avro.gel_participant_6_2_0.InterpretationRequestCancer.avdl Maven / Gradle / Ivy
@namespace("org.gel.models.report.avro")
/**
This protocol defines the mechanism that Genomics England uses to trigger a clinical interpretation process from a third
party in the cancer program
The record report is the top level class. This includes clinical information + various version
The annotation provided by Genomics England is created using CellBase https://github.com/opencb/cellbase/wiki
All annotations are against Ensembl gene models
*/
protocol CancerInterpretationRequests {
import idl "CancerParticipant.avdl";
import idl "CommonRequest.avdl";
import idl "CommonInterpreted.avdl";
import idl "ReportVersionControl.avdl";
/**
This record represents basic information for this report
*/
record CancerInterpretationRequest {
/**
Model version number
*/
ReportVersionControl versionControl;
/**
Identifier for this interpretation request
*/
string interpretationRequestId;
/**
Version for this interpretation request
*/
int interpretationRequestVersion;
/**
Internal study identifier
*/
string internalStudyId;
/**
Participant internal identifier
*/
union {null, string} participantInternalId;
/**
This is the version of the assembly used to align the reads
*/
Assembly genomeAssembly;
/**
The genome shall be assigned to the workspaces(projects or domains with a predefined set of users) to control user access
*/
array workspace;
/**
BAMs Files
*/
union {null, array} bams;
/**
VCFs Files where SVs and CNVs are represented
*/
union {null, array} vcfs;
/**
BigWig Files
*/
union {null, array} bigWigs;
/**
Variant Annotation File
*/
union {null, File} annotationFile;
/**
Other files that may be vendor specific
map of key: type of file, value: record of type File
*/
union {null, map} otherFiles;
/**
Cancer Particiapnt Data.
*/
union {null, org.gel.models.participant.avro.CancerParticipant} cancerParticipant;
/**
It is paternal or maternal with reference to the participant.
*/
union {null, OtherFamilyHistory} otherFamilyHistory;
/**
This map of key: panel_name, value: (map of key: gene, value: (map of metrics of key: metric name, value: float))
That is: a map of tables of genes and metrics
*/
union {null, map>>} genePanelsCoverage;
/**
Flags about this case relevant for interpretation
*/
union {null, array} interpretationFlags;
/**
Additional information
*/
union {null, map} additionalInfo;
}
}