LICENSE
MANIFEST.in
README.md
pyproject.toml
vntyper/__init__.py
vntyper/cli.py
vntyper/config.json
vntyper/version.py
vntyper.egg-info/PKG-INFO
vntyper.egg-info/SOURCES.txt
vntyper.egg-info/dependency_links.txt
vntyper.egg-info/entry_points.txt
vntyper.egg-info/requires.txt
vntyper.egg-info/top_level.txt
vntyper/assets/NOTICE.md
vntyper/assets/igv-3.0.2.min.js.gz
vntyper/data/length/grch38-count-conversions-v2.json
vntyper/data/length/grch38-length-annotation-v1.json
vntyper/dependencies/kestrel/commons-lang3-3.4.jar
vntyper/dependencies/kestrel/java-getopt-1.0.14.jar
vntyper/dependencies/kestrel/kanalyze.jar
vntyper/dependencies/kestrel/kestrel.jar
vntyper/dependencies/kestrel/logback-classic-1.1.3.jar
vntyper/dependencies/kestrel/logback-core-1.1.3.jar
vntyper/dependencies/kestrel/slf4j-api-1.7.12.jar
vntyper/modules/__init__.py
vntyper/modules/advntr/__init__.py
vntyper/modules/advntr/advntr_artifact_evidence.json
vntyper/modules/advntr/advntr_artifact_evidence.sha256
vntyper/modules/advntr/advntr_background.py
vntyper/modules/advntr/advntr_calibration.json
vntyper/modules/advntr/advntr_calibration_policy.py
vntyper/modules/advntr/advntr_capture.py
vntyper/modules/advntr/advntr_command_builder.py
vntyper/modules/advntr/advntr_config.json
vntyper/modules/advntr/advntr_decision_config.py
vntyper/modules/advntr/advntr_genotyping.py
vntyper/modules/advntr/advntr_options.py
vntyper/modules/advntr/advntr_replay.py
vntyper/modules/advntr/advntr_result_io.py
vntyper/modules/advntr/advntr_variant_annotations.py
vntyper/modules/advntr/artifact_evidence.py
vntyper/modules/advntr/model_provenance.py
vntyper/modules/shark/__init__.py
vntyper/modules/shark/shark_config.json
vntyper/modules/shark/shark_filtering.py
vntyper/profiles/decision_profile.json
vntyper/profiles/decision_profile.sha256
vntyper/profiles/decision_projection.json
vntyper/scripts/__init__.py
vntyper/scripts/algorithm_rules.py
vntyper/scripts/alignment_binding.py
vntyper/scripts/alignment_consumer_commands.py
vntyper/scripts/alignment_contract.py
vntyper/scripts/alignment_fastq_conversion.py
vntyper/scripts/alignment_index.py
vntyper/scripts/alignment_index_binding.py
vntyper/scripts/alignment_index_provenance.py
vntyper/scripts/alignment_preflight.py
vntyper/scripts/alignment_preflight_logs.py
vntyper/scripts/alignment_processing.py
vntyper/scripts/alignment_scan.py
vntyper/scripts/alignment_target_io.py
vntyper/scripts/archive_safety.py
vntyper/scripts/artifact_names.py
vntyper/scripts/artifact_publish.py
vntyper/scripts/assembly_guard.py
vntyper/scripts/calibration.json
vntyper/scripts/calibration_advntr_runtime_policy.py
vntyper/scripts/calibration_artifact_io.py
vntyper/scripts/calibration_artifacts.py
vntyper/scripts/calibration_atomic_io.py
vntyper/scripts/calibration_baseline.py
vntyper/scripts/calibration_caller_acceptance.py
vntyper/scripts/calibration_caller_artifacts.py
vntyper/scripts/calibration_caller_background_training.py
vntyper/scripts/calibration_caller_bundle.py
vntyper/scripts/calibration_caller_controller.py
vntyper/scripts/calibration_caller_curves.py
vntyper/scripts/calibration_caller_metrics.py
vntyper/scripts/calibration_caller_observations.py
vntyper/scripts/calibration_caller_policy.py
vntyper/scripts/calibration_caller_profile.py
vntyper/scripts/calibration_caller_profile_io.py
vntyper/scripts/calibration_caller_protocol.py
vntyper/scripts/calibration_caller_report.py
vntyper/scripts/calibration_caller_roster.py
vntyper/scripts/calibration_callers.py
vntyper/scripts/calibration_candidate.py
vntyper/scripts/calibration_cohort.py
vntyper/scripts/calibration_cohort_callers.py
vntyper/scripts/calibration_cohort_manifest.py
vntyper/scripts/calibration_cohort_metrics.py
vntyper/scripts/calibration_confirmation_controller.py
vntyper/scripts/calibration_contract.py
vntyper/scripts/calibration_custodian_import.py
vntyper/scripts/calibration_custody.py
vntyper/scripts/calibration_cutoff_advntr.py
vntyper/scripts/calibration_cutoff_axes.py
vntyper/scripts/calibration_cutoff_curves.py
vntyper/scripts/calibration_cutoff_document.py
vntyper/scripts/calibration_cutoff_evaluation.py
vntyper/scripts/calibration_cutoff_grid.py
vntyper/scripts/calibration_cutoff_inputs.py
vntyper/scripts/calibration_cutoff_kestrel.py
vntyper/scripts/calibration_cutoff_kestrel_parity.py
vntyper/scripts/calibration_cutoff_observations.py
vntyper/scripts/calibration_cutoff_optimize.py
vntyper/scripts/calibration_cutoff_report.py
vntyper/scripts/calibration_cutoff_selection.py
vntyper/scripts/calibration_development_source.py
vntyper/scripts/calibration_export.py
vntyper/scripts/calibration_exposure.py
vntyper/scripts/calibration_exposure_io.py
vntyper/scripts/calibration_features.py
vntyper/scripts/calibration_identity.py
vntyper/scripts/calibration_intake_contract.py
vntyper/scripts/calibration_intake_io.py
vntyper/scripts/calibration_kestrel_capture.py
vntyper/scripts/calibration_kestrel_replay.py
vntyper/scripts/calibration_length.py
vntyper/scripts/calibration_length_acceptance.py
vntyper/scripts/calibration_length_artifacts.py
vntyper/scripts/calibration_length_assessment.py
vntyper/scripts/calibration_length_controller.py
vntyper/scripts/calibration_length_evaluation.py
vntyper/scripts/calibration_length_evidence.py
vntyper/scripts/calibration_length_metrics.py
vntyper/scripts/calibration_length_policy.py
vntyper/scripts/calibration_length_profile.py
vntyper/scripts/calibration_length_protocol.py
vntyper/scripts/calibration_length_report.py
vntyper/scripts/calibration_locked_artifacts.py
vntyper/scripts/calibration_locked_baseline.py
vntyper/scripts/calibration_locked_evaluation.py
vntyper/scripts/calibration_manifest.py
vntyper/scripts/calibration_objective.py
vntyper/scripts/calibration_payload.py
vntyper/scripts/calibration_portable_background.py
vntyper/scripts/calibration_portable_projection.py
vntyper/scripts/calibration_profiles.py
vntyper/scripts/calibration_read_fingerprints.py
vntyper/scripts/calibration_read_identity.py
vntyper/scripts/calibration_read_io.py
vntyper/scripts/calibration_read_sources.py
vntyper/scripts/calibration_report.py
vntyper/scripts/calibration_reporting.py
vntyper/scripts/calibration_result_artifacts.py
vntyper/scripts/calibration_role_inputs.py
vntyper/scripts/calibration_role_source.py
vntyper/scripts/calibration_run_commitments.py
vntyper/scripts/calibration_run_extraction.py
vntyper/scripts/calibration_run_projection.py
vntyper/scripts/calibration_scalar_replay.py
vntyper/scripts/calibration_secure_io.py
vntyper/scripts/calibration_standard_length.py
vntyper/scripts/calibration_statistics.py
vntyper/scripts/calibration_study_binding.py
vntyper/scripts/calibration_target_access.py
vntyper/scripts/calibration_target_asset_io.py
vntyper/scripts/calibration_target_attestation.py
vntyper/scripts/calibration_target_authority.py
vntyper/scripts/calibration_target_completion.py
vntyper/scripts/calibration_target_contract.py
vntyper/scripts/calibration_target_custody.py
vntyper/scripts/calibration_target_evidence.py
vntyper/scripts/calibration_target_runs.py
vntyper/scripts/calibration_target_sources.py
vntyper/scripts/calibration_truth.py
vntyper/scripts/calibration_validation_attestation.py
vntyper/scripts/calibration_workflow.py
vntyper/scripts/caller_profile_provenance.py
vntyper/scripts/canonical_json.py
vntyper/scripts/chromosome_utils.py
vntyper/scripts/cli_calibrate.py
vntyper/scripts/cli_calibration_intake.py
vntyper/scripts/cli_calibration_parser.py
vntyper/scripts/cli_handlers.py
vntyper/scripts/cli_lazy_imports.py
vntyper/scripts/cli_logging_safety.py
vntyper/scripts/cli_parser.py
vntyper/scripts/cli_report.py
vntyper/scripts/cohort_categories.py
vntyper/scripts/cohort_exports.py
vntyper/scripts/cohort_frequency.py
vntyper/scripts/cohort_inputs.py
vntyper/scripts/cohort_profiles.py
vntyper/scripts/cohort_pseudonyms.py
vntyper/scripts/cohort_summary.py
vntyper/scripts/cohort_summary_parsing.py
vntyper/scripts/cohort_tables.py
vntyper/scripts/command_builders.py
vntyper/scripts/comparator_rules.py
vntyper/scripts/confidence_assignment.py
vntyper/scripts/confidence_rules.py
vntyper/scripts/coverage_presentation.py
vntyper/scripts/coverage_qc.py
vntyper/scripts/coverage_stats.py
vntyper/scripts/cross_match.py
vntyper/scripts/cross_match_presentation.py
vntyper/scripts/css_escaping.py
vntyper/scripts/decision_profile.py
vntyper/scripts/decision_profile_schema.py
vntyper/scripts/decision_profile_semantics.py
vntyper/scripts/extract_unmapped_from_offset.py
vntyper/scripts/failure_help.py
vntyper/scripts/fastp_cutoffs.py
vntyper/scripts/fastq_bam_processing.py
vntyper/scripts/file_processing.py
vntyper/scripts/flagging.py
vntyper/scripts/generate_report.py
vntyper/scripts/identity_candidate_persistence.py
vntyper/scripts/identity_candidates.py
vntyper/scripts/identity_dominance_selection.py
vntyper/scripts/identity_reconciliation.py
vntyper/scripts/idxstats_parsing.py
vntyper/scripts/igv_report.py
vntyper/scripts/install_references.py
vntyper/scripts/install_references_config.json
vntyper/scripts/install_references_logging.py
vntyper/scripts/kestrel_command.py
vntyper/scripts/kestrel_config.json
vntyper/scripts/kestrel_count.py
vntyper/scripts/kestrel_counting.py
vntyper/scripts/kestrel_decision_config.py
vntyper/scripts/kestrel_dominance_candidates.py
vntyper/scripts/kestrel_execution.py
vntyper/scripts/kestrel_genotyping.py
vntyper/scripts/kestrel_input_preflight.py
vntyper/scripts/kestrel_log_contract.py
vntyper/scripts/kestrel_postprocessing.py
vntyper/scripts/kestrel_result_artifacts.py
vntyper/scripts/kestrel_vcf_contract.py
vntyper/scripts/length_annotation.py
vntyper/scripts/length_depth_io.py
vntyper/scripts/length_estimation.py
vntyper/scripts/length_feature_artifact.py
vntyper/scripts/length_feature_provenance.py
vntyper/scripts/length_features.py
vntyper/scripts/length_model.py
vntyper/scripts/length_model_bundle.py
vntyper/scripts/length_presentation.py
vntyper/scripts/length_reference_annotation.py
vntyper/scripts/length_sensitivity.py
vntyper/scripts/length_standard_features.py
vntyper/scripts/length_standard_io.py
vntyper/scripts/length_standard_model.py
vntyper/scripts/length_standard_presentation.py
vntyper/scripts/molecular_identity.py
vntyper/scripts/molecular_identity_presentation.py
vntyper/scripts/molecular_identity_translation.py
vntyper/scripts/motif_decisions.py
vntyper/scripts/motif_processing.py
vntyper/scripts/nomenclature.py
vntyper/scripts/nomenclature_annotate.py
vntyper/scripts/nomenclature_bam.py
vntyper/scripts/nomenclature_bam_adapter.py
vntyper/scripts/nomenclature_bam_evidence.py
vntyper/scripts/nomenclature_bam_replay.py
vntyper/scripts/nomenclature_bam_universe.py
vntyper/scripts/nomenclature_config.json
vntyper/scripts/nomenclature_decision_config.py
vntyper/scripts/nomenclature_dominance.py
vntyper/scripts/nomenclature_dominance_runtime.py
vntyper/scripts/nomenclature_evidence.py
vntyper/scripts/nomenclature_frame_presentation.py
vntyper/scripts/nomenclature_identity_projection.py
vntyper/scripts/nomenclature_presentation.py
vntyper/scripts/online_mode.py
vntyper/scripts/output_paths.py
vntyper/scripts/pipeline.py
vntyper/scripts/pipeline_advntr_cleanup.py
vntyper/scripts/pipeline_advntr_execution.py
vntyper/scripts/pipeline_advntr_preflight.py
vntyper/scripts/pipeline_advntr_run_context.py
vntyper/scripts/pipeline_alignment.py
vntyper/scripts/pipeline_caller_activation.py
vntyper/scripts/pipeline_caller_configuration.py
vntyper/scripts/pipeline_caller_native.py
vntyper/scripts/pipeline_cleanup.py
vntyper/scripts/pipeline_coverage.py
vntyper/scripts/pipeline_guards.py
vntyper/scripts/pipeline_inputs.py
vntyper/scripts/pipeline_kestrel.py
vntyper/scripts/pipeline_kestrel_capture.py
vntyper/scripts/pipeline_length.py
vntyper/scripts/pipeline_length_execution.py
vntyper/scripts/pipeline_length_routing.py
vntyper/scripts/pipeline_read_routing.py
vntyper/scripts/pipeline_resume_planning.py
vntyper/scripts/pipeline_standard_length.py
vntyper/scripts/preflight_command_io.py
vntyper/scripts/preflight_error_io.py
vntyper/scripts/preflight_input_io.py
vntyper/scripts/profile_provenance.py
vntyper/scripts/read_layout.py
vntyper/scripts/reconciled_identity_persistence.py
vntyper/scripts/reference_binding.py
vntyper/scripts/reference_bundle.py
vntyper/scripts/reference_cache_binding.py
vntyper/scripts/reference_download.py
vntyper/scripts/reference_integrity.py
vntyper/scripts/reference_provenance.py
vntyper/scripts/reference_registry.py
vntyper/scripts/reference_resolution.py
vntyper/scripts/reference_resolution_environment.py
vntyper/scripts/reference_uri_policy.py
vntyper/scripts/region_utils.py
vntyper/scripts/report_assets.py
vntyper/scripts/report_config.json
vntyper/scripts/report_context_contract.py
vntyper/scripts/report_formatting.py
vntyper/scripts/report_identity.py
vntyper/scripts/report_integrity.py
vntyper/scripts/representation_disposition.py
vntyper/scripts/resume.py
vntyper/scripts/run_configuration.py
vntyper/scripts/samtools_command_fragments.py
vntyper/scripts/scoring.py
vntyper/scripts/screening_summary.py
vntyper/scripts/shark_version.py
vntyper/scripts/subthreshold.py
vntyper/scripts/summary.py
vntyper/scripts/summary_flattening.py
vntyper/scripts/summary_steps.py
vntyper/scripts/utils.py
vntyper/scripts/variant_parsing.py
vntyper/scripts/verify_seeds.py
vntyper/templates/_report_base.html
vntyper/templates/calibration_caller_report.html
vntyper/templates/calibration_cohort_report.html
vntyper/templates/calibration_length_report.html
vntyper/templates/calibration_report.html
vntyper/templates/cohort_summary_template.html
vntyper/templates/igv_report_template.html
vntyper/templates/report_template.html