MANIFEST.in
setup.py
src/genomoncology/__init__.py
src/genomoncology/main.py
src/genomoncology/state.py
src/genomoncology/cli/__init__.py
src/genomoncology/cli/commands.py
src/genomoncology/cli/const.py
src/genomoncology/cli/options.py
src/genomoncology/cli/types.py
src/genomoncology/cli/utils.py
src/genomoncology/kms/__init__.py
src/genomoncology/kms/annotations.py
src/genomoncology/kms/contents.py
src/genomoncology/kms/factory.py
src/genomoncology/kms/genes.py
src/genomoncology/kms/match.py
src/genomoncology/kms/therapies.py
src/genomoncology/kms/transcripts.py
src/genomoncology/kms/trials.py
src/genomoncology/parse/__init__.py
src/genomoncology/parse/doctypes.py
src/genomoncology/parse/ensures.py
src/genomoncology/parse/fieldtypes.py
src/genomoncology/parse/fusions.py
src/genomoncology/pipeline/__init__.py
src/genomoncology/pipeline/comparators.py
src/genomoncology/pipeline/converters.py
src/genomoncology/pipeline/filters.py
src/genomoncology/pipeline/runner.py
src/genomoncology/pipeline/sinks/__init__.py
src/genomoncology/pipeline/sinks/alterations.py
src/genomoncology/pipeline/sinks/annotations.py
src/genomoncology/pipeline/sinks/base.py
src/genomoncology/pipeline/sinks/excel.py
src/genomoncology/pipeline/sinks/tsv.py
src/genomoncology/pipeline/sinks/vcf.py
src/genomoncology/pipeline/sinks/warehouse.py
src/genomoncology/pipeline/sources/__init__.py
src/genomoncology/pipeline/sources/aggregated.py
src/genomoncology/pipeline/sources/base.py
src/genomoncology/pipeline/sources/bed.py
src/genomoncology/pipeline/sources/const.py
src/genomoncology/pipeline/sources/delimited.py
src/genomoncology/pipeline/sources/excel.py
src/genomoncology/pipeline/sources/maf.py
src/genomoncology/pipeline/sources/paths.py
src/genomoncology/pipeline/sources/smart_lazy_file.py
src/genomoncology/pipeline/sources/one_off_sources/__init__.py
src/genomoncology/pipeline/sources/one_off_sources/mitomap.py
src/genomoncology/pipeline/sources/one_off_sources/uniprot.py
src/genomoncology/pipeline/transformers/__init__.py
src/genomoncology/pipeline/transformers/functions.py
src/genomoncology/pipeline/transformers/mapper_classes.py
src/genomoncology/pipeline/transformers/registry.py
src/genomoncology/pipeline/transformers/tx/__init__.py
src/genomoncology/pipeline/transformers/tx/baylor_decipher.py
src/genomoncology/pipeline/transformers/tx/baylor_wgl.py
src/genomoncology/pipeline/transformers/tx/clinvar.py
src/genomoncology/pipeline/transformers/tx/cosmic.py
src/genomoncology/pipeline/transformers/tx/dbnsfp.py
src/genomoncology/pipeline/transformers/tx/dbsnp.py
src/genomoncology/pipeline/transformers/tx/evs.py
src/genomoncology/pipeline/transformers/tx/exac.py
src/genomoncology/pipeline/transformers/tx/genie_maf.py
src/genomoncology/pipeline/transformers/tx/gnomad.py
src/genomoncology/pipeline/transformers/tx/hgmd.py
src/genomoncology/pipeline/transformers/tx/hpo.py
src/genomoncology/pipeline/transformers/tx/markers.py
src/genomoncology/pipeline/transformers/tx/mitomap.py
src/genomoncology/pipeline/transformers/tx/omim.py
src/genomoncology/pipeline/transformers/tx/splicing.py
src/genomoncology/pipeline/transformers/tx/thousandgenomes.py
src/genomoncology/pipeline/transformers/tx/uniprot.py
src/genomoncology/pipeline/transformers/tx/uniprot_domains.py
src/genomoncology/pipeline/transformers/tx/uniprot_protein_name.py
src/gocli.egg-info/PKG-INFO
src/gocli.egg-info/SOURCES.txt
src/gocli.egg-info/dependency_links.txt
src/gocli.egg-info/entry_points.txt
src/gocli.egg-info/requires.txt
src/gocli.egg-info/top_level.txt
src/gosdk/__init__.py
src/gosdk/construct.py
src/gosdk/logger.py
src/gosdk/models.py
src/gosdk/variables.py
src/gosdk/specs/specd.yaml
src/gosdk/specs/definitions/Alteration.yaml
src/gosdk/specs/definitions/AlterationList.yaml
src/gosdk/specs/definitions/AlterationsDocument.yaml
src/gosdk/specs/definitions/AlterationsDocumentList.yaml
src/gosdk/specs/definitions/Annotation.yaml
src/gosdk/specs/definitions/AnnotationBundleVersion.yaml
src/gosdk/specs/definitions/AnnotationList.yaml
src/gosdk/specs/definitions/AnnotationsDocument.yaml
src/gosdk/specs/definitions/AnnotationsDocumentAndNotFoundList.yaml
src/gosdk/specs/definitions/AnnotationsDocumentList.yaml
src/gosdk/specs/definitions/Annotations_MergedDocument.yaml
src/gosdk/specs/definitions/Annotations_MergedDocumentList.yaml
src/gosdk/specs/definitions/Arguments.yaml
src/gosdk/specs/definitions/Case.yaml
src/gosdk/specs/definitions/CaseList.yaml
src/gosdk/specs/definitions/CasesDocument.yaml
src/gosdk/specs/definitions/CasesDocumentList.yaml
src/gosdk/specs/definitions/Classification.yaml
src/gosdk/specs/definitions/ClassificationsDocument.yaml
src/gosdk/specs/definitions/ClassificationsDocumentList.yaml
src/gosdk/specs/definitions/Content.yaml
src/gosdk/specs/definitions/ContentsDocument.yaml
src/gosdk/specs/definitions/ContentsDocumentList.yaml
src/gosdk/specs/definitions/Counts.yaml
src/gosdk/specs/definitions/CountsList.yaml
src/gosdk/specs/definitions/DetectedAlteration.yaml
src/gosdk/specs/definitions/Document.yaml
src/gosdk/specs/definitions/DrugBase.yaml
src/gosdk/specs/definitions/DrugClassification.yaml
src/gosdk/specs/definitions/DrugCondition.yaml
src/gosdk/specs/definitions/DrugData.yaml
src/gosdk/specs/definitions/DrugExternalLink.yaml
src/gosdk/specs/definitions/DrugFdaLabel.yaml
src/gosdk/specs/definitions/DrugGFInclude.yaml
src/gosdk/specs/definitions/DrugGFIncludeComponent.yaml
src/gosdk/specs/definitions/DrugGeneralReferences.yaml
src/gosdk/specs/definitions/DrugGeneticFactors.yaml
src/gosdk/specs/definitions/DrugGoClass.yaml
src/gosdk/specs/definitions/DrugIngredient.yaml
src/gosdk/specs/definitions/DrugIngredientStrength.yaml
src/gosdk/specs/definitions/DrugLabeller.yaml
src/gosdk/specs/definitions/DrugLiteratureReference.yaml
src/gosdk/specs/definitions/DrugModificationOf.yaml
src/gosdk/specs/definitions/DrugPfam.yaml
src/gosdk/specs/definitions/DrugPharmacology.yaml
src/gosdk/specs/definitions/DrugPolypeptide.yaml
src/gosdk/specs/definitions/DrugProduct.yaml
src/gosdk/specs/definitions/DrugSeverity.yaml
src/gosdk/specs/definitions/DrugStructuredIndications.yaml
src/gosdk/specs/definitions/DrugSynonym.yaml
src/gosdk/specs/definitions/DrugTarget.yaml
src/gosdk/specs/definitions/DrugWithDrugs.yaml
src/gosdk/specs/definitions/EligibilitiesAsCurated.yaml
src/gosdk/specs/definitions/Eligibility.yaml
src/gosdk/specs/definitions/Error.yaml
src/gosdk/specs/definitions/Evidence.yaml
src/gosdk/specs/definitions/Facets.yaml
src/gosdk/specs/definitions/Gene.yaml
src/gosdk/specs/definitions/GeneBoundaries.yaml
src/gosdk/specs/definitions/GeneBoundariesList.yaml
src/gosdk/specs/definitions/GenesList.yaml
src/gosdk/specs/definitions/HgvsGMetadata.yaml
src/gosdk/specs/definitions/LabResult.yaml
src/gosdk/specs/definitions/LabResultAttachmentFile.yaml
src/gosdk/specs/definitions/LabResultDataFile.yaml
src/gosdk/specs/definitions/LabResultDataFileList.yaml
src/gosdk/specs/definitions/Location.yaml
src/gosdk/specs/definitions/LogicSet.yaml
src/gosdk/specs/definitions/Marker.yaml
src/gosdk/specs/definitions/MarkerList.yaml
src/gosdk/specs/definitions/MarkersDocument.yaml
src/gosdk/specs/definitions/MarkersDocumentList.yaml
src/gosdk/specs/definitions/MatchedDisease.yaml
src/gosdk/specs/definitions/NDGenes.yaml
src/gosdk/specs/definitions/NewAlteration.yaml
src/gosdk/specs/definitions/NewCase.yaml
src/gosdk/specs/definitions/NewClassification.yaml
src/gosdk/specs/definitions/NewContent.yaml
src/gosdk/specs/definitions/NewDocument.yaml
src/gosdk/specs/definitions/NewLabResult.yaml
src/gosdk/specs/definitions/NewLabResultAttachmentFile.yaml
src/gosdk/specs/definitions/NewLabResultDataFile.yaml
src/gosdk/specs/definitions/NewMarker.yaml
src/gosdk/specs/definitions/NewOncologicTreatment.yaml
src/gosdk/specs/definitions/NewPatient.yaml
src/gosdk/specs/definitions/NewPatientDiagnosis.yaml
src/gosdk/specs/definitions/NewPatientMetaData.yaml
src/gosdk/specs/definitions/NewRecommendation.yaml
src/gosdk/specs/definitions/NewRecommendationsReport.yaml
src/gosdk/specs/definitions/NewReferenceAttachment.yaml
src/gosdk/specs/definitions/NewSample.yaml
src/gosdk/specs/definitions/NewSelectedMarker.yaml
src/gosdk/specs/definitions/NormalizedHGVS.yaml
src/gosdk/specs/definitions/NormalizedHGVSList.yaml
src/gosdk/specs/definitions/OutOnlyGenesOffPanel.yaml
src/gosdk/specs/definitions/OutcomeCohorts.yaml
src/gosdk/specs/definitions/OverallContact.yaml
src/gosdk/specs/definitions/Pagination.yaml
src/gosdk/specs/definitions/Patient.yaml
src/gosdk/specs/definitions/PatientList.yaml
src/gosdk/specs/definitions/PatientMetaData.yaml
src/gosdk/specs/definitions/Phenotype.yaml
src/gosdk/specs/definitions/PrognosesDocument.yaml
src/gosdk/specs/definitions/PrognosesDocumentList.yaml
src/gosdk/specs/definitions/QuickAdd.yaml
src/gosdk/specs/definitions/Recommendation.yaml
src/gosdk/specs/definitions/RecommendationList.yaml
src/gosdk/specs/definitions/Reference.yaml
src/gosdk/specs/definitions/ReferenceAttachment.yaml
src/gosdk/specs/definitions/RefreshCursor.yaml
src/gosdk/specs/definitions/Refs.yaml
src/gosdk/specs/definitions/ResponseList.yaml
src/gosdk/specs/definitions/Sample.yaml
src/gosdk/specs/definitions/SelectedMarker.yaml
src/gosdk/specs/definitions/Settings.yaml
src/gosdk/specs/definitions/TherapiesDocument.yaml
src/gosdk/specs/definitions/TherapiesDocumentList.yaml
src/gosdk/specs/definitions/TimeCourse.yaml
src/gosdk/specs/definitions/TranscriptList.yaml
src/gosdk/specs/definitions/TreatmentContexts.yaml
src/gosdk/specs/definitions/TrialsDocument.yaml
src/gosdk/specs/definitions/TrialsDocumentList.yaml
src/gosdk/specs/definitions/Upload.yaml
src/gosdk/specs/definitions/User.yaml
src/gosdk/specs/definitions/UserCredentials.yaml
src/gosdk/specs/definitions/UserToken.yaml
src/gosdk/specs/definitions/WarehouseFeature.yaml
src/gosdk/specs/definitions/WarehouseFeatureList.yaml
src/gosdk/specs/definitions/WarehouseVariant.yaml
src/gosdk/specs/definitions/WarehouseVariantJoin.yaml
src/gosdk/specs/definitions/WarehouseVariantList.yaml
src/gosdk/specs/definitions/WarehouseVariantPage.yaml
src/gosdk/specs/paths/api/alterations/get.yaml
src/gosdk/specs/paths/api/alterations/{pk}/get.yaml
src/gosdk/specs/paths/api/annotations/get.yaml
src/gosdk/specs/paths/api/annotations/actionability/{build_id}/{chromosome}/{start}/{ref}/{alt}/get.yaml
src/gosdk/specs/paths/api/annotations/delete/{data_set}#fs/delete.yaml
src/gosdk/specs/paths/api/annotations/generate_hgvs_g/get.yaml
src/gosdk/specs/paths/api/annotations/hgvs/get.yaml
src/gosdk/specs/paths/api/annotations/hgvs_overrides/post.yaml
src/gosdk/specs/paths/api/annotations/load/{data_set}/{data_set_version}#fs/post.yaml
src/gosdk/specs/paths/api/annotations/merged/{pk}/get.yaml
src/gosdk/specs/paths/api/annotations/refresh/get.yaml
src/gosdk/specs/paths/api/annotations/{build_id}/{chromosome}/{start}/{ref}/{alt}/get.yaml
src/gosdk/specs/paths/api/annotations/{data_set}/batch/get.yaml
src/gosdk/specs/paths/api/annotations/{data_set}/{hgvs_g}/delete.yaml
src/gosdk/specs/paths/api/annotations/{data_set}/{hgvs_g}/get.yaml
src/gosdk/specs/paths/api/annotations/{data_set}/{hgvs_g}/patch.yaml
src/gosdk/specs/paths/api/annotations/{data_set}/{hgvs_g}/put.yaml
src/gosdk/specs/paths/api/annotations/{identifier}/proximity/get.yaml
src/gosdk/specs/paths/api/annotations/{pk}/get.yaml
src/gosdk/specs/paths/api/annotations/{pk}/collapsed/get.yaml
src/gosdk/specs/paths/api/cases/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/annotations/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/annotations-time-courses/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/classifications/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/classifications-match/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/content/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/disease-alterations/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/filtered-trials/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/like-mine/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/markers/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/off-label/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/prognoses/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/therapies/get.yaml
src/gosdk/specs/paths/api/cases/{pk}/trials/get.yaml
src/gosdk/specs/paths/api/classifications/get.yaml
src/gosdk/specs/paths/api/classifications/match/post.yaml
src/gosdk/specs/paths/api/classifications/{pk}/get.yaml
src/gosdk/specs/paths/api/contents/get.yaml
src/gosdk/specs/paths/api/contents/counts/get.yaml
src/gosdk/specs/paths/api/contents/detail/{uuid}/get.yaml
src/gosdk/specs/paths/api/contents/match/post.yaml
src/gosdk/specs/paths/api/contents/set/get.yaml
src/gosdk/specs/paths/api/genes/get.yaml
src/gosdk/specs/paths/api/genes/filter_genes/get.yaml
src/gosdk/specs/paths/api/genes/gene_boundaries/get.yaml
src/gosdk/specs/paths/api/info/annotation_bundle/get.yaml
src/gosdk/specs/paths/api/prognoses/matches/post.yaml
src/gosdk/specs/paths/api/therapies/matches/post.yaml
src/gosdk/specs/paths/api/transcripts/get.yaml
src/gosdk/specs/paths/api/trials/matches/post.yaml
src/gosdk/specs/paths/api/users/login/post.yaml
src/gosdk/specs/paths/api/warehouse_features/post.yaml
src/gosdk/specs/paths/api/warehouse_variants/get.yaml
src/gosdk/specs/paths/api/warehouse_variants/post.yaml
src/gosdk/specs/paths/api/warehouse_variants/{pk}/get.yaml
src/gosdk/specs/paths/consult/cases/get.yaml
src/gosdk/specs/paths/consult/cases/post.yaml
src/gosdk/specs/paths/consult/cases/{case_uuid}/generate-recommendations/post.yaml
src/gosdk/specs/paths/consult/cases/{case_uuid}/lab-results/post.yaml
src/gosdk/specs/paths/consult/cases/{case_uuid}/markers/get.yaml
src/gosdk/specs/paths/consult/cases/{case_uuid}/recommendations/get.yaml
src/gosdk/specs/paths/consult/cases/{case_uuid}/selected_markers/post.yaml
src/gosdk/specs/paths/consult/cases/{uuid}/delete.yaml
src/gosdk/specs/paths/consult/patients/get.yaml
src/gosdk/specs/paths/consult/patients/post.yaml
src/gosdk/specs/paths/consult/patients/lab-result-attachments/post.yaml
src/gosdk/specs/paths/consult/patients/quick-add/post.yaml
src/gosdk/specs/paths/consult/patients/search/get.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/delete.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/data-files/{data_file_uuid}/markers/get.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/data-files/{data_file_uuid}/markers/post.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/lab-results/post.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/lab-results/{lab_result_uuid}/data-files/get.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/lab-results/{lab_result_uuid}/data-files/post.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/patient_meta_data/post.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/samples/post.yaml
src/gosdk/specs/paths/consult/patients/{uuid}/samples/{barcode_id}/get.yaml
src/gosdk/specs/paths/consult/uploads/post.yaml
src/gosdk/specs/paths/consult/uploads/{id}/get.yaml
src/gosdk/specs/paths/curation/classifications/post.yaml
src/gosdk/specs/paths/curation/concepts/alterations/get.yaml
src/gosdk/specs/paths/curation/concepts/alterations/post.yaml
src/gosdk/specs/paths/curation/contents/post.yaml
src/gosdk/specs/paths/curation/contents/{uuid}/delete.yaml
src/govcf/__init__.py
src/govcf/bed_filter.py
src/govcf/variant_files.py
src/govcf/calculate_vaf/__init__.py
src/govcf/calculate_vaf/ad_rd_dp.py
src/govcf/calculate_vaf/ao_ro_dp.py
src/govcf/calculate_vaf/base.py
src/govcf/calculate_vaf/brli.py
src/govcf/calculate_vaf/clcbio.py
src/govcf/calculate_vaf/pheo.py
src/govcf/calculate_vaf/strelka.py
src/govcf/calculate_vaf/usc.py
src/govcf/calculate_vaf/utils.py