org.opencb.biodata.models.variant.metadata.VariantFileMetadata Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.metadata;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class VariantFileMetadata 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\":\"VariantFileMetadata\",\"namespace\":\"org.opencb.biodata.models.variant.metadata\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"File id. Will match with the {@link org.opencb.biodata.models.variant.avro.FileEntry#getFileId}\"},{\"name\":\"path\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Path to the original file\",\"default\":null},{\"name\":\"sampleIds\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"Ordered list of sample ids contained in the file\",\"default\":[]},{\"name\":\"stats\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantSetStats\",\"doc\":\"Variant statistics for a set of variants.\\n The variants set can be contain a whole study, a cohort, a sample, a region, ...\",\"fields\":[{\"name\":\"variantCount\",\"type\":\"long\",\"doc\":\"Number of variants in the variant set\"},{\"name\":\"sampleCount\",\"type\":\"long\",\"doc\":\"Number of samples in the variant set\"},{\"name\":\"filterCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"* The number of occurrences for each FILTER value in files from this set.\\n * Each file can contain more than one filter value (usually separated by ';').\\n *\"},{\"name\":\"genotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Number of genotypes found for all samples in variants set\",\"default\":{}},{\"name\":\"filesCount\",\"type\":\"long\",\"doc\":\"Number of files in the variant set\"},{\"name\":\"tiTvRatio\",\"type\":\"float\",\"doc\":\"TiTvRatio = num. transitions / num. transversions\"},{\"name\":\"qualityAvg\",\"type\":\"float\",\"doc\":\"Mean Quality for all the variants with quality\"},{\"name\":\"qualityStdDev\",\"type\":\"float\",\"doc\":\"Standard Deviation of the quality\"},{\"name\":\"typeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by type. e.g. SNP, INDEL, MNP, SNV, ...\",\"default\":{}},{\"name\":\"biotypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by biotype. e.g. protein-coding, miRNA, lncRNA, ...\",\"default\":{}},{\"name\":\"consequenceTypeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Variants count group by consequence type. e.g. synonymous_variant, missense_variant, stop_lost, ...\",\"default\":{}},{\"name\":\"chromosomeCount\",\"type\":{\"type\":\"map\",\"values\":\"long\",\"avro.java.string\":\"String\"},\"doc\":\"Number of variants per chromosome\",\"default\":{}},{\"name\":\"chromosomeDensity\",\"type\":{\"type\":\"map\",\"values\":\"float\",\"avro.java.string\":\"String\"},\"doc\":\"Total density of variants within the chromosome. counts / chromosome.length\",\"default\":{}}]}],\"doc\":\"Global statistics calculated for this file\",\"default\":null},{\"name\":\"header\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantFileHeader\",\"doc\":\"Variant File Header. Contains simple and complex metadata lines describing the content of the file.\\n This header matches with the VCF header.\\n A header may have multiple Simple or Complex lines with the same key\",\"fields\":[{\"name\":\"version\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"complexLines\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantFileHeaderComplexLine\",\"fields\":[{\"name\":\"key\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Key of group of the Complex Header Line, e.g. INFO, FORMAT, FILTER, ALT, ...\"},{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"ID or Name of the line\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The description\",\"default\":null},{\"name\":\"number\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Arity of the values associated with this metadata line.\\n Only present if the metadata line describes data fields, i.e. key == INFO or FORMAT\\n Accepted values:\\n - : The field has always this number of values.\\n - A: The field has one value per alternate allele.\\n - R: The field has one value for each possible allele, including the reference.\\n - G: The field has one value for each possible genotype\\n - .: The number of possible values varies, is unknown or unbounded.\",\"default\":null},{\"name\":\"type\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Type of the values associated with this metadata line.\\n Only present if the metadata line describes data fields, i.e. key == INFO or FORMAT\\n Accepted values:\\n - Integer\\n - Float\\n - String\\n - Character\\n - Flag\",\"default\":null},{\"name\":\"genericFields\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"Other optional fields\",\"default\":{}}]}},\"doc\":\"complex lines, e.g. INFO=\",\"default\":[]},{\"name\":\"simpleLines\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantFileHeaderSimpleLine\",\"fields\":[{\"name\":\"key\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Key of group of the Simple Header Line, e.g. source, assembly, pedigreeDB, ...\"},{\"name\":\"value\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Value\"}]}},\"doc\":\"simple lines, e.g. fileDate=20090805\",\"default\":[]}]}],\"doc\":\"The Variant File Header\",\"default\":null},{\"name\":\"attributes\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"},\"doc\":\"Other user defined attributes related with the file\",\"default\":{}}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** File id. Will match with the {@link org.opencb.biodata.models.variant.avro.FileEntry#getFileId} */
private java.lang.String id;
/** Path to the original file */
private java.lang.String path;
/** Ordered list of sample ids contained in the file */
private java.util.List sampleIds;
/** Global statistics calculated for this file */
private org.opencb.biodata.models.variant.metadata.VariantSetStats stats;
/** The Variant File Header */
private org.opencb.biodata.models.variant.metadata.VariantFileHeader header;
/** Other user defined attributes related with the file */
private java.util.Map attributes;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public VariantFileMetadata() {}
/**
* All-args constructor.
*/
public VariantFileMetadata(java.lang.String id, java.lang.String path, java.util.List sampleIds, org.opencb.biodata.models.variant.metadata.VariantSetStats stats, org.opencb.biodata.models.variant.metadata.VariantFileHeader header, java.util.Map attributes) {
this.id = id;
this.path = path;
this.sampleIds = sampleIds;
this.stats = stats;
this.header = header;
this.attributes = attributes;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return id;
case 1: return path;
case 2: return sampleIds;
case 3: return stats;
case 4: return header;
case 5: return attributes;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: id = (java.lang.String)value$; break;
case 1: path = (java.lang.String)value$; break;
case 2: sampleIds = (java.util.List)value$; break;
case 3: stats = (org.opencb.biodata.models.variant.metadata.VariantSetStats)value$; break;
case 4: header = (org.opencb.biodata.models.variant.metadata.VariantFileHeader)value$; break;
case 5: attributes = (java.util.Map)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'id' field.
* File id. Will match with the {@link org.opencb.biodata.models.variant.avro.FileEntry#getFileId} */
public java.lang.String getId() {
return id;
}
/**
* Sets the value of the 'id' field.
* File id. Will match with the {@link org.opencb.biodata.models.variant.avro.FileEntry#getFileId} * @param value the value to set.
*/
public void setId(java.lang.String value) {
this.id = value;
}
/**
* Gets the value of the 'path' field.
* Path to the original file */
public java.lang.String getPath() {
return path;
}
/**
* Sets the value of the 'path' field.
* Path to the original file * @param value the value to set.
*/
public void setPath(java.lang.String value) {
this.path = value;
}
/**
* Gets the value of the 'sampleIds' field.
* Ordered list of sample ids contained in the file */
public java.util.List getSampleIds() {
return sampleIds;
}
/**
* Sets the value of the 'sampleIds' field.
* Ordered list of sample ids contained in the file * @param value the value to set.
*/
public void setSampleIds(java.util.List value) {
this.sampleIds = value;
}
/**
* Gets the value of the 'stats' field.
* Global statistics calculated for this file */
public org.opencb.biodata.models.variant.metadata.VariantSetStats getStats() {
return stats;
}
/**
* Sets the value of the 'stats' field.
* Global statistics calculated for this file * @param value the value to set.
*/
public void setStats(org.opencb.biodata.models.variant.metadata.VariantSetStats value) {
this.stats = value;
}
/**
* Gets the value of the 'header' field.
* The Variant File Header */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader getHeader() {
return header;
}
/**
* Sets the value of the 'header' field.
* The Variant File Header * @param value the value to set.
*/
public void setHeader(org.opencb.biodata.models.variant.metadata.VariantFileHeader value) {
this.header = value;
}
/**
* Gets the value of the 'attributes' field.
* Other user defined attributes related with the file */
public java.util.Map getAttributes() {
return attributes;
}
/**
* Sets the value of the 'attributes' field.
* Other user defined attributes related with the file * @param value the value to set.
*/
public void setAttributes(java.util.Map value) {
this.attributes = value;
}
/** Creates a new VariantFileMetadata RecordBuilder */
public static org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder newBuilder() {
return new org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder();
}
/** Creates a new VariantFileMetadata RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder other) {
return new org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder(other);
}
/** Creates a new VariantFileMetadata RecordBuilder by copying an existing VariantFileMetadata instance */
public static org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder newBuilder(org.opencb.biodata.models.variant.metadata.VariantFileMetadata other) {
return new org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder(other);
}
/**
* RecordBuilder for VariantFileMetadata instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String id;
private java.lang.String path;
private java.util.List sampleIds;
private org.opencb.biodata.models.variant.metadata.VariantSetStats stats;
private org.opencb.biodata.models.variant.metadata.VariantFileHeader header;
private java.util.Map attributes;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.metadata.VariantFileMetadata.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder other) {
super(other);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.path)) {
this.path = data().deepCopy(fields()[1].schema(), other.path);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.sampleIds)) {
this.sampleIds = data().deepCopy(fields()[2].schema(), other.sampleIds);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.stats)) {
this.stats = data().deepCopy(fields()[3].schema(), other.stats);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.header)) {
this.header = data().deepCopy(fields()[4].schema(), other.header);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.attributes)) {
this.attributes = data().deepCopy(fields()[5].schema(), other.attributes);
fieldSetFlags()[5] = true;
}
}
/** Creates a Builder by copying an existing VariantFileMetadata instance */
private Builder(org.opencb.biodata.models.variant.metadata.VariantFileMetadata other) {
super(org.opencb.biodata.models.variant.metadata.VariantFileMetadata.SCHEMA$);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.path)) {
this.path = data().deepCopy(fields()[1].schema(), other.path);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.sampleIds)) {
this.sampleIds = data().deepCopy(fields()[2].schema(), other.sampleIds);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.stats)) {
this.stats = data().deepCopy(fields()[3].schema(), other.stats);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.header)) {
this.header = data().deepCopy(fields()[4].schema(), other.header);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.attributes)) {
this.attributes = data().deepCopy(fields()[5].schema(), other.attributes);
fieldSetFlags()[5] = true;
}
}
/** Gets the value of the 'id' field */
public java.lang.String getId() {
return id;
}
/** Sets the value of the 'id' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setId(java.lang.String value) {
validate(fields()[0], value);
this.id = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'id' field has been set */
public boolean hasId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'id' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearId() {
id = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'path' field */
public java.lang.String getPath() {
return path;
}
/** Sets the value of the 'path' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setPath(java.lang.String value) {
validate(fields()[1], value);
this.path = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'path' field has been set */
public boolean hasPath() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'path' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearPath() {
path = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'sampleIds' field */
public java.util.List getSampleIds() {
return sampleIds;
}
/** Sets the value of the 'sampleIds' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setSampleIds(java.util.List value) {
validate(fields()[2], value);
this.sampleIds = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'sampleIds' field has been set */
public boolean hasSampleIds() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'sampleIds' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearSampleIds() {
sampleIds = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'stats' field */
public org.opencb.biodata.models.variant.metadata.VariantSetStats getStats() {
return stats;
}
/** Sets the value of the 'stats' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setStats(org.opencb.biodata.models.variant.metadata.VariantSetStats value) {
validate(fields()[3], value);
this.stats = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'stats' field has been set */
public boolean hasStats() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'stats' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearStats() {
stats = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'header' field */
public org.opencb.biodata.models.variant.metadata.VariantFileHeader getHeader() {
return header;
}
/** Sets the value of the 'header' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setHeader(org.opencb.biodata.models.variant.metadata.VariantFileHeader value) {
validate(fields()[4], value);
this.header = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'header' field has been set */
public boolean hasHeader() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'header' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearHeader() {
header = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'attributes' field */
public java.util.Map getAttributes() {
return attributes;
}
/** Sets the value of the 'attributes' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder setAttributes(java.util.Map value) {
validate(fields()[5], value);
this.attributes = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'attributes' field has been set */
public boolean hasAttributes() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'attributes' field */
public org.opencb.biodata.models.variant.metadata.VariantFileMetadata.Builder clearAttributes() {
attributes = null;
fieldSetFlags()[5] = false;
return this;
}
@Override
public VariantFileMetadata build() {
try {
VariantFileMetadata record = new VariantFileMetadata();
record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]);
record.path = fieldSetFlags()[1] ? this.path : (java.lang.String) defaultValue(fields()[1]);
record.sampleIds = fieldSetFlags()[2] ? this.sampleIds : (java.util.List) defaultValue(fields()[2]);
record.stats = fieldSetFlags()[3] ? this.stats : (org.opencb.biodata.models.variant.metadata.VariantSetStats) defaultValue(fields()[3]);
record.header = fieldSetFlags()[4] ? this.header : (org.opencb.biodata.models.variant.metadata.VariantFileHeader) defaultValue(fields()[4]);
record.attributes = fieldSetFlags()[5] ? this.attributes : (java.util.Map) defaultValue(fields()[5]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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