.dockerignore
AUTHORS.md
CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
SECURITY.md
SUPPORT.md
pyproject.toml
config/actinidia_external_contamination_audit_v0.5.tsv
config/actinidia_external_event_definition_v0.5.tsv
config/actinidia_external_input_sources_v0.5.tsv
config/actinidia_external_validation_policy_v0.5.tsv
config/apple_external_validation_policy_v0.3.tsv
config/baseline_registry_v0.1.tsv
config/benchmark_dataset_plan.tsv
config/bna_daae_progenitor_chromosome_pairs_v0.1.tsv
config/bna_daae_sampling_plan_v0.1.tsv
config/bna_darmor_daae_chromosome_pairs_v0.1.tsv
config/coffea_et39_homoeolog_groups_v1.0.tsv
config/coffea_external_event_definition_v1.0.tsv
config/coffea_external_input_sources_v1.0.tsv
config/coffea_external_validation_policy_v1.0.tsv
config/coffea_gardenia_seqid_aliases_v1.0.tsv
config/copy_collapse_zero_retuning_policy_v0.1.tsv
config/core_scaling_workloads_v0.1.json
config/event_ontology_v0.1.tsv
config/gma_v21_heldout_freeze_v0.1.txt
config/gma_v21_heldout_postscore_freeze_v0.1.txt
config/gma_v21_sampling_plan_v0.1.tsv
config/hawthorn_rna_sample_groups_v0.1.tsv
config/helianthus_applicability_input_sources_v0.6.tsv
config/helianthus_wgd_source_registry_v0.6.tsv
config/maize_nam5_te_seqid_map_v0.1.tsv
config/maize_natural_validation_v0.1.tsv
config/maize_v2_source_files.tsv
config/maize_v2_zero_retuning_policy.tsv
config/pav_evidence_freeze_v0.1.txt
config/populus_external_input_sources_v0.4.tsv
config/populus_external_validation_policy_v0.4.tsv
config/source_genomes.tsv
config/species_applicability_policy_v0.6.tsv
config/structure_benchmark_public_models_v0.1.tsv
config/structure_benchmark_v0.1.tsv
config/v0.4_external_species_contamination_registry.tsv
config/v0.4_external_species_eligibility_registry.tsv
config/v0.4_external_species_selection_rule.tsv
config/walnut_external_event_definition_v0.8.tsv
config/walnut_external_input_sources_v0.8.tsv
config/walnut_external_validation_policy_v0.8.tsv
config/wgdi_brassica_blind_pairs_v0.1.tsv
config/wgdi_brassica_pairs_v0.1.tsv
config/holdouts/actinidia_red5_v0.5/contract.json
config/holdouts/coffea_et39_v1.0/contract.json
config/holdouts/coffea_et39_v1.0/no_ranker/SHA256SUMS
config/holdouts/coffea_et39_v1.0/no_ranker/composite_manifest.json
config/holdouts/walnut_walnut2_v0.8/contract.json
config/holdouts/walnut_walnut2_v0.8/no_ranker/SHA256SUMS
config/holdouts/walnut_walnut2_v0.8/no_ranker/composite_manifest.json
config/primary_seqids/actinidia_chinensis_red5.tsv
config/primary_seqids/actinidia_eriantha_white_v1.0.tsv
config/primary_seqids/actinidia_rufa_aru_r1.0.tsv
config/primary_seqids/brassica_oleracea_ensembl62.tsv
config/primary_seqids/brassica_rapa_ensembl62.tsv
config/primary_seqids/carya_illinoinensis_pawnee_v1.tsv
config/primary_seqids/castanea_mollissima_nanking_hap2_v1.0.tsv
config/primary_seqids/coffea_arabica_et39_hifi.tsv
config/primary_seqids/coffea_eugenioides_bua_v1.tsv
config/primary_seqids/coffea_mauritiana_v1.tsv
config/primary_seqids/corylus_avellana_cavtom2pms_1.0.tsv
config/primary_seqids/diospyros_oleifera_v1.0.tsv
config/primary_seqids/fragaria_vesca_v4.0.tsv
config/primary_seqids/gardenia_jasminoides_asm1310374v1.tsv
config/primary_seqids/gossypium_arboreum_pgcp_v240.tsv
config/primary_seqids/gossypium_barbadense_pgcp_v242.tsv
config/primary_seqids/gossypium_hirsutum_pgcp_v245.tsv
config/primary_seqids/gossypium_raimondii_pgcp_v247.tsv
config/primary_seqids/helianthus_annuus_hanxrq_r2.0.tsv
config/primary_seqids/juglans_mandshurica_gwhbeun_v1.tsv
config/primary_seqids/juglans_regia_walnut_2.0.tsv
config/primary_seqids/malus_gddh13_v1.1.tsv
config/primary_seqids/manihot_esculenta_v6.tsv
config/primary_seqids/ophiorrhiza_pumila_v1.tsv
config/primary_seqids/populus_trichocarpa_v4.0.tsv
config/primary_seqids/prunus_persica_ncbiv2.tsv
config/primary_seqids/pyrus_bartlettdh_v2.0.tsv
config/primary_seqids/rhododendron_simsii_gca_014282245.1.tsv
config/primary_seqids/ricinus_communis_wild_castor.tsv
config/primary_seqids/rosa_chinensis_rchiobhm_v2.tsv
config/primary_seqids/salix_purpurea_v5.0.tsv
config/primary_seqids/salix_suchowensis_GCA_017552425.1.tsv
config/primary_seqids/setaria_italica_ensembl62.tsv
config/primary_seqids/sorghum_bicolor_ensembl62.tsv
config/primary_seqids/zea_mays_ensembl62.tsv
config/source_groups/osa_cultivars_v0.1.tsv
config/source_groups/osa_phylo_v0.1.tsv
containers/Dockerfile
docs/ACTINIDIA_BLIND_EXECUTION_PATCH_1_v0.5.md
docs/ACTINIDIA_EXTERNAL_REPLICATION_PROTOCOL_v0.5.md
docs/ACTINIDIA_EXTERNAL_VALIDATION_RESULT_v0.5.md
docs/ACTINIDIA_REFERENCE_DESIGN_RATIONALE_v0.5.md
docs/ALGORITHM_QUALITY_STRATEGY_v0.1.md
docs/APPLE_EXTERNAL_VALIDATION_EXECUTION_AMENDMENT_v0.3.1.md
docs/APPLE_EXTERNAL_VALIDATION_EXECUTION_AMENDMENT_v0.3.2.md
docs/APPLE_EXTERNAL_VALIDATION_PROTOCOL_v0.3.md
docs/APPLE_EXTERNAL_VALIDATION_RESULT_v0.3.md
docs/APPLE_NATURAL_ONT_VALIDATION_PROTOCOL_v0.4.md
docs/ASSEMBLY_GAP_NEGATIVE_CONTROL_v0.2.md
docs/BASELINE_COMPARISON_PROTOCOL_v0.1.md
docs/BASELINE_INPUTS_GLYCINE_v0.1.md
docs/BENCHMARK_PROTOCOL_v0.1.md
docs/BENCHMARK_PROTOCOL_v0.2.md
docs/BENCHMARK_SMOKE_2026-08-07.md
docs/BRASSICA_WGD_EVIDENCE_2026-08-07.md
docs/CANDIDATE_POOL_RANKER_V0.3_RESULT_2026-08-08.md
docs/CANDIDATE_POOL_V0.3_RESULT_2026-08-08.md
docs/CLI_COMMAND_INVENTORY_v0.1.json
docs/CLI_PARAMETERS.md
docs/CLI_REFERENCE.md
docs/COFFEA_BLIND_REPRODUCIBILITY_AMENDMENT_v1.1.md
docs/COFFEA_CUSTODY_LINEAGE_PATCH_v1.3.md
docs/COFFEA_EXECUTION_PATCH_MANIFEST_ALIAS_v1.0.md
docs/COFFEA_EXECUTION_PATCH_SINGLE_REFERENCE_SCOPE_v1.0.md
docs/COFFEA_EXTERNAL_CORE_H1_PROTOCOL_v1.0.md
docs/COFFEA_EXTERNAL_SELECTION_AND_CONTAMINATION_RATIONALE_v1.0.md
docs/COFFEA_REVEAL_EXECUTION_PATCH_v1.2.md
docs/COMPETITOR_LANDSCAPE_2026-08-07.md
docs/CONFLICT_WINNER_GUARD_RESULT_v0.4.md
docs/CONTAINER_GUIDE.md
docs/CONTAINER_SMOKE_2026-08-10.md
docs/COTTON_ZERO_RETUNING_HOLDOUT_v0.1.md
docs/DATA_AUDIT_2026-08-07.md
docs/DECISIONS.md
docs/EVENT_GRAPH_AND_PATCH_v0.1.md
docs/FORMAL_BENCHMARK_FREEZE_v0.1.md
docs/GEMOMA_LIFTON_ENVIRONMENTS_v0.1.md
docs/HAWTHORN_RNA_EVIDENCE_AUDIT_v0.1.md
docs/HELDOUT_SOYBEAN_v0.1.md
docs/HELIANTHUS_APPLICABILITY_PREFLIGHT_v0.6.md
docs/HOMEOLOG_TOPOLOGY_v0.2.md
docs/INCIDENTS.md
docs/INPUT_QC_2026-08-07.md
docs/INSTALLATION.md
docs/MAIZE_NATURAL_ISOSEQ_RESULT_2026-08-08.md
docs/MAIZE_NATURAL_VALIDATION_PROTOCOL_v0.1.md
docs/MAIZE_V2_FORMAL_RESULT_2026-08-08.md
docs/MAIZE_V2_ZERO_RETUNING_HOLDOUT.md
docs/MATCHED_BASELINES_GLYCINE_v0.1.md
docs/MINIPROT_BASELINE_v0.1.md
docs/NATURAL_HAWTHORN_PROTOCOL_v0.2.md
docs/PAIRED_BENCHMARK_AND_SYNTENY_v0.1.md
docs/PLOIDYPATCH_GOAL_COMPLETION_AUDIT_2026-08-10.md
docs/POPULUS_EXECUTION_PATCH_v0.4.1.md
docs/POPULUS_EXECUTION_PATCH_v0.4.2.md
docs/POPULUS_EXTERNAL_VALIDATION_PROTOCOL_v0.4.md
docs/POPULUS_EXTERNAL_VALIDATION_RESULT_v0.4.md
docs/PROJECT_CHARTER.md
docs/PUBLIC_DATA_CATALOG_2026-08-07.md
docs/PUBLIC_MODEL_STRUCTURE_MATRIX_v0.1.md
docs/PUBLIC_REPOSITORY_BOUNDARY.md
docs/PYCHOPPER_ENVIRONMENT_v2.7.10.md
docs/QUALITY_STATUS_2026-08-08.md
docs/RANKER_V0.3_DEVELOPMENT_PROTOCOL.md
docs/REAL_PAV_EVIDENCE_v0.1.md
docs/RELEASE_READINESS_v1.0.md
docs/RELEASE_WHEEL_SMOKE_2026-08-08.md
docs/REPRODUCIBILITY_GUIDE.md
docs/RESEARCH_STATUS_2026-08-10.md
docs/RESULT_REPORT.md
docs/REVIEWED_COPY_PATCH_v0.1.md
docs/SCALING_BENCHMARK_PROTOCOL_v0.1.md
docs/SPECIES_APPLICABILITY_FRAMEWORK_v0.6.md
docs/STABLE_REFERENCE_RANKER_V0.9_DEVELOPMENT_PROTOCOL.md
docs/STRUCTURE_HYPOTHESES_AND_RICE_HOLDOUT_v0.1.md
docs/STRUCTURE_PATCH_VALIDATION_v0.1.md
docs/SYNGAP_ENVIRONMENT_v1.2.5.md
docs/TESTING.md
docs/TUTORIAL.md
docs/USER_GUIDE.md
docs/VERSIONING_AND_PAPER_RELEASE_v1.0.md
docs/WALNUT_BLIND_MANIFEST_SEQID_PATCH_v0.8.md
docs/WALNUT_CANDIDATE_FASTA_HEADER_PATCH_v0.8.md
docs/WALNUT_CARYA_TRANSCRIPT_HIERARCHY_PATCH_v0.8.md
docs/WALNUT_EXTERNAL_CORE_H1_PROTOCOL_v0.8.md
docs/WALNUT_EXTERNAL_CORE_H1_RESULT_v0.8.md
docs/WALNUT_EXTERNAL_SELECTION_AND_CONTAMINATION_RATIONALE_v0.8.md
docs/WALNUT_STRUCTURE_HOLDOUT_ELIGIBILITY_PATCH_v0.8.md
docs/WGD_COPY_COLLAPSE_v0.1.md
docs/audits/ACTINIDIA_SYNTAX_PREFLIGHT_v0.5.md
docs/examples/report_preview/SHA256SUMS
docs/examples/report_preview/candidates.tsv
docs/examples/report_preview/index.html
docs/examples/report_preview/report.json
docs/examples/report_preview/review_ledger_template.tsv
docs/release_evidence/CITATION_cff_validation_v1.0.json
docs/release_evidence/README.md
docs/release_evidence/container_core_v0.1/README.md
docs/release_evidence/container_core_v0.1/cli_help.txt
docs/release_evidence/container_core_v0.1/container_smoke.json
docs/release_evidence/container_core_v0.1/example_stdout.json
docs/release_evidence/container_core_v0.1/image_inspect.json
docs/release_evidence/container_core_v0.1/package_SHA256SUMS
docs/release_evidence/container_core_v0.1/upstream_SHA256SUMS
docs/release_evidence/container_core_v0.1/version.txt
docs/release_evidence/wheel_core_v0.2/SHA256SUMS
docs/release_evidence/wheel_core_v0.2/command_audit.jsonl
docs/release_evidence/wheel_core_v0.2/example_output_SHA256SUMS
docs/release_evidence/wheel_core_v0.2/example_run_summary.json
docs/release_evidence/wheel_core_v0.2/release_manifest.json
docs/release_evidence/wheel_core_v0.2/sdist_members.txt
docs/release_evidence/wheel_core_v0.2/wheel_members.txt
docs/release_evidence/wheel_core_v0.3/SHA256SUMS
docs/release_evidence/wheel_core_v0.3/command_audit.jsonl
docs/release_evidence/wheel_core_v0.3/example_output_SHA256SUMS
docs/release_evidence/wheel_core_v0.3/example_run_summary.json
docs/release_evidence/wheel_core_v0.3/release_manifest.json
docs/release_evidence/wheel_core_v0.3/reproducibility_report.json
docs/release_evidence/wheel_core_v0.3/sdist_members.txt
docs/release_evidence/wheel_core_v0.3/wheel_members.txt
examples/minimal_reviewed_patch/README.md
examples/minimal_reviewed_patch/candidate.gff3
examples/minimal_reviewed_patch/candidate.gff3.manifest.json
examples/minimal_reviewed_patch/decisions.tsv
examples/minimal_reviewed_patch/input_manifest.tsv
examples/minimal_reviewed_patch/report_copy_features.tsv
examples/minimal_reviewed_patch/report_scores.tsv
examples/minimal_reviewed_patch/report_topology.tsv
examples/minimal_reviewed_patch/review_decisions.tsv
examples/minimal_reviewed_patch/run_example.py
examples/minimal_reviewed_patch/source.gff3
packaging/conda/meta.yaml
scripts/audit_actinidia_topology_gate_v0.5.py
scripts/audit_copy_pair_selection_truth.py
scripts/audit_gemoma_environment.sh
scripts/audit_hawthorn_rna.sh
scripts/audit_lifton_environment.sh
scripts/audit_source_dataset.sh
scripts/audit_staged_bundles.sh
scripts/audit_syngap_environment.sh
scripts/build_actinidia_complete_control_reveal_inputs_v0.5.sh
scripts/build_actinidia_method_trio_candidate_pools_v0.5.sh
scripts/build_apple_method_trio_candidate_pools_v0.3.sh
scripts/build_candidate_pool_v0.3_features.sh
scripts/build_coffea_blind_role_root_v1.0.py
scripts/build_coffea_complete_control_reveal_inputs_v1.0.py
scripts/build_coffea_evaluator_role_root_v1.0.py
scripts/build_coffea_h1_candidate_pools_v1.0.py
scripts/build_coffea_protein_supported_universes_v1.0.py
scripts/build_coffea_structure_holdout_v1.0.py
scripts/build_external_holdout_blind_role_root_v0.5.py
scripts/build_maize_v2_method_trio_blind.sh
scripts/build_maize_v2_natural_method_trio.sh
scripts/build_populus_complete_control_reveal_inputs_v0.4.sh
scripts/build_populus_method_trio_candidate_pools_v0.4.sh
scripts/build_primary_protein_quality_subset_v0.6.py
scripts/build_release_candidate_v0.2.py
scripts/build_release_candidate_v0.3.py
scripts/build_species_applicability_metrics_v0.6.py
scripts/build_walnut_blind_role_root_v0.8.py
scripts/build_walnut_complete_control_reveal_inputs_v0.8.py
scripts/build_walnut_h1_candidate_pools_v0.8.py
scripts/build_walnut_structure_holdout_v0.8.py
scripts/build_wgdi_source_alias_gff.py
scripts/compare_primary_translation_quality_v0.6.py
scripts/continue_after_apple_flnc_v0.1.sh
scripts/core_scaling_common_v0_1.py
scripts/diagnose_maize_v2_homeolog_ranker.py
scripts/download_apple_gddh13_te_annotation_v0.1.sh
scripts/download_apple_golden_delicious_ont_v0.1.sh
scripts/download_maize_isophase_validation.sh
scripts/download_maize_nam5_te_annotation_v0.1.sh
scripts/evaluate_actinidia_external_v0.5.py
scripts/evaluate_apple_external_v0.3.py
scripts/evaluate_brassica_glycine_copy_model_transfer_v0.1.sh
scripts/evaluate_candidate_pool_rankers_v0.3.py
scripts/evaluate_chain_preserving_pool_v0.3.sh
scripts/evaluate_coffea_external_h1_v1.0.py
scripts/evaluate_conflict_winner_guard_v0.4.py
scripts/evaluate_copy_collapse_transfer_glycine_v0.1.sh
scripts/evaluate_cotton_glycine_copy_model_transfer_v0.1.sh
scripts/evaluate_cotton_syngap_v0.1.sh
scripts/evaluate_external_v0.4.py
scripts/evaluate_external_v0.5.py
scripts/evaluate_frozen_homeolog_ranker_v0.2.py
scripts/evaluate_glycine_candidate_self_wgd_v0.1.sh
scripts/evaluate_glycine_copy_collapse_syngap_v0.1.sh
scripts/evaluate_glycine_copy_model_v0.1.sh
scripts/evaluate_homeolog_topology_v0.2.py
scripts/evaluate_maize_v2_homeolog_ranker.sh
scripts/evaluate_maize_v2_method_trio.sh
scripts/evaluate_stable_reference_ranker_v0.9.py
scripts/evaluate_syngap_glycine_v0.1.sh
scripts/evaluate_transfer_glycine_v0.1.sh
scripts/evaluate_walnut_external_h1_v0.8.py
scripts/export_cli_inventory_v0.1.py
scripts/export_cli_parameters_v1.py
scripts/extract_fasta_seqids.sh
scripts/filter_fastq_length_quality.py
scripts/finalize_coffea_blind_custody_v1.0.py
scripts/finalize_docx_visual_qa_v0.3.py
scripts/finalize_external_holdout_blind_custody_v0.5.py
scripts/finalize_formatted_review_v0.2.py
scripts/finalize_populus_blind_custody_v0.4.py
scripts/finalize_walnut_blind_custody_v0.8.py
scripts/finalize_walnut_evaluator_only_inputs_v0.8.py
scripts/freeze_apple_execution_implementation_v0.3.sh
scripts/freeze_apple_external_protocol_v0.3.sh
scripts/freeze_apple_ont_csv_limit_failed_attempt_v0.1.sh
scripts/freeze_coffea_external_execution_v1.0.py
scripts/freeze_coffea_external_protocol_v1.0.py
scripts/freeze_conflict_guard_ranker_v0.4.py
scripts/freeze_core_scaling_references_v0.1.py
scripts/freeze_external_holdout_execution_v0.5.py
scripts/freeze_external_holdout_protocol_v0.5.py
scripts/freeze_file_list.sh
scripts/freeze_populus_execution_implementation_v0.4.py
scripts/freeze_populus_external_protocol_v0.4.py
scripts/freeze_publication_environment_v0.1.py
scripts/freeze_support_conditioned_ranker_v0.3.py
scripts/freeze_walnut_external_execution_v0.8.py
scripts/freeze_walnut_external_protocol_v0.8.py
scripts/infer_actinidia_external_pairs_v0.5.sh
scripts/infer_apple_external_pairs_v0.3.sh
scripts/infer_brassica_homeolog_pairs_v0.1.sh
scripts/infer_coffea_external_pairs_v1.0.py
scripts/infer_cotton_holdout_homeolog_pairs_v0.1.sh
scripts/infer_glycine_self_wgd_pairs_v0.1.sh
scripts/infer_maize_v2_outgroup_pairs.sh
scripts/infer_populus_external_pairs_v0.4.sh
scripts/infer_walnut_external_pairs_v0.8.py
scripts/inspect_cds_frame_outliers.py
scripts/launch_apple_external_validation_v0.3.sh
scripts/launch_apple_v0.3_phase1.sh
scripts/launch_brassica_accelerated_pipeline_v0.1.sh
scripts/launch_brassica_multireference_upstream_v0.1.sh
scripts/launch_brassica_union_self_wgd_v0.1.sh
scripts/launch_cotton_holdout_upstreams_v0.1.sh
scripts/launch_cotton_syngap_v0.1.sh
scripts/launch_glycine_candidate_self_wgd_union_dev_v0.1.sh
scripts/launch_glycine_candidate_self_wgd_v0.1.sh
scripts/launch_glycine_copy_collapse_syngap_v0.1.sh
scripts/launch_maize_v2_evaluator_pairs.sh
scripts/launch_maize_v2_upstreams.sh
scripts/launch_structure_benchmark_matrix.sh
scripts/launch_structure_benchmark_public_models.sh
scripts/launch_syngap_glycine_v0.1.sh
scripts/launch_transfer_glycine_method_v0.1.sh
scripts/launch_transfer_glycine_v0.1.sh
scripts/normalize_maker_transcript_hierarchy_v0.5.py
scripts/parallel_resume_apple_ont_final_accession_v0.1.sh
scripts/plot_actinidia_external_v0.5.py
scripts/plot_apple_flnc_validation_v0.1.py
scripts/plot_core_scaling_benchmark_v0.1.py
scripts/plot_cross_species_h1_v0.1.py
scripts/plot_populus_confirmatory_v0.4.py
scripts/plot_system_architecture_v0.1.py
scripts/preflight_coffea_external_inputs_v1.0.py
scripts/preflight_external_inputs_v0.4.py
scripts/preflight_syngap_annotation.sh
scripts/preflight_walnut_external_inputs_v0.8.py
scripts/prepare_actinidia_evaluator_wgdi_inputs_v0.5.sh
scripts/prepare_actinidia_external_normalized_inputs_v0.5.sh
scripts/prepare_apple_evaluator_wgdi_inputs_v0.3.sh
scripts/prepare_apple_external_normalized_inputs_v0.3.sh
scripts/prepare_brassica_multireference_inputs_v0.1.sh
scripts/prepare_brassica_wgdi_inputs.sh
scripts/prepare_coffea_blind_candidate_inputs_v1.0.py
scripts/prepare_coffea_evaluator_wgdi_inputs_v1.0.py
scripts/prepare_coffea_external_normalized_inputs_v1.0.py
scripts/prepare_coffea_target_ks_inputs_v1.0.py
scripts/prepare_cotton_holdout_normalized_inputs_v0.1.sh
scripts/prepare_cotton_holdout_wgdi_inputs_v0.1.sh
scripts/prepare_cotton_syngap_inputs_v0.1.sh
scripts/prepare_maize_v2_normalized_inputs.sh
scripts/prepare_maize_v2_wgdi_inputs.sh
scripts/prepare_populus_evaluator_wgdi_inputs_v0.4.sh
scripts/prepare_populus_external_normalized_inputs_v0.4.sh
scripts/prepare_public_model_structure_sources.sh
scripts/prepare_walnut_blind_candidate_inputs_v0.8.py
scripts/prepare_walnut_evaluator_wgdi_inputs_v0.8.py
scripts/prepare_walnut_external_normalized_inputs_v0.8.py
scripts/prepare_walnut_target_ks_inputs_v0.8.py
scripts/publish_gemoma_working.sh
scripts/reconcile_coffea_blind_replicates_v1.1.py
scripts/remap_glycine_self_wgd_pairs_v0.2.sh
scripts/resolve_ensembl_bundles.sh
scripts/resume_apple_golden_delicious_ont_v0.1.sh
scripts/resume_apple_ont_post_alignment_patch1_v0.1.sh
scripts/resume_apple_ont_transcript_strand_patch2_v0.1.sh
scripts/run_actinidia_blind_pipeline_v0.5.sh
scripts/run_actinidia_blind_union_self_wgd_v0.5.sh
scripts/run_actinidia_copy_collapse_benchmark_v0.5.sh
scripts/run_actinidia_evaluator_wgdi_v0.5.sh
scripts/run_actinidia_miniprot_upstream_v0.5.sh
scripts/run_apple_blind_union_self_wgd_v0.3.sh
scripts/run_apple_copy_collapse_benchmark_v0.3.sh
scripts/run_apple_evaluator_wgdi_v0.3.sh
scripts/run_apple_external_reveal_v0.3.sh
scripts/run_apple_golden_delicious_ont_flnc_validation_v0.1.sh
scripts/run_apple_golden_delicious_ont_validation_v0.1.sh
scripts/run_apple_miniprot_upstream_v0.3.sh
scripts/run_apple_natural_self_wgd_v0.4.sh
scripts/run_arabidopsis_missing_gene_miniprot_v0.1.sh
scripts/run_ath_structure_candidates_v0.1.sh
scripts/run_ath_structure_hypotheses_v0.1.sh
scripts/run_blind_brassica_wgdi.sh
scripts/run_brassica_copy_collapse_benchmark_v0.1.sh
scripts/run_brassica_copy_collapse_miniprot_v0.1.sh
scripts/run_brassica_copy_collapse_support_tier_v0.1.sh
scripts/run_brassica_copy_collapse_wgdi_gap_v0.1.sh
scripts/run_brassica_full_statistics_when_ready_v0.1.sh
scripts/run_brassica_multireference_method_trio_v0.1.sh
scripts/run_brassica_union_self_wgd_one_v0.1.sh
scripts/run_brassica_wgdi.sh
scripts/run_candidate_pool_ranker_evaluation_v0.3.sh
scripts/run_chromosome_alignments.sh
scripts/run_coffea_blind_isolated_v1.0.sh
scripts/run_coffea_blind_pipeline_v1.0.sh
scripts/run_coffea_candidate_methods_v1.0.sh
scripts/run_coffea_evaluator_pipeline_v1.0.sh
scripts/run_coffea_evaluator_wgdi_v1.0.sh
scripts/run_coffea_external_reveal_v1.0.py
scripts/run_coffea_reconciliation_isolated_v1.1.sh
scripts/run_copy_collapse_statistics_v0.1.sh
scripts/run_core_scaling_benchmark_v0.1.py
scripts/run_cotton_copy_collapse_holdout_v0.1.sh
scripts/run_cotton_evaluator_freeze_v0.1.sh
scripts/run_cotton_extended_statistics_when_ready_v0.1.sh
scripts/run_cotton_full_statistics_v0.1.sh
scripts/run_cotton_holdout_homeolog_wgdi_v0.1.sh
scripts/run_cotton_holdout_method_trio_v0.1.sh
scripts/run_cotton_miniprot_upstream_v0.1.sh
scripts/run_cotton_union_self_wgd_one_v0.1.sh
scripts/run_external_holdout_blind_isolated_v0.5.sh
scripts/run_external_holdout_reveal_v0.5.sh
scripts/run_gemoma_homology.sh
scripts/run_glycine_candidate_self_wgd_one_v0.1.sh
scripts/run_glycine_copy_addition_patch_validation_v0.1.sh
scripts/run_glycine_copy_collapse_benchmark_v0.1.sh
scripts/run_glycine_copy_collapse_consensus_union_dev_v0.1.sh
scripts/run_glycine_copy_collapse_consensus_v0.1.sh
scripts/run_glycine_copy_collapse_full_statistics_v0.1.sh
scripts/run_glycine_copy_collapse_miniprot_v0.1.sh
scripts/run_glycine_copy_collapse_syngap_v0.1.sh
scripts/run_glycine_copy_feature_development_v0.1.sh
scripts/run_glycine_copy_model_training_v0.1.sh
scripts/run_hawthorn_assembly_context.sh
scripts/run_hawthorn_grouped_junctions.sh
scripts/run_hawthorn_haplotype_projection.sh
scripts/run_hawthorn_natural_validation.sh
scripts/run_hawthorn_primary_junctions.sh
scripts/run_hawthorn_secondary_graph.sh
scripts/run_hawthorn_secondary_junctions.sh
scripts/run_hawthorn_secondary_validation.sh
scripts/run_helianthus_fixed_backbone_preflight_v0.6.sh
scripts/run_homeolog_ranker_freeze_v0.2.sh
scripts/run_homeolog_topology_development_v0.2.sh
scripts/run_homeolog_topology_evaluation_v0.2.sh
scripts/run_lifton_transfer.sh
scripts/run_maize_isophase_statistics_v0.1.sh
scripts/run_maize_isophase_validation_v0.1.sh
scripts/run_maize_v2_copy_collapse_holdout.sh
scripts/run_maize_v2_homeolog_diagnostics.sh
scripts/run_maize_v2_method_statistics.sh
scripts/run_maize_v2_miniprot_upstream.sh
scripts/run_maize_v2_natural_biological_audit_v0.1.sh
scripts/run_maize_v2_natural_self_wgd.sh
scripts/run_maize_v2_outgroup_wgdi.sh
scripts/run_maize_v2_union_self_wgd.sh
scripts/run_matched_baseline_bootstrap_glycine_v0.1.sh
scripts/run_one_chromosome_alignment.sh
scripts/run_populus_blind_isolated_v0.4.sh
scripts/run_populus_blind_pipeline_v0.4.sh
scripts/run_populus_blind_union_self_wgd_v0.4.sh
scripts/run_populus_copy_collapse_benchmark_v0.4.sh
scripts/run_populus_evaluator_wgdi_v0.4.sh
scripts/run_populus_external_reveal_v0.4.sh
scripts/run_populus_miniprot_upstream_v0.4.sh
scripts/run_public_test_suite_v1.py
scripts/run_pychopper_seeded.py
scripts/run_rice_multisource_projection_v0.1.sh
scripts/run_rice_phylo_projection_v0.1.sh
scripts/run_rice_structure_validation_v0.1.sh
scripts/run_structure_benchmark_matrix.sh
scripts/run_structure_benchmark_one.sh
scripts/run_structure_hypothesis_bootstrap_v0.1.sh
scripts/run_structure_patch_one_v0.1.sh
scripts/run_support_conditioned_ranker_freeze_v0.3.sh
scripts/run_syngap_dual.sh
scripts/run_syngap_glycine_v0.1.sh
scripts/run_transfer_glycine_v0.1.sh
scripts/run_walnut_blind_isolated_v0.8.sh
scripts/run_walnut_blind_pipeline_v0.8.sh
scripts/run_walnut_candidate_methods_v0.8.sh
scripts/run_walnut_evaluator_wgdi_v0.8.sh
scripts/run_walnut_external_reveal_v0.8.py
scripts/score_actinidia_candidates_blind_v0.5.sh
scripts/score_apple_candidates_blind_v0.3.sh
scripts/score_apple_natural_candidates_v0.4.sh
scripts/score_ath_structure_hypotheses_v0.1.sh
scripts/score_candidate_pool_v0.3_with_v0.2.sh
scripts/score_maize_v2_homeolog_ranker_blind.sh
scripts/score_maize_v2_natural_homeolog_ranker.sh
scripts/score_populus_candidates_blind_v0.4.sh
scripts/smoke_container_v0.1.sh
scripts/stage_apple_external_v0.3.sh
scripts/stage_bna_daae_bundle.sh
scripts/stage_cotton_holdout_inputs_v0.1.sh
scripts/stage_ensembl_bundles.sh
scripts/stage_external_holdout_inputs_v0.5.py
scripts/stage_maize_v2_holdout_inputs.sh
scripts/stage_oryza_phylo_references_v0.1.sh
scripts/stage_populus_external_inputs_v0.4.py
scripts/stage_species_applicability_inputs_v0.6.py
scripts/summarize_audit_reports.py
scripts/summarize_core_scaling_benchmark_v0.1.py
scripts/synthesize_missing_transcript_exons.py
scripts/synthesize_root_transcript_genes.py
scripts/train_copy_model_v0.1.py
scripts/train_homeolog_ranker_v0.2.py
scripts/verify_apple_flnc_result_v0.1.py
scripts/verify_conflict_guard_production_replay_v0.4.py
scripts/verify_external_holdout_blind_context_v0.5.py
scripts/verify_homeolog_ranker_evaluator_numeric.py
scripts/verify_published_method_output_v0.8.py
scripts/verify_support_ranker_replay_v0.3.py
scripts/watch_brassica_accelerated_pipeline_v0.1.sh
scripts/watch_cotton_holdout_candidates_v0.1.sh
scripts/watch_cotton_post_methods_v0.1.sh
scripts/watch_cotton_syngap_pipeline_v0.1.sh
scripts/watch_maize_v2_homeolog_pipeline.sh
scripts/watch_maize_v2_method_pipeline.sh
scripts/watch_maize_v2_method_statistics.sh
scripts/watch_maize_v2_natural_discovery.sh
src/ploidypatch/__init__.py
src/ploidypatch/artifact_manifest.py
src/ploidypatch/audit.py
src/ploidypatch/baseline.py
src/ploidypatch/bootstrap.py
src/ploidypatch/calibration.py
src/ploidypatch/candidate_merge.py
src/ploidypatch/catalog.py
src/ploidypatch/catalog_summary.py
src/ploidypatch/cli.py
src/ploidypatch/coffea_h1_framework.py
src/ploidypatch/conflict_guard.py
src/ploidypatch/confusion_bootstrap.py
src/ploidypatch/consensus.py
src/ploidypatch/copy_features.py
src/ploidypatch/copy_model.py
src/ploidypatch/copy_model_eval.py
src/ploidypatch/copy_pair_sampling.py
src/ploidypatch/copy_patch.py
src/ploidypatch/core_h1_evaluation.py
src/ploidypatch/core_h1_pools.py
src/ploidypatch/event_graph.py
src/ploidypatch/external_evaluation.py
src/ploidypatch/fixed_backbone_projection.py
src/ploidypatch/fixed_target_backbone.py
src/ploidypatch/gff.py
src/ploidypatch/gff_compat.py
src/ploidypatch/holdout_contract.py
src/ploidypatch/homeolog_pairs.py
src/ploidypatch/homeolog_ranker.py
src/ploidypatch/homeolog_topology.py
src/ploidypatch/io.py
src/ploidypatch/isoseq_validation.py
src/ploidypatch/known_subgenome_h1.py
src/ploidypatch/localization.py
src/ploidypatch/natural.py
src/ploidypatch/natural_audit.py
src/ploidypatch/negative.py
src/ploidypatch/normalize.py
src/ploidypatch/pair_consensus.py
src/ploidypatch/patch.py
src/ploidypatch/pav.py
src/ploidypatch/perturb.py
src/ploidypatch/projection_select.py
src/ploidypatch/protein_universe.py
src/ploidypatch/published_output.py
src/ploidypatch/reference_anchored.py
src/ploidypatch/reproducible_projection.py
src/ploidypatch/review_report.py
src/ploidypatch/rna.py
src/ploidypatch/safe_tar_fasta.py
src/ploidypatch/sampling.py
src/ploidypatch/score.py
src/ploidypatch/self_wgd_pairs.py
src/ploidypatch/seqid_alias.py
src/ploidypatch/species_applicability.py
src/ploidypatch/stable_ranker.py
src/ploidypatch/structure_bootstrap.py
src/ploidypatch/structure_candidate.py
src/ploidypatch/structure_hypothesis.py
src/ploidypatch/structure_hypothesis_score.py
src/ploidypatch/structure_patch.py
src/ploidypatch/structure_perturb.py
src/ploidypatch/support_ranker.py
src/ploidypatch/synteny_gap.py
src/ploidypatch/synteny_io.py
src/ploidypatch/walnut_h1.py
src/ploidypatch/walnut_h1_framework.py
src/ploidypatch/wgd_candidate_select.py
src/ploidypatch/wgdi_summary.py
src/ploidypatch.egg-info/PKG-INFO
src/ploidypatch.egg-info/SOURCES.txt
src/ploidypatch.egg-info/dependency_links.txt
src/ploidypatch.egg-info/entry_points.txt
src/ploidypatch.egg-info/requires.txt
src/ploidypatch.egg-info/top_level.txt
src/ploidypatch/report_assets/report.css
src/ploidypatch/report_assets/report.html
src/ploidypatch/report_assets/report.js
tests/test_actinidia_blind_candidate_scripts_v0_5.py
tests/test_actinidia_evaluator_pipeline_v0_5.py
tests/test_apple_flnc_pipeline_v0_1.py
tests/test_apple_natural_scripts_v0_4.py
tests/test_audit.py
tests/test_baseline.py
tests/test_bootstrap.py
tests/test_build_wgdi_source_alias_gff.py
tests/test_calibration.py
tests/test_candidate_merge.py
tests/test_candidate_pool_ranker_v0_3.py
tests/test_catalog.py
tests/test_catalog_summary.py
tests/test_cli_contract.py
tests/test_coffea_external_metadata_v1_0.py
tests/test_coffea_h1_execution_v1_0.py
tests/test_coffea_normalizer.py
tests/test_coffea_protocol_freeze_v1_0.py
tests/test_coffea_reproducibility_amendment_v1_1.py
tests/test_coffea_scientific_pipeline_v1_0.py
tests/test_conflict_guard.py
tests/test_conflict_guard_evaluator.py
tests/test_consensus.py
tests/test_container_release.py
tests/test_copy_features.py
tests/test_copy_model.py
tests/test_copy_model_eval.py
tests/test_copy_pair_sampling.py
tests/test_copy_patch.py
tests/test_core_h1_pools.py
tests/test_evaluate_actinidia_wrapper_v0_5.py
tests/test_evaluate_apple_external_v0_3.py
tests/test_evaluate_external_v0_4.py
tests/test_evaluate_external_v0_5.py
tests/test_event_graph.py
tests/test_external_evaluation.py
tests/test_external_holdout_contract_v0_5.py
tests/test_external_holdout_execution_isolation_v0_5.py
tests/test_external_holdout_stage_v0_5.py
tests/test_fastq_filter_script.py
tests/test_fixed_backbone_projection.py
tests/test_fixed_target_backbone.py
tests/test_freeze_conflict_guard_ranker_v0_4.py
tests/test_freeze_populus_external_protocol_v0_4.py
tests/test_gff_compat.py
tests/test_helianthus_fixed_backbone_preflight_v0_6.py
tests/test_homeolog_pairs.py
tests/test_homeolog_ranker.py
tests/test_homeolog_topology.py
tests/test_independent_bootstrap.py
tests/test_isoseq_validation.py
tests/test_known_subgenome_h1.py
tests/test_localization.py
tests/test_minimal_reviewed_patch_example.py
tests/test_natural.py
tests/test_natural_audit.py
tests/test_negative.py
tests/test_normalize.py
tests/test_normalize_maker_transcript_hierarchy_v0_5.py
tests/test_pair_consensus.py
tests/test_patch.py
tests/test_pav.py
tests/test_perturb.py
tests/test_populus_blind_candidate_scripts_v0_4.py
tests/test_populus_evaluator_pipeline_v0_4.py
tests/test_populus_execution_isolation_v0_4.py
tests/test_preflight_external_inputs_v0_4.py
tests/test_projection_select.py
tests/test_protein_universe.py
tests/test_public_release_docs.py
tests/test_pychopper_seed_wrapper.py
tests/test_reference_anchored.py
tests/test_release_candidate_builder_v0_2.py
tests/test_release_candidate_builder_v0_3.py
tests/test_release_candidate_evidence_v0_2.py
tests/test_release_candidate_evidence_v0_3.py
tests/test_release_metadata.py
tests/test_report_frontend_assets.py
tests/test_report_public_assets.py
tests/test_reproducible_projection.py
tests/test_review_report.py
tests/test_rna.py
tests/test_safe_tar_fasta.py
tests/test_sampling.py
tests/test_score.py
tests/test_self_wgd_pairs.py
tests/test_seqid_alias.py
tests/test_species_applicability_metrics_builder_v0_6.py
tests/test_species_applicability_v0_6.py
tests/test_stable_ranker.py
tests/test_stable_reference_ranker_v0_9.py
tests/test_stage_populus_external_inputs_v0_4.py
tests/test_structure_bootstrap.py
tests/test_structure_candidate.py
tests/test_structure_hypothesis.py
tests/test_structure_hypothesis_score.py
tests/test_structure_patch.py
tests/test_structure_perturb.py
tests/test_support_ranker.py
tests/test_synteny_gap.py
tests/test_synteny_io.py
tests/test_v1_release_package.py
tests/test_verify_apple_flnc_result_v0_1.py
tests/test_verify_conflict_guard_production_replay_v0_4.py
tests/test_walnut_external_contract_v0_8.py
tests/test_walnut_external_execution_v0_8.py
tests/test_walnut_external_stage_v0_8.py
tests/test_walnut_h1_scientific_primitives_v0_8.py
tests/test_walnut_metadata_v0_8.py
tests/test_walnut_method_output_manifest_v0_8.py
tests/test_walnut_scientific_pipeline_v0_8.py
tests/test_wgd_candidate_select.py
tests/test_wgdi_summary.py