org.gel.models.report.avro.CommonRequest Maven / Gradle / Ivy

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/**
 * Autogenerated by Avro
 * 
 * DO NOT EDIT DIRECTLY
 */
package org.gel.models.report.avro;

@SuppressWarnings("all")
/** This protocol defines the Commons for GEL models */
@org.apache.avro.specific.AvroGenerated
public interface CommonRequest {
  public static final org.apache.avro.Protocol PROTOCOL = org.apache.avro.Protocol.parse("{\"protocol\":\"CommonRequest\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"This protocol defines the Commons for GEL models\",\"types\":[{\"type\":\"enum\",\"name\":\"FileType\",\"symbols\":[\"BAM\",\"gVCF\",\"VCF_small\",\"VCF_somatic_small\",\"VCF_CNV\",\"VCF_somatic_CNV\",\"VCF_SV\",\"VCF_somatic_SV\",\"VCF_SV_CNV\",\"SVG\",\"ANN\",\"BigWig\",\"MD5Sum\",\"ROH\",\"OTHER\",\"PARTITION\",\"VARIANT_FREQUENCIES\",\"COVERAGE\"]},{\"type\":\"record\",\"name\":\"File\",\"doc\":\"This defines a file\\n    This record is uniquely defined by the sample identfier and an URI\\n    Currently sample identifier can be a single string or a list of strings if multiple samples are associated with the same file\\n    *\",\"fields\":[{\"name\":\"sampleId\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Unique identifier(s) of the sample. For example in a multisample vcf this would have an array of all the sample identifiers\"},{\"name\":\"uriFile\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"URI path of the file\"},{\"name\":\"fileType\",\"type\":\"FileType\",\"doc\":\"The type of the file\"},{\"name\":\"md5Sum\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The MD5 checksum\"}]},{\"type\":\"record\",\"name\":\"OtherFamilyHistory\",\"doc\":\"Family history for secondary findings.\\n    Arrays of strings describing discrete family history phenotypes.\\n    Usually: `EndocrineTumours`, `colorectal`, `BreastOvarian` and `HDOrStroke` but can be others\",\"fields\":[{\"name\":\"maternalFamilyHistory\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Relevant Maternal family history\"},{\"name\":\"paternalFamilyHistory\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Relevant Maternal family history\"}]},{\"type\":\"enum\",\"name\":\"Program\",\"doc\":\"The Genomics England program\",\"symbols\":[\"cancer\",\"rare_disease\"]},{\"type\":\"enum\",\"name\":\"InterpretationFlags\",\"doc\":\"Some flags relevant to the interpretation of a case\",\"symbols\":[\"mixed_chemistries\",\"mixedLab_preparation\",\"low_tumour_purity\",\"uniparental_isodisomy\",\"uniparental_heterodisomy\",\"unusual_karyotype\",\"high_cnv_count\",\"high_estimate_human_contamination_fraction\",\"mixed_recruiting_gmc\",\"suspected_mosaicism\",\"low_quality_sample\",\"ffpe_tumour_sample\",\"ff_nano_tumour_sample\",\"missing_values_for_proband_in_reported_variant\",\"reissued\",\"supplementary_report_errors\",\"internal_use_only\",\"high_priority\",\"suspected_increased_number_of_false_positive_heterozygous_loss_calls\",\"suspected_poor_quality_cnv_calls\",\"cnv_calls_assumed_xx_karyo\",\"cnv_calls_assumed_xy_karyo\",\"other\"]},{\"type\":\"record\",\"name\":\"InterpretationFlag\",\"doc\":\"A given interpretation flag together with an optional description\",\"fields\":[{\"name\":\"interpretationFlag\",\"type\":\"InterpretationFlags\",\"doc\":\"The interpretation flag\"},{\"name\":\"additionalDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The description for the flag\"}]},{\"type\":\"record\",\"name\":\"ParticipantInterpretationFlags\",\"doc\":\"Interpretation flags at the participant level\",\"fields\":[{\"name\":\"interpretationFlag\",\"type\":\"InterpretationFlags\",\"doc\":\"The interpretation flag\"},{\"name\":\"additionalDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The description for the flag\"},{\"name\":\"SampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample Id fron which this flag was reported\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Participant Id as appeared in the pedigree\"}]}],\"messages\":{}}");

  @SuppressWarnings("all")
  /** This protocol defines the Commons for GEL models */
  public interface Callback extends CommonRequest {
    public static final org.apache.avro.Protocol PROTOCOL = org.gel.models.report.avro.CommonRequest.PROTOCOL;
  }
}