org.opencb.biodata.models.variant.avro.Variants 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 interface Variants {
public static final org.apache.avro.Protocol PROTOCOL = org.apache.avro.Protocol.parse("{\"protocol\":\"Variants\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"types\":[{\"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.\"}]},{\"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\"}]},{\"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\"}]},{\"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\"]},{\"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\",\"ModeOfInheritance\"],\"doc\":\"The mode of inheritance\"}]},{\"type\":\"enum\",\"name\":\"FeatureTypes\",\"doc\":\"The feature types\",\"symbols\":[\"regulatory_region\",\"gene\",\"transcript\",\"protein\"]},{\"type\":\"record\",\"name\":\"GenomicFeature\",\"doc\":\"The genomic feature\",\"fields\":[{\"name\":\"featureType\",\"type\":[\"null\",\"FeatureTypes\"],\"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\"}]},{\"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\"]},{\"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\"]},{\"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\"]},{\"type\":\"enum\",\"name\":\"TumorigenesisClassification\",\"doc\":\"Variant classification according to its relation to cancer aetiology.\\n* `driver` : Driver variants\\n* `passenger` : Passenger variants\\n* `modifier` : Modifier variants\",\"symbols\":[\"driver\",\"passenger\",\"modifier\"]},{\"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\"]},{\"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\"]},{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetrance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]},{\"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\"]},{\"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\"]},{\"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\"]},{\"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\"]},{\"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\\\")\"}]},{\"type\":\"record\",\"name\":\"VariantClassification\",\"doc\":\"The variant classification according to different properties.\",\"fields\":[{\"name\":\"clinicalSignificance\",\"type\":[\"null\",\"ClinicalSignificance\"],\"doc\":\"The variant's clinical significance.\"},{\"name\":\"drugResponseClassification\",\"type\":[\"null\",\"DrugResponseClassification\"],\"doc\":\"The variant's pharmacogenomics classification",".\"},{\"name\":\"traitAssociation\",\"type\":[\"null\",\"TraitAssociation\"],\"doc\":\"The variant's trait association.\"},{\"name\":\"tumorigenesisClassification\",\"type\":[\"null\",\"TumorigenesisClassification\"],\"doc\":\"The variant's tumorigenesis classification.\"},{\"name\":\"functionalEffect\",\"type\":[\"null\",\"VariantFunctionalEffect\"],\"doc\":\"The variant functional effect\"}]},{\"type\":\"record\",\"name\":\"EvidenceEntry\",\"doc\":\"An entry for an evidence\",\"fields\":[{\"name\":\"source\",\"type\":\"EvidenceSource\",\"doc\":\"Source of the evidence\"},{\"name\":\"submissions\",\"type\":{\"type\":\"array\",\"items\":\"EvidenceSubmission\"},\"doc\":\"The list of submissions\",\"default\":[]},{\"name\":\"somaticInformation\",\"type\":[\"null\",\"SomaticInformation\"],\"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\":\"AlleleOrigin\"}],\"doc\":\"List of allele origins\"},{\"name\":\"heritableTraits\",\"type\":{\"type\":\"array\",\"items\":\"HeritableTrait\"},\"doc\":\"Heritable traits associated to this evidence\",\"default\":[]},{\"name\":\"genomicFeatures\",\"type\":{\"type\":\"array\",\"items\":\"GenomicFeature\"},\"doc\":\"The transcript to which the evidence refers\",\"default\":[]},{\"name\":\"variantClassification\",\"type\":[\"null\",\"VariantClassification\"],\"doc\":\"The variant classification\"},{\"name\":\"impact\",\"type\":[\"null\",\"EvidenceImpact\"],\"doc\":\"Impact of evidence. Should be coherent with the classification of impact if provided.\"},{\"name\":\"confidence\",\"type\":[\"null\",\"Confidence\"],\"doc\":\"The curation confidence.\"},{\"name\":\"consistencyStatus\",\"type\":[\"null\",\"ConsistencyStatus\"],\"doc\":\"The consistency status. This is applicable to complex evidences (e.g.: ClinVar)\"},{\"name\":\"ethnicity\",\"type\":\"EthnicCategory\",\"doc\":\"Ethnicity\"},{\"name\":\"penetrance\",\"type\":[\"null\",\"Penetrance\"],\"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\":\"Property\"},\"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\":[]}]},{\"type\":\"enum\",\"name\":\"ExpressionCall\",\"symbols\":[\"UP\",\"DOWN\"],\"javaAnnotation\":\"Deprecated\"},{\"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\"}}]}]},{\"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\",\"ExpressionCall\"]},{\"name\":\"pvalue\",\"type\":[\"null\",\"float\"]}]},{\"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\"]}]},{\"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\"}]}]},{\"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\"}}]},{\"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\"]}]},{\"type\":\"record\",\"name\":\"SequenceOntologyTerm\",\"fields\":[{\"name\":\"accession\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},{\"name\":\"name\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"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\"}]}]},{\"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\"}]}]},{\"type\":\"record\",\"name\":\"ProteinVariantAnnotation\",\"fields\":[{\"name\":\"uniprotAccession\",\"type\":[\"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\":\"Score\"}]},{\"name\":\"keywords\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}]},{\"name\":\"features\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"ProteinFeature\"}]}]},{\"type\":\"record\",\"name\":\"ExonOverlap\",\"fields\":[{\"name\":\"number\",\"type\":[\"nu","ll\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"percentage\",\"type\":[\"null\",\"float\"]}]},{\"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\"}}]},{\"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\":\"ExonOverlap\"}]},{\"name\":\"spliceScores\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"SpliceScores\"}]},{\"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\",\"ProteinVariantAnnotation\"]},{\"name\":\"sequenceOntologyTerms\",\"type\":{\"type\":\"array\",\"items\":\"SequenceOntologyTerm\"}}]},{\"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\"}]}]},{\"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\"]}]},{\"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\":\"consensusSize\",\"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\"}]}]},{\"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\"}}]}]},{\"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\"}]}]},{\"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\":\"PharmacogenomicsAlleles\"}]}]},{\"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\":\"PharmacogenomicsClinicalAnnotation\"}]}]},{\"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\"}}]}]},{\"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\"}]}]},{\"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\"}]}]},{\"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\":\"OntologyTermAnno","tation\"}]},{\"name\":\"scores\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GwasAssociationStudyTraitScores\"}]}]},{\"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\":\"GwasAssociationStudyTrait\"}]}]},{\"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\":\"GwasAssociationStudy\"}]}]},{\"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\"}]}]},{\"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\":\"CancerHotspotAlternateAnnotation\"}]},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]},{\"type\":\"record\",\"name\":\"AdditionalAttribute\",\"fields\":[{\"name\":\"attribute\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}}]},{\"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\":\"Xref\"}]},{\"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\":\"ConsequenceType\"},\"default\":[]},{\"name\":\"populationFrequencies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"PopulationFrequency\"}]},{\"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\":\"Expression\"}]},{\"name\":\"geneTraitAssociation\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GeneTraitAssociation\"}]},{\"name\":\"geneDrugInteraction\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GeneDrugInteraction\"}]},{\"name\":\"geneConstraints\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Constraint\"}]},{\"name\":\"geneMirnaTargets\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GeneMirnaTarget\"}]},{\"name\":\"geneCancerAssociations\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GeneCancerAssociation\"}]},{\"name\":\"traitAssociation\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"EvidenceEntry\"}]},{\"name\":\"pharmacogenomics\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Pharmacogenomics\"}]},{\"name\":\"gwas\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GwasAssociation\"}]},{\"name\":\"cancerHotspots\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"CancerHotspotVariantAnnotation\"}]},{\"name\":\"functionalScore\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Score\"}]},{\"name\":\"cytoband\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Cytoband\"}]},{\"name\":\"repeat\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Repeat\"}]},{\"name\":\"drugs\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Drug\"}]},{\"name\":\"additionalAttributes\",\"type\":[\"null\",{\"type\":\"map\",\"values\":\"AdditionalAttribute\",\"avro.java.string\":\"String\"}],\"default\":null}]},{\"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\"]},{\"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 *\"}]},{\"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}]},{\"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.\"}]},{\"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\",\"OriginalCall\"],\"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.\"}]},{\"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\"}]},{\"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\"}}}]},{\"type\":\"enum\",\"name\":\"IssueType\",\"symbols\":[\"DUPLICATION\",\"DISCREPANCY\",\"MENDELIAN_ERROR\",\"DE_NOVO\",\"COMPOUND_HETEROZYGOUS\"]},{\"type\":\"record\",\"name\":\"IssueEntry\",\"fields\":[{\"name\":\"type\",\"type\":\"IssueType\"},{\"name\":\"sample\",\"type\":\"SampleEntry\"},{\"name\":\"data\",\"type\":{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}}]},{\"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\":\"FileEntry\"},\"doc\":\"* List of files from the study where the variant was present.\",\"default\":[]},{\"name\":\"secondaryAlternates\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"AlternateCoordinate\"}],\"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\":\"SampleEntry\"},\"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\":\"IssueEntry\"},\"default\":[]},{\"name\":\"stats\",\"type\":{\"type\":\"array\",\"items\":\"VariantStats\"},\"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\":\"VariantScore\"},\"default\":[]}]},{\"type\":\"enum\",\"name\":\"StructuralVariantType\",\"doc\":\"* @Deprecated, use VariantType instead\",\"symbols\":[\"COPY_NUMBER_GAIN\",\"COPY_NUMBER_LOSS\",\"TANDEM_DUPLICATION\"],\"javaAnnotation\":\"Deprecated\"},{\"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\"]},{\"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\"]}]},{\"type\":\"record\",\"name\":\"Breakend\",\"fields\":[{\"name\":\"mate\",\"type\":[\"null\",\"BreakendMate\"]},{\"name\":\"orientation\",\"type\":[\"null\",\"BreakendOrientation\"]},{\"name\":\"insSeq\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]}]},{\"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\",\"StructuralVariantType\"],\"doc\":\"*"," @deprecated\",\"javaAnnotation\":\"Deprecated\"},{\"name\":\"breakend\",\"type\":[\"null\",\"Breakend\"],\"default\":null}]},{\"type\":\"record\",\"name\":\"VariantAvro\",\"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\",\"StructuralVariation\"],\"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\":\"VariantType\",\"doc\":\"* Type of variation: single nucleotide, indel or structural variation.\"},{\"name\":\"studies\",\"type\":{\"type\":\"array\",\"items\":\"StudyEntry\"},\"doc\":\"* Information specific to each study the variant was read from, such as\\n * samples or statistics.\"},{\"name\":\"annotation\",\"type\":[\"null\",\"VariantAnnotation\"],\"doc\":\"* Annotations of the genomic variation.\",\"default\":null}]}],\"messages\":{}}");
@SuppressWarnings("all")
public interface Callback extends Variants {
public static final org.apache.avro.Protocol PROTOCOL = org.opencb.biodata.models.variant.avro.Variants.PROTOCOL;
}
}