\"DUPLICATION\",\"TANDEM_DUPLICATION\",\"BREAKEND\",\"NO_VARIATION\",\"SYMBOLIC\",\"MIXED\",\"SNP\",\"MNP\",\"CNV\"]}}]}}],\"doc\":\"* Alternate alleles that appear along with a variant alternate.\",\"default\":null},{\"name\":\"sampleDataKeys\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"* Fields stored for each sample.\"},{\"name\":\"samples\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"SampleEntry\",\"fields\":[{\"name\":\"sampleId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"fileIndex\",\"type\":[\"null\",\"int\"]},{\"name\":\"data\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}}]}},\"doc\":\"* Genotypes and other sample-related information. Each position is related\\n * with one sample. The content are lists of values in the same order than the\\n * sampleDataKeys array. The length of this lists must be the same as the sampleDataKeys field.\"},{\"name\":\"issues\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"IssueEntry\",\"fields\":[{\"name\":\"type\",\"type\":{\"type\":\"enum\",\"name\":\"IssueType\",\"symbols\":[\"DUPLICATION\",\"DISCREPANCY\",\"MENDELIAN_ERROR\",\"DE_NOVO\",\"COMPOUND_HETEROZYGOUS\"]}},{\"name\":\"sample\",\"type\":\"SampleEntry\"},{\"name\":\"data\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}}]}},\"default\":[]},{\"name\":\"stats\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantStats\",\"fields\":[{\"name\":\"cohortId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Unique cohort identifier within the study.\\n *\"},{\"name\":\"sampleCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Count of samples with non-missing genotypes in this variant from the cohort.\\n * This value is used as denominator for genotypeFreq.\\n *\"},{\"name\":\"fileCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Count of files with samples from the cohort that reported this variant.\\n * This value is used as denominator for filterFreq.\\n *\"},{\"name\":\"alleleCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Total number of alleles in called genotypes. It does not include missing alleles.\\n * This value is used as denominator for refAlleleFreq and altAlleleFreq.\\n *\"},{\"name\":\"refAlleleCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Number of reference alleles found in this variant.\\n *\"},{\"name\":\"altAlleleCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Number of main alternate alleles found in this variants. It does not include secondary alternates.\\n *\"},{\"name\":\"refAlleleFreq\",\"type\":[\"null\",\"float\"],\"doc\":\"* Reference allele frequency calculated from refAlleleCount and alleleCount, in the range [0,1]\\n *\"},{\"name\":\"altAlleleFreq\",\"type\":[\"null\",\"float\"],\"doc\":\"* Alternate allele frequency calculated from altAlleleCount and alleleCount, in the range [0,1]\\n *\"},{\"name\":\"missingAlleleCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Number of missing alleles.\\n *\"},{\"name\":\"missingGenotypeCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* Number of genotypes with all alleles missing (e.g. ./.). It does not count partially missing genotypes like \\\"./0\\\" or \\\"./1\\\".\\n *\"},{\"name\":\"genotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"* Number of occurrences for each genotype.\\n * This does not include genotype with all alleles missing (e.g. ./.), but it includes partially missing genotypes like \\\"./0\\\" or \\\"./1\\\".\\n * Total sum of counts should be equal to the count of samples.\\n *\",\"default\":{}},{\"name\":\"genotypeFreq\",\"type\":{\"type\":\"map\",\"values\":\"float\",\"avro.java.string\":\"String\"},\"doc\":\"* Genotype frequency for each genotype found calculated from the genotypeCount and samplesCount, in the range [0,1]\\n * The sum of frequencies should be 1.\\n *\",\"default\":{}},{\"name\":\"filterCount\",\"type\":{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"},\"doc\":\"* The number of occurrences for each FILTER value in files from samples in this cohort reporting this variant.\\n * As each file can contain more than one filter value (usually separated by ';'), the total sum of counts could be greater than the count of files.\\n *\"},{\"name\":\"filterFreq\",\"type\":{\"type\":\"map\",\"values\":\"float\",\"avro.java.string\":\"String\"},\"doc\":\"* Frequency of each filter calculated from the filterCount and filesCount, in the range [0,1]\\n *\"},{\"name\":\"qualityCount\",\"type\":[\"null\",\"int\"],\"doc\":\"* The number of files from samples in this cohort reporting this variant with valid QUAL values.\\n * This value is used as denominator to obtain the qualityAvg.\"},{\"name\":\"qualityAvg\",\"type\":[\"null\",\"float\"],\"doc\":\"* The average Quality value for files with valid QUAL values from samples in this cohort reporting this variant.\\n * Some files may not have defined the QUAL value, so the sampling could be less than the filesCount.\\n *\"},{\"name\":\"maf\",\"type\":[\"null\",\"float\"],\"doc\":\"* Minor allele frequency. Frequency of the less common allele between the reference and the main alternate alleles.\\n * This value does not take into acconunt secondary alternates.\\n *\"},{\"name\":\"mgf\",\"type\":[\"null\",\"float\"],\"doc\":\"* Minor genotype frequency. Frequency of the less common genotype seen in this variant.\\n * This value takes into account all values from the genotypeFreq map.\\n *\"},{\"na","me\":\"mafAllele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Allele with minor frequency.\\n *\"},{\"name\":\"mgfGenotype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Genotype with minor frequency.\\n *\"}]}},\"doc\":\"* Statistics of the genomic variation, such as its alleles/genotype count\\n * or its minimum allele frequency, grouped by cohort name.\"},{\"name\":\"scores\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantScore\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Variant score ID.\"},{\"name\":\"cohort1\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Main cohort used for calculating the score.\"},{\"name\":\"cohort2\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Optional secondary cohort used for calculating the score.\",\"default\":null},{\"name\":\"score\",\"type\":\"float\",\"doc\":\"* Score value\"},{\"name\":\"pValue\",\"type\":[\"null\",\"float\"],\"doc\":\"* Score p value\",\"default\":null}]}},\"default\":[]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** * Unique identifier of the study. */
private java.lang.String studyId;
/** * List of files from the study where the variant was present. */
private java.util.List files;
/** * Alternate alleles that appear along with a variant alternate. */
private java.util.List secondaryAlternates;
/** * Fields stored for each sample. */
private java.util.List sampleDataKeys;
/** * Genotypes and other sample-related information. Each position is related
* with one sample. The content are lists of values in the same order than the
* sampleDataKeys array. The length of this lists must be the same as the sampleDataKeys field. */
private java.util.List samples;
private java.util.List issues;
/** * Statistics of the genomic variation, such as its alleles/genotype count
* or its minimum allele frequency, grouped by cohort name. */
private java.util.List stats;
private java.util.List scores;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public StudyEntry() {}
/**
* All-args constructor.
*/
public StudyEntry(java.lang.String studyId, java.util.List files, java.util.List secondaryAlternates, java.util.List sampleDataKeys, java.util.List samples, java.util.List issues, java.util.List stats, java.util.List scores) {
this.studyId = studyId;
this.files = files;
this.secondaryAlternates = secondaryAlternates;
this.sampleDataKeys = sampleDataKeys;
this.samples = samples;
this.issues = issues;
this.stats = stats;
this.scores = scores;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return studyId;
case 1: return files;
case 2: return secondaryAlternates;
case 3: return sampleDataKeys;
case 4: return samples;
case 5: return issues;
case 6: return stats;
case 7: return scores;
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$) {
case 0: studyId = (java.lang.String)value$; break;
case 1: files = (java.util.List)value$; break;
case 2: secondaryAlternates = (java.util.List)value$; break;
case 3: sampleDataKeys = (java.util.List)value$; break;
case 4: samples = (java.util.List)value$; break;
case 5: issues = (java.util.List)value$; break;
case 6: stats = (java.util.List)value$; break;
case 7: scores = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'studyId' field.
* * Unique identifier of the study. */
public java.lang.String getStudyId() {
return studyId;
}
/**
* Sets the value of the 'studyId' field.
* * Unique identifier of the study. * @param value the value to set.
*/
public void setStudyId(java.lang.String value) {
this.studyId = value;
}
/**
* Gets the value of the 'files' field.
* * List of files from the study where the variant was present. */
public java.util.List getFiles() {
return files;
}
/**
* Sets the value of the 'files' field.
* * List of files from the study where the variant was present. * @param value the value to set.
*/
public void setFiles(java.util.List value) {
this.files = value;
}
/**
* Gets the value of the 'secondaryAlternates' field.
* * Alternate alleles that appear along with a variant alternate. */
public java.util.List getSecondaryAlternates() {
return secondaryAlternates;
}
/**
* Sets the value of the 'secondaryAlternates' field.
* * Alternate alleles that appear along with a variant alternate. * @param value the value to set.
*/
public void setSecondaryAlternates(java.util.List value) {
this.secondaryAlternates = value;
}
/**
* Gets the value of the 'sampleDataKeys' field.
* * Fields stored for each sample. */
public java.util.List getSampleDataKeys() {
return sampleDataKeys;
}
/**
* Sets the value of the 'sampleDataKeys' field.
* * Fields stored for each sample. * @param value the value to set.
*/
public void setSampleDataKeys(java.util.List value) {
this.sampleDataKeys = value;
}
/**
* Gets the value of the 'samples' field.
* * Genotypes and other sample-related information. Each position is related
* with one sample. The content are lists of values in the same order than the
* sampleDataKeys array. The length of this lists must be the same as the sampleDataKeys field. */
public java.util.List getSamples() {
return samples;
}
/**
* Sets the value of the 'samples' field.
* * Genotypes and other sample-related information. Each position is related
* with one sample. The content are lists of values in the same order than the
* sampleDataKeys array. The length of this lists must be the same as the sampleDataKeys field. * @param value the value to set.
*/
public void setSamples(java.util.List value) {
this.samples = value;
}
/**
* Gets the value of the 'issues' field.
*/
public java.util.List getIssues() {
return issues;
}
/**
* Sets the value of the 'issues' field.
* @param value the value to set.
*/
public void setIssues(java.util.List value) {
this.issues = value;
}
/**
* Gets the value of the 'stats' field.
* * Statistics of the genomic variation, such as its alleles/genotype count
* or its minimum allele frequency, grouped by cohort name. */
public java.util.List getStats() {
return stats;
}
/**
* Sets the value of the 'stats' field.
* * Statistics of the genomic variation, such as its alleles/genotype count
* or its minimum allele frequency, grouped by cohort name. * @param value the value to set.
*/
public void setStats(java.util.List value) {
this.stats = value;
}
/**
* Gets the value of the 'scores' field.
*/
public java.util.List getScores() {
return scores;
}
/**
* Sets the value of the 'scores' field.
* @param value the value to set.
*/
public void setScores(java.util.List value) {
this.scores = value;
}
/** Creates a new StudyEntry RecordBuilder */
public static org.opencb.biodata.models.variant.avro.StudyEntry.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.StudyEntry.Builder();
}
/** Creates a new StudyEntry RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.StudyEntry.Builder newBuilder(org.opencb.biodata.models.variant.avro.StudyEntry.Builder other) {
return new org.opencb.biodata.models.variant.avro.StudyEntry.Builder(other);
}
/** Creates a new StudyEntry RecordBuilder by copying an existing StudyEntry instance */
public static org.opencb.biodata.models.variant.avro.StudyEntry.Builder newBuilder(org.opencb.biodata.models.variant.avro.StudyEntry other) {
return new org.opencb.biodata.models.variant.avro.StudyEntry.Builder(other);
}
/**
* RecordBuilder for StudyEntry instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String studyId;
private java.util.List files;
private java.util.List secondaryAlternates;
private java.util.List sampleDataKeys;
private java.util.List samples;
private java.util.List issues;
private java.util.List stats;
private java.util.List scores;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.StudyEntry.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.StudyEntry.Builder other) {
super(other);
if (isValidValue(fields()[0], other.studyId)) {
this.studyId = data().deepCopy(fields()[0].schema(), other.studyId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.files)) {
this.files = data().deepCopy(fields()[1].schema(), other.files);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.secondaryAlternates)) {
this.secondaryAlternates = data().deepCopy(fields()[2].schema(), other.secondaryAlternates);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.sampleDataKeys)) {
this.sampleDataKeys = data().deepCopy(fields()[3].schema(), other.sampleDataKeys);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.samples)) {
this.samples = data().deepCopy(fields()[4].schema(), other.samples);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.issues)) {
this.issues = data().deepCopy(fields()[5].schema(), other.issues);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.stats)) {
this.stats = data().deepCopy(fields()[6].schema(), other.stats);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.scores)) {
this.scores = data().deepCopy(fields()[7].schema(), other.scores);
fieldSetFlags()[7] = true;
}
}
/** Creates a Builder by copying an existing StudyEntry instance */
private Builder(org.opencb.biodata.models.variant.avro.StudyEntry other) {
super(org.opencb.biodata.models.variant.avro.StudyEntry.SCHEMA$);
if (isValidValue(fields()[0], other.studyId)) {
this.studyId = data().deepCopy(fields()[0].schema(), other.studyId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.files)) {
this.files = data().deepCopy(fields()[1].schema(), other.files);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.secondaryAlternates)) {
this.secondaryAlternates = data().deepCopy(fields()[2].schema(), other.secondaryAlternates);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.sampleDataKeys)) {
this.sampleDataKeys = data().deepCopy(fields()[3].schema(), other.sampleDataKeys);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.samples)) {
this.samples = data().deepCopy(fields()[4].schema(), other.samples);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.issues)) {
this.issues = data().deepCopy(fields()[5].schema(), other.issues);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.stats)) {
this.stats = data().deepCopy(fields()[6].schema(), other.stats);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.scores)) {
this.scores = data().deepCopy(fields()[7].schema(), other.scores);
fieldSetFlags()[7] = true;
}
}
/** Gets the value of the 'studyId' field */
public java.lang.String getStudyId() {
return studyId;
}
/** Sets the value of the 'studyId' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setStudyId(java.lang.String value) {
validate(fields()[0], value);
this.studyId = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'studyId' field has been set */
public boolean hasStudyId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'studyId' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearStudyId() {
studyId = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'files' field */
public java.util.List getFiles() {
return files;
}
/** Sets the value of the 'files' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setFiles(java.util.List value) {
validate(fields()[1], value);
this.files = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'files' field has been set */
public boolean hasFiles() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'files' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearFiles() {
files = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'secondaryAlternates' field */
public java.util.List getSecondaryAlternates() {
return secondaryAlternates;
}
/** Sets the value of the 'secondaryAlternates' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setSecondaryAlternates(java.util.List value) {
validate(fields()[2], value);
this.secondaryAlternates = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'secondaryAlternates' field has been set */
public boolean hasSecondaryAlternates() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'secondaryAlternates' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearSecondaryAlternates() {
secondaryAlternates = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'sampleDataKeys' field */
public java.util.List getSampleDataKeys() {
return sampleDataKeys;
}
/** Sets the value of the 'sampleDataKeys' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setSampleDataKeys(java.util.List value) {
validate(fields()[3], value);
this.sampleDataKeys = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'sampleDataKeys' field has been set */
public boolean hasSampleDataKeys() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'sampleDataKeys' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearSampleDataKeys() {
sampleDataKeys = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'samples' field */
public java.util.List getSamples() {
return samples;
}
/** Sets the value of the 'samples' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setSamples(java.util.List value) {
validate(fields()[4], value);
this.samples = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'samples' field has been set */
public boolean hasSamples() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'samples' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearSamples() {
samples = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'issues' field */
public java.util.List getIssues() {
return issues;
}
/** Sets the value of the 'issues' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setIssues(java.util.List value) {
validate(fields()[5], value);
this.issues = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'issues' field has been set */
public boolean hasIssues() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'issues' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearIssues() {
issues = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'stats' field */
public java.util.List getStats() {
return stats;
}
/** Sets the value of the 'stats' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setStats(java.util.List value) {
validate(fields()[6], value);
this.stats = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'stats' field has been set */
public boolean hasStats() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'stats' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearStats() {
stats = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'scores' field */
public java.util.List getScores() {
return scores;
}
/** Sets the value of the 'scores' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder setScores(java.util.List value) {
validate(fields()[7], value);
this.scores = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'scores' field has been set */
public boolean hasScores() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'scores' field */
public org.opencb.biodata.models.variant.avro.StudyEntry.Builder clearScores() {
scores = null;
fieldSetFlags()[7] = false;
return this;
}
@Override
public StudyEntry build() {
try {
StudyEntry record = new StudyEntry();
record.studyId = fieldSetFlags()[0] ? this.studyId : (java.lang.String) defaultValue(fields()[0]);
record.files = fieldSetFlags()[1] ? this.files : (java.util.List) defaultValue(fields()[1]);
record.secondaryAlternates = fieldSetFlags()[2] ? this.secondaryAlternates : (java.util.List) defaultValue(fields()[2]);
record.sampleDataKeys = fieldSetFlags()[3] ? this.sampleDataKeys : (java.util.List) defaultValue(fields()[3]);
record.samples = fieldSetFlags()[4] ? this.samples : (java.util.List) defaultValue(fields()[4]);
record.issues = fieldSetFlags()[5] ? this.issues : (java.util.List) defaultValue(fields()[5]);
record.stats = fieldSetFlags()[6] ? this.stats : (java.util.List) defaultValue(fields()[6]);
record.scores = fieldSetFlags()[7] ? this.scores : (java.util.List) defaultValue(fields()[7]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}