org.opencb.biodata.models.variant.avro.VariantAvro 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 VariantAvro 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\":\"VariantAvro\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* The variant ID.\"},{\"name\":\"names\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"* Other names used for this genomic variation.\",\"default\":[]},{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Chromosome where the genomic variation occurred.\"},{\"name\":\"start\",\"type\":\"int\",\"doc\":\"* Normalized position where the genomic variation starts.\\n * \\n * - SNVs have the same start and end position
\\n * - Insertions start in the last present position: if the first nucleotide\\n * is inserted in position 6, the start is position 5
\\n * - Deletions start in the first previously present position: if the first\\n * deleted nucleotide is in position 6, the start is position 6
\\n *
\"},{\"name\":\"end\",\"type\":\"int\",\"doc\":\"* Normalized position where the genomic variation ends.\\n * \\n * - SNVs have the same start and end positions
\\n * - Insertions end in the first present position: if the last nucleotide\\n * is inserted in position 9, the end is position 10
\\n * - Deletions ends in the last previously present position: if the last\\n * deleted nucleotide is in position 9, the end is position 9
\\n *
\"},{\"name\":\"reference\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Reference allele.\"},{\"name\":\"alternate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"* Alternate allele.\"},{\"name\":\"strand\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Reference strand for this variant\",\"default\":null},{\"name\":\"sv\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"StructuralVariation\",\"fields\":[{\"name\":\"ciStartLeft\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciStartRight\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciEndLeft\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciEndRight\",\"type\":[\"null\",\"int\"]},{\"name\":\"copyNumber\",\"type\":[\"null\",\"int\"],\"doc\":\"* Number of copies for CNV variants.\"},{\"name\":\"leftSvInsSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"* Inserted sequence for long INS\\n *\"},{\"name\":\"rightSvInsSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"type\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"StructuralVariantType\",\"doc\":\"* @Deprecated, use VariantType instead\",\"symbols\":[\"COPY_NUMBER_GAIN\",\"COPY_NUMBER_LOSS\",\"TANDEM_DUPLICATION\"],\"javaAnnotation\":\"Deprecated\"}],\"doc\":\"* @deprecated\",\"javaAnnotation\":\"Deprecated\"},{\"name\":\"breakend\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"Breakend\",\"fields\":[{\"name\":\"mate\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"BreakendMate\",\"fields\":[{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"position\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciPositionLeft\",\"type\":[\"null\",\"int\"]},{\"name\":\"ciPositionRight\",\"type\":[\"null\",\"int\"]}]}]},{\"name\":\"orientation\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"BreakendOrientation\",\"doc\":\"* SE | (Start -> End) | s | t[p[ | piece extending to the right of p is joined after t\\n * SS | (Start -> Start) | s | t]p] | reverse comp piece extending left of p is joined after t\\n * ES | (End -> Start) | s | ]p]t | piece extending to the left of p is joined before t\\n * EE | (End -> End) | s | [p[t | reverse comp piece extending right of p is joined before t\",\"symbols\":[\"SE\",\"SS\",\"ES\",\"EE\"]}]},{\"name\":\"insSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}],\"default\":null}]}],\"doc\":\"* Information regarding Structural Variants\",\"default\":null},{\"name\":\"length\",\"type\":\"int\",\"doc\":\"* Length of the genomic variation, which depends on the variation type.\\n * \\n * - SNVs have a length of 1 nucleotide
\\n * - Indels have the length of the largest allele
\\n *
\"},{\"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\":\"* Type of variation: single nucleotide, indel or structural variation.\"},{\"name\":\"studies\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"StudyEntry\",\"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\":\"VariantType\"}]}}],\"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 *\"},{\"name\":\"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\":[]}]}},\"doc\":\"* Information specific to each study the variant was read from, such as\\n * samples or statistics.\"},{\"name\":\"annotation\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantAnnotation\",\"fields\":[{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"start\",\"type\":[\"null\",\"int\"]},{\"name\":\"end\",\"type\":[\"null\",\"int\"]},{\"name\":\"reference\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"alternate\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"ancestralAllele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"xrefs\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Xref\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"hgvs\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"displayConsequenceType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"consequenceTypes\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"ConsequenceType\",\"fields\":[{\"name\":\"geneId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"geneName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"ensemblGeneId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"ensemblTranscriptId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"transcriptId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"hgvs\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"strand\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"biotype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"exonOverlap\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"ExonOverlap\",\"fields\":[{\"name\":\"number\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"percentage\",\"type\":[\"null\",\"float\"]}]}}]},{\"name\":\"spliceScores\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"SpliceScores\",\"fields\":[{\"name\":\"source\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"scores\",\"type\":{\"type\":\"map\",\"values\":\"double\",\"avro.java.string\":\"String\"}}]}}]},{\"name\":\"transcriptFlags\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"cdnaPosition\",\"type\":[\"null\",\"int\"]},{\"name\":\"cdsPosition\",\"type\":[\"null\",\"int\"]},{\"name\":\"codon\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"proteinVariantAnnotation\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"ProteinVariantAnnotation\",\"fields\":[{\"name\":\"uniprotAccession\",\"t","ype\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"uniprotName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"proteinId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"default\":null},{\"name\":\"position\",\"type\":[\"null\",\"int\"]},{\"name\":\"reference\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"alternate\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"uniprotVariantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"functionalDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"substitutionScores\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Score\",\"fields\":[{\"name\":\"score\",\"type\":\"double\"},{\"name\":\"source\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"keywords\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"features\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"ProteinFeature\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"start\",\"type\":\"int\"},{\"name\":\"end\",\"type\":\"int\"},{\"name\":\"type\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]}]}]},{\"name\":\"sequenceOntologyTerms\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"SequenceOntologyTerm\",\"fields\":[{\"name\":\"accession\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"name\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}}}]}},\"default\":[]},{\"name\":\"populationFrequencies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PopulationFrequency\",\"fields\":[{\"name\":\"study\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"population\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"refAllele\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"altAllele\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"refAlleleFreq\",\"type\":\"float\"},{\"name\":\"altAlleleFreq\",\"type\":\"float\"},{\"name\":\"refAlleleCount\",\"type\":[\"null\",\"int\"]},{\"name\":\"altAlleleCount\",\"type\":[\"null\",\"int\"]},{\"name\":\"refHomGenotypeFreq\",\"type\":[\"null\",\"float\"]},{\"name\":\"hetGenotypeFreq\",\"type\":[\"null\",\"float\"]},{\"name\":\"altHomGenotypeFreq\",\"type\":[\"null\",\"float\"]},{\"name\":\"refHomGenotypeCount\",\"type\":[\"null\",\"int\"]},{\"name\":\"hetGenotypeCount\",\"type\":[\"null\",\"int\"]},{\"name\":\"altHomGenotypeCount\",\"type\":[\"null\",\"int\"]}]}}]},{\"name\":\"minorAllele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"minorAlleleFreq\",\"type\":[\"null\",\"float\"]},{\"name\":\"conservation\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Score\"}]},{\"name\":\"geneExpression\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Expression\",\"fields\":[{\"name\":\"geneName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"transcriptId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"experimentalFactor\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"factorValue\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"experimentId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"technologyPlatform\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"expression\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ExpressionCall\",\"symbols\":[\"UP\",\"DOWN\"],\"javaAnnotation\":\"Deprecated\"}]},{\"name\":\"pvalue\",\"type\":[\"null\",\"float\"]}]}}]},{\"name\":\"geneTraitAssociation\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GeneTraitAssociation\",\"fields\":[{\"name\":\"id\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"name\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"hpo\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"score\",\"type\":[\"null\",\"float\"]},{\"name\":\"numberOfPubmeds\",\"type\":[\"null\",\"int\"]},{\"name\":\"associationTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"sources\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"source\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}}]},{\"name\":\"geneDrugInteraction\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GeneDrugInteraction\",\"fields\":[{\"name\":\"geneName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"drugName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"studyType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"type\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"interactionType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"chemblId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"publications\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}]}}]},{\"name\":\"geneConstraints\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Constraint\",\"fields\":[{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"method\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"value\",\"type\":[\"null\",\"double\"]}]}}]},{\"name\":\"geneMirnaTargets\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GeneMirnaTarget\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"biotype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"geneCancerAssociations\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GeneCancerAssociation\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"tier\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"somatic\",\"type\":[\"null\",\"boolean\"]},{\"name\":\"germline\",\"type\":[\"null\",\"boolean\"]},{\"name\":\"somaticTumourTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"germlineTumourTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"syndromes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"tissues\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"modeOfInheritance\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"roleInCancer\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"mutationTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"translocationPartners\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}]}}]},{\"name\":\"traitAssociation\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"EvidenceEntry\",\"doc\":\"An entry for an evidence\",\"fields\":[{\"name\":\"source\",\"type\":{\"type\":\"record\",\"name\":\"EvidenceSource\",\"doc\":\"The source of an evidence.\",\"fields\":[{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Name of source\"},{\"name\":\"version\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Version of source\"},{\"name\":\"date\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The source date.\"}]},\"doc\":\"Source of the evidence\"},{\"name\":\"submissions\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"EvidenceSubmission\",\"doc\":\"The submission information\",\"fields\":[{\"name\":\"submitter\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.","string\":\"String\"}],\"doc\":\"The submitter\"},{\"name\":\"date\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The submission date\"},{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The submission id\"}]}},\"doc\":\"The list of submissions\",\"default\":[]},{\"name\":\"somaticInformation\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"SomaticInformation\",\"doc\":\"The somatic information.\",\"fields\":[{\"name\":\"primarySite\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary site\"},{\"name\":\"siteSubtype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary site subtype\"},{\"name\":\"primaryHistology\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary histology\"},{\"name\":\"histologySubtype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The histology subtype\"},{\"name\":\"tumourOrigin\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The tumour origin\"},{\"name\":\"sampleSource\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The sample source, e.g. blood-bone marrow, cell-line, pancreatic\"}]}],\"doc\":\"The somatic information\"},{\"name\":\"url\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"URL of source if any\"},{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"ID of record in the source\"},{\"name\":\"assembly\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The reference genome assembly\"},{\"name\":\"alleleOrigin\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"enum\",\"name\":\"AlleleOrigin\",\"doc\":\"Variant 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\"},{\"name\":\"heritableTraits\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"HeritableTrait\",\"doc\":\"The entity representing a phenotype and its inheritance pattern.\",\"fields\":[{\"name\":\"trait\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The trait (e.g.: HPO term, MIM term, DO term etc.)\"},{\"name\":\"inheritanceMode\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ModeOfInheritance\",\"doc\":\"An enumeration for the different mode of inheritances:\\n\\n* `monoallelic_not_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, not imprinted\\n* `monoallelic_maternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed)\\n* `monoallelic_paternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed)\\n* `monoallelic`: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown\\n* `biallelic`: BIALLELIC, autosomal or pseudoautosomal\\n* `monoallelic_and_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal\\n* `monoallelic_and_more_severe_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal\\n* `xlinked_biallelic`: X-LINKED: hemizygous mutation in males, biallelic mutations in females\\n* `xlinked_monoallelic`: X linked: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\\n* `mitochondrial`: MITOCHONDRIAL\\n* `unknown`: Unknown\\n* `NA`: Not applicable\",\"symbols\":[\"monoallelic\",\"monoallelic_not_imprinted\",\"monoallelic_maternally_imprinted\",\"monoallelic_paternally_imprinted\",\"biallelic\",\"monoallelic_and_biallelic\",\"monoallelic_and_more_severe_biallelic\",\"xlinked_biallelic\",\"xlinked_monoallelic\",\"mitochondrial\",\"unknown\",\"NA\"]}],\"doc\":\"The mode of inheritance\"}]}},\"doc\":\"Heritable traits associated to this evidence\",\"default\":[]},{\"name\":\"genomicFeatures\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GenomicFeature\",\"doc\":\"The genomic feature\",\"fields\":[{\"name\":\"featureType\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"FeatureTypes\",\"doc\":\"The feature types\",\"symbols\":[\"regulatory_region\",\"gene\",\"transcript\",\"protein\"]}],\"doc\":\"Feature Type\"},{\"name\":\"ensemblId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455)\"},{\"name\":\"xrefs\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Others IDs. Fields like the HGNC symbol if available should be added here\"}]}},\"doc\":\"The transcript to which the evidence refers\",\"default\":[]},{\"name\":\"variantClassification\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"VariantClassification\",\"doc\":\"The variant classification according to different properties.\",\"fields\":[{\"name\":\"clinicalSignificance\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ClinicalSignificance\",\"doc\":\"Mendelian variants classification with ACMG terminology as defined in Richards, S. et al. (2015). Standards and\\n guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College\\n of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17(5),\\n 405–423. https://doi.org/10.1038/gim.2015.30.\\n\\n Classification for pharmacogenomic variants, variants associated to\\n disease and somatic variants based on the ACMG recommendations and ClinVar classification\\n (https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/).\\n\\n* `benign_variant` : Benign variants interpreted for Mendelian disorders\\n* `likely_benign_variant` : Likely benign variants interpreted for Mendelian disorders with a certainty of at least 90%\\n* `pathogenic_variant` : Pathogenic variants interpreted for Mendelian disorders\\n* `likely_pathogenic_variant` : Likely pathogenic variants interpreted for Mendelian disorders with a certainty of at\\nleast 90%\\n* `uncertain_significance` : Uncertain significance variants interpreted for Mendelian disorders. Variants with\\nconflicting evidences should be classified as uncertain_significance\",\"symbols\":[\"benign\",\"likely_benign\",\"VUS\",\"likely_pathogenic\",\"pathogenic\",\"uncertain_significance\"]}],\"doc\":\"The variant's clinical significance.\"},{\"name\":\"drugResponseClassification\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"DrugResponseClassification\",\"doc\":\"Pharmacogenomics drug response variant classification\",\"symbols\":[\"responsive\",\"altered_sensitivity\",\"reduced_sensitivity\",\"increased_sensitivity\",\"altered_resistance\",\"increased_resistance\",\"reduced_resistance\",\"increased_risk_of_toxicity\",\"reduced_risk_of_toxicity\",\"altered_toxicity\",\"adverse_drug_reaction\",\"indication\",\"contraindication\",\"dosing_alteration\",\"increased_dose\",\"reduced_dose\",\"increased_monitoring\",\"increased_efficacy\",\"reduced_efficacy\",\"altered_efficacy\"]}],\"doc\":\"The variant's pharmacogenomics classification.\"},{\"name\":\"traitAssociation\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"TraitAssociation\",\"doc\":\"Association of variants to a given trait.\\n* `established_risk_allele` : Established risk allele for variants associated to disease\\n* `likely_risk_allele` : Likely risk allele for variants associated to disease\\n* `uncertain_risk_allele` : Uncertain risk allele for variants associated to disease\\n* `protective` : Protective allele\",\"symbols\":[\"established_risk_allele\",\"likely_risk_allele\",\"uncertain_risk_allele\",\"protective\"]}],\"doc\":\"The variant's trait association.\"},{\"name\":\"tumorigenesisClassification\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"TumorigenesisClassification\",\"doc\":\"Variant classification according to its relation to cance","r aetiology.\\n* `driver` : Driver variants\\n* `passenger` : Passenger variants\\n* `modifier` : Modifier variants\",\"symbols\":[\"driver\",\"passenger\",\"modifier\"]}],\"doc\":\"The variant's tumorigenesis classification.\"},{\"name\":\"functionalEffect\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"VariantFunctionalEffect\",\"doc\":\"Variant effect with Sequence Ontology terms.\\n\\n* `SO_0002052`: dominant_negative_variant (http://purl.obolibrary.org/obo/SO_0002052)\\n* `SO_0002053`: gain_of_function_variant (http://purl.obolibrary.org/obo/SO_0002053)\\n* `SO_0001773`: lethal_variant (http://purl.obolibrary.org/obo/SO_0001773)\\n* `SO_0002054`: loss_of_function_variant (http://purl.obolibrary.org/obo/SO_0002054)\\n* `SO_0001786`: loss_of_heterozygosity (http://purl.obolibrary.org/obo/SO_0001786)\\n* `SO_0002055`: null_variant (http://purl.obolibrary.org/obo/SO_0002055)\",\"symbols\":[\"dominant_negative_variant\",\"gain_of_function_variant\",\"lethal_variant\",\"loss_of_function_variant\",\"loss_of_heterozygosity\",\"null_variant\"]}],\"doc\":\"The variant functional effect\"}]}],\"doc\":\"The variant classification\"},{\"name\":\"impact\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"EvidenceImpact\",\"doc\":\"Evidence of pathogenicity and benign impact as defined in Richards, S. et al. (2015). Standards and guidelines for the interpretation\\n of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and\\n the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30\\n\\nEvidence of pathogenicity:\\n* `very_strong`:\\n - PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon\\n deletion) in a gene where LOF is a known mechanism of disease\\n* `strong`:\\n - PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change\\n - PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history\\n - PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene\\n product\\n - PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence\\n in controls\\n* `moderate`:\\n - PM1 Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of\\n an enzyme) without benign variation\\n - PM2 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes\\n Project, or Exome Aggregation Consortium\\n - PM3 For recessive disorders, detected in trans with a pathogenic variant\\n - PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss\\n variants\\n - PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic\\n has been seen before\\n - PM6 Assumed de novo, but without confirmation of paternity and maternity\\n* `supporting`:\\n - PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the\\n disease\\n - PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are\\n a common mechanism of disease\\n - PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product\\n (conservation, evolutionary, splicing impact, etc.)\\n - PP4 Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology\\n - PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory\\n to perform an independent evaluation\\n\\nEvidence of benign impact:\\n* `stand_alone`:\\n - BA1 Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation\\n Consortium\\n* `strong`:\\n - BS1 Allele frequency is greater than expected for disorder\\n - BS2 Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked\\n (hemizygous) disorder, with full penetrance expected at an early age\\n - BS3 Well-established in vitro or in vivo functional studies show no damaging effect on protein function or\\n splicing\\n - BS4 Lack of segregation in affected members of a family\\n* `supporting`:\\n - BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease\\n - BP2 Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis\\n with a pathogenic variant in any inheritance pattern\\n - BP3 In-frame deletions/insertions in a repetitive region without a known function\\n - BP4 Multiple lines of computational evidence suggest no impact on gene or gene product (conservation,\\n evolutionary, splicing impact, etc.)\\n - BP5 Variant found in a case with an alternate molecular basis for disease\\n - BP6 Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to\\n perform an independent evaluation\\n - BP7 A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice\\n consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved\",\"symbols\":[\"very_strong\",\"strong\",\"moderate\",\"supporting\",\"stand_alone\"]}],\"doc\":\"Impact of evidence. Should be coherent with the classification of impact if provided.\"},{\"name\":\"confidence\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Confidence\",\"doc\":\"Confidence based on the Confidence Information Ontology\\n\\n* `CIO_0000029`: high confidence level http://purl.obolibrary.org/obo/CIO_0000029\\n* `CIO_0000031`: low confidence level http://purl.obolibrary.org/obo/CIO_0000031\\n* `CIO_0000030`: medium confidence level http://purl.obolibrary.org/obo/CIO_0000030\\n* `CIO_0000039`: rejected http://purl.obolibrary.org/obo/CIO_0000039\",\"symbols\":[\"low_confidence_level\",\"medium_confidence_level\",\"high_confidence_level\",\"rejected\"]}],\"doc\":\"The curation confidence.\"},{\"name\":\"consistencyStatus\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ConsistencyStatus\",\"doc\":\"The consistency of evidences for a given phenotype. This aggregates all evidences for a given phenotype and all\\n evidences with no phenotype associated (e.g.: in silico impact prediction, population frequency).\\n This is based on the Confidence Information Ontology terms.\\n\\n* `CIO_0000033`: congruent, all evidences are consistent. http://purl.obolibrary.org/obo/CIO_0000033\\n* `CIO_0000034`: conflict, there are conflicting evidences. This should correspond to a `VariantClassification` of\\n`uncertain_significance` for mendelian disorders. http://purl.obolibrary.org/obo/CIO_0000034\\n* `CIO_0000035`: strongly conflicting. http://purl.obolibrary.org/obo/CIO_0000035\\n* `CIO_0000036`: weakly conflicting. http://purl.obolibrary.org/obo/CIO_0000036\",\"symbols\":[\"congruent\",\"conflict\",\"weakly_conflicting\",\"strongly_conflicting\"]}],\"doc\":\"The consistency status. This is applicable to complex evidences (e.g.: ClinVar)\"},{\"name\":\"ethnicity\",\"type\":{\"type\":\"enum\",\"name\":\"EthnicCategory\",\"doc\":\"This is the list of ethnics in ONS16\\n\\n* `D`: Mixed: White and Black Caribbean\\n* `E`: Mixed: White and Black African\\n* `F`: Mixed: White and Asian\\n* `G`: Mixed: Any other mixed background\\n* `A`: White: British\\n* `B`: White: Irish\\n* `C`: White: Any other White background\\n* `L`: Asian or Asian British: Any other Asian background\\n* `M`: Black or Black British: Caribbean\\n* `N`: Black or Black British: African\\n* `H`: Asian or Asian British: Indian\\n* `J`: Asian or Asian British: Pakistani\\n* `K`: Asian or Asian British: Bangladeshi\\n* `P`: Black or Black British: Any other Black background\\n* `S`: Other Ethnic Groups: Any other ethnic group\\n* `R`: Other Ethnic Groups: Chinese\\n* `Z`: Not stated\",\"symbols\":[\"D\",\"E\",\"F\",\"G\",\"A\",\"B\",\"C\",\"L\",\"M\",\"N\",\"H\",\"J\",\"K\",\"P\",\"S\",\"R\",\"Z\"]},\"doc\":\"Ethnicity\"},{\"name\":\"penetrance\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetr","ance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]}],\"doc\":\"The penetrance of the phenotype for this genotype. Value in the range [0, 1]\"},{\"name\":\"variableExpressivity\",\"type\":[\"null\",\"boolean\"],\"doc\":\"Variable expressivity of a given phenotype for the same genotype\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Evidence description\"},{\"name\":\"additionalProperties\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Property\",\"doc\":\"A property in the form of name-value pair.\\n Names are restricted to ontology ids, they should be checked against existing ontologies in resources like\\n Ontology Lookup Service.\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)\"},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term name\"},{\"name\":\"value\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Optional value for the ontology term, the type of the value is not checked\\n (i.e.: we could set the pvalue term to \\\"significant\\\" or to \\\"0.0001\\\")\"}]}},\"doc\":\"A list of additional properties in the form name-value.\",\"default\":[]},{\"name\":\"bibliography\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"Bibliography\",\"default\":[]}]}}]},{\"name\":\"pharmacogenomics\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Pharmacogenomics\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"types\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"smiles\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"inChI\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"annotations\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PharmacogenomicsClinicalAnnotation\",\"fields\":[{\"name\":\"variantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"geneNames\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"phenotypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"phenotypeTypes\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"confidence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"score\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"url\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"summary\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"pubmed\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"alleles\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"PharmacogenomicsAlleles\",\"fields\":[{\"name\":\"allele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"annotation\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]}]}}]}]}}]},{\"name\":\"gwas\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GwasAssociation\",\"fields\":[{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"region\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"snpId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"riskAllele\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"riskAlleleFrequency\",\"type\":[\"null\",\"double\"]},{\"name\":\"studies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GwasAssociationStudy\",\"fields\":[{\"name\":\"pubmedid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"study\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"studyAccession\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"initialSampleSizeDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"initialSampleSize\",\"type\":[\"null\",\"int\"]},{\"name\":\"platform\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"genotypingTechnology\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"traits\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GwasAssociationStudyTrait\",\"fields\":[{\"name\":\"diseaseTrait\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"strongestSnpRiskAllele\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"ontologies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"OntologyTermAnnotation\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"url\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"attributes\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"scores\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GwasAssociationStudyTraitScores\",\"fields\":[{\"name\":\"pValue\",\"type\":[\"null\",\"double\"]},{\"name\":\"pValueMlog\",\"type\":[\"null\",\"double\"]},{\"name\":\"pValueText\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"orBeta\",\"type\":[\"null\",\"double\"]},{\"name\":\"percentCI\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]}]}}]}]}}]}]}}]},{\"name\":\"cancerHotspots\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"CancerHotspotVariantAnnotation\",\"fields\":[{\"name\":\"geneName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"proteinId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"aminoacidPosition\",\"type\":[\"null\",\"int\"]},{\"name\":\"aminoacidReference\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"cancerType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"scores\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"double\",\"avro.java.string\":\"String\"}]},{\"name\":\"cancerTypeCount\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"}]},{\"name\":\"organCount\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"}]},{\"name\":\"variants\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"CancerHotspotAlternateAnnotation\",\"fields\":[{\"name\":\"aminoacidAlternate\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"count\",\"type\":[\"null\",\"int\"]},{\"name\":\"sampleCount\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"int\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"functionalScore\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Score\"}]},{\"name\":\"cytoband\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Cytoband\",\"fields\":[{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"stain\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"start\",\"type\":[\"null\",\"int\"]},{\"name\":\"end\",\"type\":[\"null\",\"int\"]}]}}]},{\"name\":\"repeat\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Repeat\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"chromosome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"start\",\"type\":[\"null\",\"int\"]},{\"name\":\"end\",\"type\":[\"null\",\"int\"]},{\"name\":\"period\",\"type\":[\"null\",\"int\"]},{\"name\":\"co","nsensusSize\",\"type\":[\"null\",\"int\"]},{\"name\":\"copyNumber\",\"type\":[\"null\",\"float\"]},{\"name\":\"percentageMatch\",\"type\":[\"null\",\"float\"]},{\"name\":\"score\",\"type\":[\"null\",\"float\"]},{\"name\":\"sequence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]}}]},{\"name\":\"drugs\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Drug\",\"fields\":[{\"name\":\"therapeuticContext\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"pathway\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"effect\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"association\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"status\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"evidence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"bibliography\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]}]}}]},{\"name\":\"additionalAttributes\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"record\",\"name\":\"AdditionalAttribute\",\"fields\":[{\"name\":\"attribute\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}}]},\"avro.java.string\":\"String\"}],\"default\":null}]}],\"doc\":\"* Annotations of the genomic variation.\",\"default\":null}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** * The variant ID. */
private java.lang.String id;
/** * Other names used for this genomic variation. */
private java.util.List names;
/** * Chromosome where the genomic variation occurred. */
private java.lang.String chromosome;
/** * Normalized position where the genomic variation starts.
*
* - SNVs have the same start and end position
* - Insertions start in the last present position: if the first nucleotide
* is inserted in position 6, the start is position 5
* - Deletions start in the first previously present position: if the first
* deleted nucleotide is in position 6, the start is position 6
*
*/
private int start;
/** * Normalized position where the genomic variation ends.
*
* - SNVs have the same start and end positions
* - Insertions end in the first present position: if the last nucleotide
* is inserted in position 9, the end is position 10
* - Deletions ends in the last previously present position: if the last
* deleted nucleotide is in position 9, the end is position 9
*
*/
private int end;
/** * Reference allele. */
private java.lang.String reference;
/** * Alternate allele. */
private java.lang.String alternate;
/** * Reference strand for this variant */
private java.lang.String strand;
/** * Information regarding Structural Variants */
private org.opencb.biodata.models.variant.avro.StructuralVariation sv;
/** * Length of the genomic variation, which depends on the variation type.
*
* - SNVs have a length of 1 nucleotide
* - Indels have the length of the largest allele
*
*/
private int length;
/** * Type of variation: single nucleotide, indel or structural variation. */
private org.opencb.biodata.models.variant.avro.VariantType type;
/** * Information specific to each study the variant was read from, such as
* samples or statistics. */
private java.util.List studies;
/** * Annotations of the genomic variation. */
private org.opencb.biodata.models.variant.avro.VariantAnnotation annotation;
/**
* 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 VariantAvro() {}
/**
* All-args constructor.
*/
public VariantAvro(java.lang.String id, java.util.List names, java.lang.String chromosome, java.lang.Integer start, java.lang.Integer end, java.lang.String reference, java.lang.String alternate, java.lang.String strand, org.opencb.biodata.models.variant.avro.StructuralVariation sv, java.lang.Integer length, org.opencb.biodata.models.variant.avro.VariantType type, java.util.List studies, org.opencb.biodata.models.variant.avro.VariantAnnotation annotation) {
this.id = id;
this.names = names;
this.chromosome = chromosome;
this.start = start;
this.end = end;
this.reference = reference;
this.alternate = alternate;
this.strand = strand;
this.sv = sv;
this.length = length;
this.type = type;
this.studies = studies;
this.annotation = annotation;
}
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 names;
case 2: return chromosome;
case 3: return start;
case 4: return end;
case 5: return reference;
case 6: return alternate;
case 7: return strand;
case 8: return sv;
case 9: return length;
case 10: return type;
case 11: return studies;
case 12: return annotation;
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: names = (java.util.List)value$; break;
case 2: chromosome = (java.lang.String)value$; break;
case 3: start = (java.lang.Integer)value$; break;
case 4: end = (java.lang.Integer)value$; break;
case 5: reference = (java.lang.String)value$; break;
case 6: alternate = (java.lang.String)value$; break;
case 7: strand = (java.lang.String)value$; break;
case 8: sv = (org.opencb.biodata.models.variant.avro.StructuralVariation)value$; break;
case 9: length = (java.lang.Integer)value$; break;
case 10: type = (org.opencb.biodata.models.variant.avro.VariantType)value$; break;
case 11: studies = (java.util.List)value$; break;
case 12: annotation = (org.opencb.biodata.models.variant.avro.VariantAnnotation)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'id' field.
* * The variant ID. */
public java.lang.String getId() {
return id;
}
/**
* Sets the value of the 'id' field.
* * The variant ID. * @param value the value to set.
*/
public void setId(java.lang.String value) {
this.id = value;
}
/**
* Gets the value of the 'names' field.
* * Other names used for this genomic variation. */
public java.util.List getNames() {
return names;
}
/**
* Sets the value of the 'names' field.
* * Other names used for this genomic variation. * @param value the value to set.
*/
public void setNames(java.util.List value) {
this.names = value;
}
/**
* Gets the value of the 'chromosome' field.
* * Chromosome where the genomic variation occurred. */
public java.lang.String getChromosome() {
return chromosome;
}
/**
* Sets the value of the 'chromosome' field.
* * Chromosome where the genomic variation occurred. * @param value the value to set.
*/
public void setChromosome(java.lang.String value) {
this.chromosome = value;
}
/**
* Gets the value of the 'start' field.
* * Normalized position where the genomic variation starts.
*
* - SNVs have the same start and end position
* - Insertions start in the last present position: if the first nucleotide
* is inserted in position 6, the start is position 5
* - Deletions start in the first previously present position: if the first
* deleted nucleotide is in position 6, the start is position 6
*
*/
public java.lang.Integer getStart() {
return start;
}
/**
* Sets the value of the 'start' field.
* * Normalized position where the genomic variation starts.
*
* - SNVs have the same start and end position
* - Insertions start in the last present position: if the first nucleotide
* is inserted in position 6, the start is position 5
* - Deletions start in the first previously present position: if the first
* deleted nucleotide is in position 6, the start is position 6
*
* @param value the value to set.
*/
public void setStart(java.lang.Integer value) {
this.start = value;
}
/**
* Gets the value of the 'end' field.
* * Normalized position where the genomic variation ends.
*
* - SNVs have the same start and end positions
* - Insertions end in the first present position: if the last nucleotide
* is inserted in position 9, the end is position 10
* - Deletions ends in the last previously present position: if the last
* deleted nucleotide is in position 9, the end is position 9
*
*/
public java.lang.Integer getEnd() {
return end;
}
/**
* Sets the value of the 'end' field.
* * Normalized position where the genomic variation ends.
*
* - SNVs have the same start and end positions
* - Insertions end in the first present position: if the last nucleotide
* is inserted in position 9, the end is position 10
* - Deletions ends in the last previously present position: if the last
* deleted nucleotide is in position 9, the end is position 9
*
* @param value the value to set.
*/
public void setEnd(java.lang.Integer value) {
this.end = value;
}
/**
* Gets the value of the 'reference' field.
* * Reference allele. */
public java.lang.String getReference() {
return reference;
}
/**
* Sets the value of the 'reference' field.
* * Reference allele. * @param value the value to set.
*/
public void setReference(java.lang.String value) {
this.reference = value;
}
/**
* Gets the value of the 'alternate' field.
* * Alternate allele. */
public java.lang.String getAlternate() {
return alternate;
}
/**
* Sets the value of the 'alternate' field.
* * Alternate allele. * @param value the value to set.
*/
public void setAlternate(java.lang.String value) {
this.alternate = value;
}
/**
* Gets the value of the 'strand' field.
* * Reference strand for this variant */
public java.lang.String getStrand() {
return strand;
}
/**
* Sets the value of the 'strand' field.
* * Reference strand for this variant * @param value the value to set.
*/
public void setStrand(java.lang.String value) {
this.strand = value;
}
/**
* Gets the value of the 'sv' field.
* * Information regarding Structural Variants */
public org.opencb.biodata.models.variant.avro.StructuralVariation getSv() {
return sv;
}
/**
* Sets the value of the 'sv' field.
* * Information regarding Structural Variants * @param value the value to set.
*/
public void setSv(org.opencb.biodata.models.variant.avro.StructuralVariation value) {
this.sv = value;
}
/**
* Gets the value of the 'length' field.
* * Length of the genomic variation, which depends on the variation type.
*
* - SNVs have a length of 1 nucleotide
* - Indels have the length of the largest allele
*
*/
public java.lang.Integer getLength() {
return length;
}
/**
* Sets the value of the 'length' field.
* * Length of the genomic variation, which depends on the variation type.
*
* - SNVs have a length of 1 nucleotide
* - Indels have the length of the largest allele
*
* @param value the value to set.
*/
public void setLength(java.lang.Integer value) {
this.length = value;
}
/**
* Gets the value of the 'type' field.
* * Type of variation: single nucleotide, indel or structural variation. */
public org.opencb.biodata.models.variant.avro.VariantType getType() {
return type;
}
/**
* Sets the value of the 'type' field.
* * Type of variation: single nucleotide, indel or structural variation. * @param value the value to set.
*/
public void setType(org.opencb.biodata.models.variant.avro.VariantType value) {
this.type = value;
}
/**
* Gets the value of the 'studies' field.
* * Information specific to each study the variant was read from, such as
* samples or statistics. */
public java.util.List getStudies() {
return studies;
}
/**
* Sets the value of the 'studies' field.
* * Information specific to each study the variant was read from, such as
* samples or statistics. * @param value the value to set.
*/
public void setStudies(java.util.List value) {
this.studies = value;
}
/**
* Gets the value of the 'annotation' field.
* * Annotations of the genomic variation. */
public org.opencb.biodata.models.variant.avro.VariantAnnotation getAnnotation() {
return annotation;
}
/**
* Sets the value of the 'annotation' field.
* * Annotations of the genomic variation. * @param value the value to set.
*/
public void setAnnotation(org.opencb.biodata.models.variant.avro.VariantAnnotation value) {
this.annotation = value;
}
/** Creates a new VariantAvro RecordBuilder */
public static org.opencb.biodata.models.variant.avro.VariantAvro.Builder newBuilder() {
return new org.opencb.biodata.models.variant.avro.VariantAvro.Builder();
}
/** Creates a new VariantAvro RecordBuilder by copying an existing Builder */
public static org.opencb.biodata.models.variant.avro.VariantAvro.Builder newBuilder(org.opencb.biodata.models.variant.avro.VariantAvro.Builder other) {
return new org.opencb.biodata.models.variant.avro.VariantAvro.Builder(other);
}
/** Creates a new VariantAvro RecordBuilder by copying an existing VariantAvro instance */
public static org.opencb.biodata.models.variant.avro.VariantAvro.Builder newBuilder(org.opencb.biodata.models.variant.avro.VariantAvro other) {
return new org.opencb.biodata.models.variant.avro.VariantAvro.Builder(other);
}
/**
* RecordBuilder for VariantAvro instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String id;
private java.util.List names;
private java.lang.String chromosome;
private int start;
private int end;
private java.lang.String reference;
private java.lang.String alternate;
private java.lang.String strand;
private org.opencb.biodata.models.variant.avro.StructuralVariation sv;
private int length;
private org.opencb.biodata.models.variant.avro.VariantType type;
private java.util.List studies;
private org.opencb.biodata.models.variant.avro.VariantAnnotation annotation;
/** Creates a new Builder */
private Builder() {
super(org.opencb.biodata.models.variant.avro.VariantAvro.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.opencb.biodata.models.variant.avro.VariantAvro.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.names)) {
this.names = data().deepCopy(fields()[1].schema(), other.names);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[2].schema(), other.chromosome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.start)) {
this.start = data().deepCopy(fields()[3].schema(), other.start);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.end)) {
this.end = data().deepCopy(fields()[4].schema(), other.end);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.reference)) {
this.reference = data().deepCopy(fields()[5].schema(), other.reference);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.alternate)) {
this.alternate = data().deepCopy(fields()[6].schema(), other.alternate);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.strand)) {
this.strand = data().deepCopy(fields()[7].schema(), other.strand);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.sv)) {
this.sv = data().deepCopy(fields()[8].schema(), other.sv);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.length)) {
this.length = data().deepCopy(fields()[9].schema(), other.length);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.type)) {
this.type = data().deepCopy(fields()[10].schema(), other.type);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.studies)) {
this.studies = data().deepCopy(fields()[11].schema(), other.studies);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.annotation)) {
this.annotation = data().deepCopy(fields()[12].schema(), other.annotation);
fieldSetFlags()[12] = true;
}
}
/** Creates a Builder by copying an existing VariantAvro instance */
private Builder(org.opencb.biodata.models.variant.avro.VariantAvro other) {
super(org.opencb.biodata.models.variant.avro.VariantAvro.SCHEMA$);
if (isValidValue(fields()[0], other.id)) {
this.id = data().deepCopy(fields()[0].schema(), other.id);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.names)) {
this.names = data().deepCopy(fields()[1].schema(), other.names);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.chromosome)) {
this.chromosome = data().deepCopy(fields()[2].schema(), other.chromosome);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.start)) {
this.start = data().deepCopy(fields()[3].schema(), other.start);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.end)) {
this.end = data().deepCopy(fields()[4].schema(), other.end);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.reference)) {
this.reference = data().deepCopy(fields()[5].schema(), other.reference);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.alternate)) {
this.alternate = data().deepCopy(fields()[6].schema(), other.alternate);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.strand)) {
this.strand = data().deepCopy(fields()[7].schema(), other.strand);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.sv)) {
this.sv = data().deepCopy(fields()[8].schema(), other.sv);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.length)) {
this.length = data().deepCopy(fields()[9].schema(), other.length);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.type)) {
this.type = data().deepCopy(fields()[10].schema(), other.type);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.studies)) {
this.studies = data().deepCopy(fields()[11].schema(), other.studies);
fieldSetFlags()[11] = true;
}
if (isValidValue(fields()[12], other.annotation)) {
this.annotation = data().deepCopy(fields()[12].schema(), other.annotation);
fieldSetFlags()[12] = 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.avro.VariantAvro.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.avro.VariantAvro.Builder clearId() {
id = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'names' field */
public java.util.List getNames() {
return names;
}
/** Sets the value of the 'names' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setNames(java.util.List value) {
validate(fields()[1], value);
this.names = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'names' field has been set */
public boolean hasNames() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'names' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearNames() {
names = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'chromosome' field */
public java.lang.String getChromosome() {
return chromosome;
}
/** Sets the value of the 'chromosome' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setChromosome(java.lang.String value) {
validate(fields()[2], value);
this.chromosome = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'chromosome' field has been set */
public boolean hasChromosome() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'chromosome' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearChromosome() {
chromosome = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'start' field */
public java.lang.Integer getStart() {
return start;
}
/** Sets the value of the 'start' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setStart(int value) {
validate(fields()[3], value);
this.start = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'start' field has been set */
public boolean hasStart() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'start' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearStart() {
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'end' field */
public java.lang.Integer getEnd() {
return end;
}
/** Sets the value of the 'end' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setEnd(int value) {
validate(fields()[4], value);
this.end = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'end' field has been set */
public boolean hasEnd() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'end' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearEnd() {
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'reference' field */
public java.lang.String getReference() {
return reference;
}
/** Sets the value of the 'reference' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setReference(java.lang.String value) {
validate(fields()[5], value);
this.reference = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'reference' field has been set */
public boolean hasReference() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'reference' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearReference() {
reference = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'alternate' field */
public java.lang.String getAlternate() {
return alternate;
}
/** Sets the value of the 'alternate' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setAlternate(java.lang.String value) {
validate(fields()[6], value);
this.alternate = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'alternate' field has been set */
public boolean hasAlternate() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'alternate' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearAlternate() {
alternate = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'strand' field */
public java.lang.String getStrand() {
return strand;
}
/** Sets the value of the 'strand' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setStrand(java.lang.String value) {
validate(fields()[7], value);
this.strand = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'strand' field has been set */
public boolean hasStrand() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'strand' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearStrand() {
strand = null;
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'sv' field */
public org.opencb.biodata.models.variant.avro.StructuralVariation getSv() {
return sv;
}
/** Sets the value of the 'sv' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setSv(org.opencb.biodata.models.variant.avro.StructuralVariation value) {
validate(fields()[8], value);
this.sv = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'sv' field has been set */
public boolean hasSv() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'sv' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearSv() {
sv = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'length' field */
public java.lang.Integer getLength() {
return length;
}
/** Sets the value of the 'length' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setLength(int value) {
validate(fields()[9], value);
this.length = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'length' field has been set */
public boolean hasLength() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'length' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearLength() {
fieldSetFlags()[9] = false;
return this;
}
/** Gets the value of the 'type' field */
public org.opencb.biodata.models.variant.avro.VariantType getType() {
return type;
}
/** Sets the value of the 'type' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setType(org.opencb.biodata.models.variant.avro.VariantType value) {
validate(fields()[10], value);
this.type = value;
fieldSetFlags()[10] = true;
return this;
}
/** Checks whether the 'type' field has been set */
public boolean hasType() {
return fieldSetFlags()[10];
}
/** Clears the value of the 'type' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearType() {
type = null;
fieldSetFlags()[10] = false;
return this;
}
/** Gets the value of the 'studies' field */
public java.util.List getStudies() {
return studies;
}
/** Sets the value of the 'studies' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setStudies(java.util.List value) {
validate(fields()[11], value);
this.studies = value;
fieldSetFlags()[11] = true;
return this;
}
/** Checks whether the 'studies' field has been set */
public boolean hasStudies() {
return fieldSetFlags()[11];
}
/** Clears the value of the 'studies' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearStudies() {
studies = null;
fieldSetFlags()[11] = false;
return this;
}
/** Gets the value of the 'annotation' field */
public org.opencb.biodata.models.variant.avro.VariantAnnotation getAnnotation() {
return annotation;
}
/** Sets the value of the 'annotation' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder setAnnotation(org.opencb.biodata.models.variant.avro.VariantAnnotation value) {
validate(fields()[12], value);
this.annotation = value;
fieldSetFlags()[12] = true;
return this;
}
/** Checks whether the 'annotation' field has been set */
public boolean hasAnnotation() {
return fieldSetFlags()[12];
}
/** Clears the value of the 'annotation' field */
public org.opencb.biodata.models.variant.avro.VariantAvro.Builder clearAnnotation() {
annotation = null;
fieldSetFlags()[12] = false;
return this;
}
@Override
public VariantAvro build() {
try {
VariantAvro record = new VariantAvro();
record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]);
record.names = fieldSetFlags()[1] ? this.names : (java.util.List) defaultValue(fields()[1]);
record.chromosome = fieldSetFlags()[2] ? this.chromosome : (java.lang.String) defaultValue(fields()[2]);
record.start = fieldSetFlags()[3] ? this.start : (java.lang.Integer) defaultValue(fields()[3]);
record.end = fieldSetFlags()[4] ? this.end : (java.lang.Integer) defaultValue(fields()[4]);
record.reference = fieldSetFlags()[5] ? this.reference : (java.lang.String) defaultValue(fields()[5]);
record.alternate = fieldSetFlags()[6] ? this.alternate : (java.lang.String) defaultValue(fields()[6]);
record.strand = fieldSetFlags()[7] ? this.strand : (java.lang.String) defaultValue(fields()[7]);
record.sv = fieldSetFlags()[8] ? this.sv : (org.opencb.biodata.models.variant.avro.StructuralVariation) defaultValue(fields()[8]);
record.length = fieldSetFlags()[9] ? this.length : (java.lang.Integer) defaultValue(fields()[9]);
record.type = fieldSetFlags()[10] ? this.type : (org.opencb.biodata.models.variant.avro.VariantType) defaultValue(fields()[10]);
record.studies = fieldSetFlags()[11] ? this.studies : (java.util.List) defaultValue(fields()[11]);
record.annotation = fieldSetFlags()[12] ? this.annotation : (org.opencb.biodata.models.variant.avro.VariantAnnotation) defaultValue(fields()[12]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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