CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
docs/reference/cli.md
fiberhmm/__init__.py
fiberhmm/_update_check.py
fiberhmm/advisories.json
fiberhmm/advisories.py
fiberhmm/identity.py
fiberhmm.egg-info/PKG-INFO
fiberhmm.egg-info/SOURCES.txt
fiberhmm.egg-info/dependency_links.txt
fiberhmm.egg-info/entry_points.txt
fiberhmm.egg-info/requires.txt
fiberhmm.egg-info/top_level.txt
fiberhmm/cli/__init__.py
fiberhmm/cli/_entry.py
fiberhmm/cli/apply.py
fiberhmm/cli/call.py
fiberhmm/cli/call_m5c.py
fiberhmm/cli/check.py
fiberhmm/cli/common.py
fiberhmm/cli/crossstrand.py
fiberhmm/cli/daf_encode.py
fiberhmm/cli/daf_snps.py
fiberhmm/cli/dedup.py
fiberhmm/cli/duplex.py
fiberhmm/cli/export_posteriors.py
fiberhmm/cli/extract_tags.py
fiberhmm/cli/footprint_model.py
fiberhmm/cli/generate_probs.py
fiberhmm/cli/merge.py
fiberhmm/cli/pair.py
fiberhmm/cli/pipeline.py
fiberhmm/cli/provenance.py
fiberhmm/cli/qc.py
fiberhmm/cli/recall_tfs.py
fiberhmm/cli/strand_rescue.py
fiberhmm/cli/strand_rescue_annotate.py
fiberhmm/cli/strand_rescue_audit.py
fiberhmm/cli/tag_families.py
fiberhmm/cli/tag_m5c.py
fiberhmm/cli/train.py
fiberhmm/cli/utils.py
fiberhmm/core/__init__.py
fiberhmm/core/bam_reader.py
fiberhmm/core/hmm.py
fiberhmm/core/model_io.py
fiberhmm/core/progress.py
fiberhmm/crossstrand/__init__.py
fiberhmm/crossstrand/consensus.py
fiberhmm/crossstrand/duplex.py
fiberhmm/crossstrand/pairing.py
fiberhmm/crossstrand/recall.py
fiberhmm/daf/__init__.py
fiberhmm/daf/aligned_arrays.py
fiberhmm/daf/encoder.py
fiberhmm/daf/insert_consensus.py
fiberhmm/daf/m5c.py
fiberhmm/daf/snps.py
fiberhmm/inference/__init__.py
fiberhmm/inference/bam_output.py
fiberhmm/inference/circular.py
fiberhmm/inference/depth_cap.py
fiberhmm/inference/engine.py
fiberhmm/inference/fixed_likelihood_mixture.py
fiberhmm/inference/footprint_pair_edge_tolerance.py
fiberhmm/inference/fused_stages.py
fiberhmm/inference/geometry_uncertainty.py
fiberhmm/inference/hierarchical_state_model.py
fiberhmm/inference/joint_geometry_catalog.py
fiberhmm/inference/latent_tiling.py
fiberhmm/inference/legacy_annotations.py
fiberhmm/inference/legacy_pipeline.py
fiberhmm/inference/mixed_geometry_graph.py
fiberhmm/inference/molecule_footprint_pair.py
fiberhmm/inference/mp_context.py
fiberhmm/inference/native_footprint_grouping.py
fiberhmm/inference/no_evidence.py
fiberhmm/inference/nrl_estimate.py
fiberhmm/inference/nuc_recaller.py
fiberhmm/inference/parallel.py
fiberhmm/inference/read_filters.py
fiberhmm/inference/region_pipeline.py
fiberhmm/inference/region_planning.py
fiberhmm/inference/region_resume.py
fiberhmm/inference/region_types.py
fiberhmm/inference/region_workers.py
fiberhmm/inference/soft_footprint_pair_groups.py
fiberhmm/inference/state_conflict_graph.py
fiberhmm/inference/state_factor_graph.py
fiberhmm/inference/state_geometry.py
fiberhmm/inference/state_intervals.py
fiberhmm/inference/stats.py
fiberhmm/inference/strand_boundary_normalization.py
fiberhmm/inference/strand_rescue.py
fiberhmm/inference/strand_rescue_validation.py
fiberhmm/inference/streaming_drain.py
fiberhmm/inference/streaming_pipeline.py
fiberhmm/inference/streaming_workers.py
fiberhmm/inference/tagging.py
fiberhmm/inference/tf_family_ids.py
fiberhmm/inference/tf_recaller.py
fiberhmm/inference/tf_sites.py
fiberhmm/inference/worker_results.py
fiberhmm/inference/accessibility/__init__.py
fiberhmm/inference/accessibility/analysis.py
fiberhmm/inference/accessibility/cli.py
fiberhmm/inference/accessibility/coaccess.py
fiberhmm/inference/accessibility/gaps.py
fiberhmm/inference/accessibility/variants.py
fiberhmm/inference/accessibility/workflow.py
fiberhmm/inference/consensus/__init__.py
fiberhmm/inference/consensus/accelerated_fit.py
fiberhmm/inference/consensus/accelerated_predictive.py
fiberhmm/inference/consensus/adapter.py
fiberhmm/inference/consensus/artifacts.py
fiberhmm/inference/consensus/bam.py
fiberhmm/inference/consensus/bam_export.py
fiberhmm/inference/consensus/batch.py
fiberhmm/inference/consensus/cli.py
fiberhmm/inference/consensus/clustering.py
fiberhmm/inference/consensus/comparability.py
fiberhmm/inference/consensus/context.py
fiberhmm/inference/consensus/cross_evidence.py
fiberhmm/inference/consensus/cross_joint.py
fiberhmm/inference/consensus/cross_preparation.py
fiberhmm/inference/consensus/cross_quantification.py
fiberhmm/inference/consensus/cuda_predictive.py
fiberhmm/inference/consensus/execution.py
fiberhmm/inference/consensus/fit_cache.py
fiberhmm/inference/consensus/fit_execution.py
fiberhmm/inference/consensus/geometry.py
fiberhmm/inference/consensus/geometry_transfer.py
fiberhmm/inference/consensus/lattice.py
fiberhmm/inference/consensus/loader_sampling.py
fiberhmm/inference/consensus/measurement_catalog.py
fiberhmm/inference/consensus/measurement_compatibility.py
fiberhmm/inference/consensus/measurement_distribution.py
fiberhmm/inference/consensus/measurement_edge_tolerance.py
fiberhmm/inference/consensus/measurement_family.py
fiberhmm/inference/consensus/measurement_geometry.py
fiberhmm/inference/consensus/measurement_grouping.py
fiberhmm/inference/consensus/measurement_nomination.py
fiberhmm/inference/consensus/native_auxiliary.py
fiberhmm/inference/consensus/native_auxiliary_shape.py
fiberhmm/inference/consensus/native_catalog_update.py
fiberhmm/inference/consensus/native_compound.py
fiberhmm/inference/consensus/native_compound_catalog.py
fiberhmm/inference/consensus/native_cross.py
fiberhmm/inference/consensus/native_cross_counts.py
fiberhmm/inference/consensus/native_family_consolidation.py
fiberhmm/inference/consensus/native_family_mixture.py
fiberhmm/inference/consensus/native_gap_pair_bounds.py
fiberhmm/inference/consensus/native_internal_refinement.py
fiberhmm/inference/consensus/native_predictive_mixture.py
fiberhmm/inference/consensus/native_presentation.py
fiberhmm/inference/consensus/native_resolution.py
fiberhmm/inference/consensus/native_workflow.py
fiberhmm/inference/consensus/nomination.py
fiberhmm/inference/consensus/nonparametric_fit.py
fiberhmm/inference/consensus/numerics.py
fiberhmm/inference/consensus/observations.py
fiberhmm/inference/consensus/parameters.py
fiberhmm/inference/consensus/population_comparison.py
fiberhmm/inference/consensus/population_posterior.py
fiberhmm/inference/consensus/population_rescue.py
fiberhmm/inference/consensus/progress.py
fiberhmm/inference/consensus/projection.py
fiberhmm/inference/consensus/recall.py
fiberhmm/inference/consensus/recall_action.py
fiberhmm/inference/consensus/regions.py
fiberhmm/inference/consensus/report.py
fiberhmm/inference/consensus/rescue_geometry.py
fiberhmm/inference/consensus/scoring_execution.py
fiberhmm/inference/consensus/separable_fit.py
fiberhmm/inference/consensus/splitting.py
fiberhmm/inference/consensus/stages.py
fiberhmm/inference/consensus/target_mixture.py
fiberhmm/inference/consensus/transfer.py
fiberhmm/inference/consensus/transfer_cli.py
fiberhmm/inference/consensus/upstream_recall.py
fiberhmm/inference/consensus/vectorized_predictive.py
fiberhmm/inference/consensus/workflow.py
fiberhmm/inference/consensus/call_clustering/__init__.py
fiberhmm/inference/consensus/call_clustering/__main__.py
fiberhmm/inference/consensus/call_clustering/comparison.py
fiberhmm/inference/consensus/call_clustering/workflow.py
fiberhmm/inference/consensus/harmonized_families/__init__.py
fiberhmm/inference/consensus/harmonized_families/checkpoints.py
fiberhmm/inference/consensus/harmonized_families/evidence.py
fiberhmm/inference/consensus/harmonized_families/nomination.py
fiberhmm/inference/consensus/harmonized_families/parallel.py
fiberhmm/inference/consensus/harmonized_families/presentation.py
fiberhmm/inference/consensus/harmonized_families/workflow.py
fiberhmm/inference/consensus/harmonized_families/reference/SOURCE_MANIFEST.json
fiberhmm/inference/consensus/harmonized_families/reference/__init__.py
fiberhmm/inference/consensus/harmonized_families/reference/bounded_parent_prototype.py
fiberhmm/inference/consensus/harmonized_families/reference/cross_source_family_consolidation.py
fiberhmm/inference/consensus/harmonized_families/reference/family_retirement.py
fiberhmm/inference/consensus/harmonized_families/reference/fitted_geometry_nomination.py
fiberhmm/inference/consensus/harmonized_families/reference/native_cell_consolidation.py
fiberhmm/inference/consensus/harmonized_families/reference/native_support_nomination.py
fiberhmm/inference/consensus/harmonized_families/reference/overlapping_family_update.py
fiberhmm/inference/consensus/harmonized_families/reference/raw_family_segmented_region.py
fiberhmm/inference/consensus/harmonized_families/reference/refine_consensus_parents.py
fiberhmm/inference/consensus/harmonized_families/reference/resolve_consensus_representatives.py
fiberhmm/inference/consensus/harmonized_families/reference/resolve_fit_aliases.py
fiberhmm/inference/consensus/harmonized_families/reference/reuse_consensus_fits.py
fiberhmm/inference/consensus/harmonized_families/reference/run_bounded_parent_panel.py
fiberhmm/inference/consensus/harmonized_families/reference/run_native_cell_consolidation.py
fiberhmm/inference/consensus/harmonized_families/reference/run_native_locus_map.py
fiberhmm/inference/consensus/harmonized_families/reference/synthetic_state_benchmark.py
fiberhmm/inference/consensus/harmonized_families/reference/windowless_llr_inventory.py
fiberhmm/inference/consensus/lattice_recaller/__init__.py
fiberhmm/inference/consensus/lattice_recaller/discovery.py
fiberhmm/inference/consensus/lattice_recaller/frozen.py
fiberhmm/inference/consensus/lattice_recaller/model.py
fiberhmm/inference/consensus/lattice_recaller/units.py
fiberhmm/inference/consensus/lattice_recaller/workflow.py
fiberhmm/io/__init__.py
fiberhmm/io/annotation_frame.py
fiberhmm/io/autosql.py
fiberhmm/io/bam_header.py
fiberhmm/io/circular_bed.py
fiberhmm/io/footprint_bam.py
fiberhmm/io/frame_carry.py
fiberhmm/io/ma_tags.py
fiberhmm/io/output_files.py
fiberhmm/io/provenance.py
fiberhmm/io/run_state.py
fiberhmm/io/tf_models.py
fiberhmm/models/SUPPORTED_MODES.json
fiberhmm/models/__init__.py
fiberhmm/models/cpg_nanopore.json
fiberhmm/models/ddda_TF.MODEL_CARD.md
fiberhmm/models/ddda_TF.json
fiberhmm/models/ddda_duplex_rotational_v1.json
fiberhmm/models/ddda_duplex_v1.json
fiberhmm/models/ddda_nuc.json
fiberhmm/models/ddda_nuc_profile.json
fiberhmm/models/ddda_nuc_refine.json
fiberhmm/models/dddb_nanopore.json
fiberhmm/models/ecogii_pacbio.json
fiberhmm/models/hia5_nanopore.json
fiberhmm/models/hia5_pacbio.json
fiberhmm/models/legacy/ddda_nuc_refine_context_v2.6.json
fiberhmm/models/legacy/ddda_pacbio.json
fiberhmm/models/legacy/dddb_nanopore_gt_swapped_legacy.json
fiberhmm/models/legacy/dddb_nanopore_naked_2f10003c.json
fiberhmm/models/legacy/hia5_nanopore_gt_swapped_legacy.json
fiberhmm/models/legacy/hia5_nanopore_v2.9_reindexed_legacy.json
fiberhmm/models/legacy/hia5_pacbio_fp0.1x.json
fiberhmm/pipeline/__init__.py
fiberhmm/pipeline/aligner.py
fiberhmm/pipeline/basecall.py
fiberhmm/pipeline/circular.py
fiberhmm/pipeline/headers.py
fiberhmm/pipeline/progress.py
fiberhmm/pipeline/reference.py
fiberhmm/pipeline/runner.py
fiberhmm/posteriors/__init__.py
fiberhmm/posteriors/hdf5_backend.py
fiberhmm/posteriors/region_tsv.py
fiberhmm/posteriors/tsv_backend.py
fiberhmm/posteriors/writer.py
fiberhmm/probabilities/__init__.py
fiberhmm/probabilities/context_counter.py
fiberhmm/probabilities/stats.py
fiberhmm/probabilities/utils.py
fiberhmm/qc/README.md
fiberhmm/qc/__init__.py
fiberhmm/qc/control_curves.json
fiberhmm/qc/control_examples.json
fiberhmm/qc/core.py
fiberhmm/qc/references.json
fiberhmm/qc/states.py
models/ddda_TF.json
models/ddda_nuc.json
models/ddda_nuc_profile.json
models/dddb_nanopore.json
models/hia5_nanopore.json
models/hia5_pacbio.json
scripts/run_targeted_strand_rescue.py
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tests/conftest.py
tests/daf_mismatch_reference.py
tests/test_accessibility_analysis.py
tests/test_accessibility_bed_cli.py
tests/test_accessibility_nfr.py
tests/test_accessibility_nfr_perf.py
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tests/test_advisories.py
tests/test_apply_legacy_harmonize.py
tests/test_bam_header.py
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tests/test_bam_reader.py
tests/test_call_cli.py
tests/test_call_entrypoint_regressions.py
tests/test_call_pipeline.py
tests/test_call_resume.py
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tests/test_cli_input_errors.py
tests/test_cli_path_aliases.py
tests/test_cli_reference.py
tests/test_cli_streams.py
tests/test_consensus_acceleration.py
tests/test_consensus_adapter.py
tests/test_consensus_alignment_gap.py
tests/test_consensus_annotation_frame.py
tests/test_consensus_bam_export.py
tests/test_consensus_bed_cli.py
tests/test_consensus_bounded_cr_workflow.py
tests/test_consensus_bounded_edge_tolerance.py
tests/test_consensus_call_clustering.py
tests/test_consensus_chemistry_declaration.py
tests/test_consensus_comparability.py
tests/test_consensus_confirmation_training.py
tests/test_consensus_continue.py
tests/test_consensus_cross_evidence.py
tests/test_consensus_cross_preparation.py
tests/test_consensus_cross_quantification.py
tests/test_consensus_duplex.py
tests/test_consensus_evidence_integrity.py
tests/test_consensus_execution_signals.py
tests/test_consensus_fit_execution.py
tests/test_consensus_frozen_regression.py
tests/test_consensus_geometry_transfer.py
tests/test_consensus_grouping_tolerance.py
tests/test_consensus_harmonization.py
tests/test_consensus_lattice.py
tests/test_consensus_lattice_recaller.py
tests/test_consensus_lattice_stability.py
tests/test_consensus_measurement_catalog.py
tests/test_consensus_measurement_compatibility.py
tests/test_consensus_measurement_distribution.py
tests/test_consensus_measurement_family.py
tests/test_consensus_measurement_geometry.py
tests/test_consensus_measurement_grouping.py
tests/test_consensus_measurement_nomination.py
tests/test_consensus_napa_regression.py
tests/test_consensus_native_append_workflow.py
tests/test_consensus_native_auxiliary.py
tests/test_consensus_native_catalog_update.py
tests/test_consensus_native_compound.py
tests/test_consensus_native_compound_catalog.py
tests/test_consensus_native_cross.py
tests/test_consensus_native_cross_controls.py
tests/test_consensus_native_cross_counts.py
tests/test_consensus_native_family_consolidation.py
tests/test_consensus_native_family_mixture.py
tests/test_consensus_native_gap_pair_bounds.py
tests/test_consensus_native_internal_refinement.py
tests/test_consensus_native_predictive_mixture.py
tests/test_consensus_native_presentation.py
tests/test_consensus_native_resolution.py
tests/test_consensus_nonparametric_fit.py
tests/test_consensus_numerics.py
tests/test_consensus_order_robustness.py
tests/test_consensus_predictive_bounds.py
tests/test_consensus_recall_action.py
tests/test_consensus_rescue_geometry.py
tests/test_consensus_scoring_execution.py
tests/test_consensus_separable_fit.py
tests/test_consensus_speed_equivalence.py
tests/test_consensus_speed_second.py
tests/test_consensus_splitting.py
tests/test_consensus_tabulated_transfer.py
tests/test_consensus_target_mixture.py
tests/test_consensus_tie_set_membership.py
tests/test_consensus_unit_identity.py
tests/test_consensus_upstream_recall.py
tests/test_consensus_vectorized_predictive.py
tests/test_consensus_workflow.py
tests/test_consensus_xcr_units.py
tests/test_coordinate_frame.py
tests/test_core_model_guards.py
tests/test_cpg_mask_policy.py
tests/test_crossstrand_consensus.py
tests/test_crossstrand_extract.py
tests/test_crossstrand_pairing.py
tests/test_crossstrand_recall.py
tests/test_daf_chimera.py
tests/test_daf_encoder_lifecycle.py
tests/test_daf_insert_consensus.py
tests/test_daf_iupac.py
tests/test_daf_mismatch_fastpath.py
tests/test_daf_run_mask.py
tests/test_daf_snp_determinism.py
tests/test_daf_snps.py
tests/test_daf_table_indexing.py
tests/test_daf_unaligned_mask.py
tests/test_dedup.py
tests/test_depth_cap.py
tests/test_documented_cli_fixes.py
tests/test_duplex.py
tests/test_engine_daf_extraction.py
tests/test_export_posteriors_cli.py
tests/test_export_posteriors_frames.py
tests/test_export_posteriors_robustness.py
tests/test_extract_block_scores.py
tests/test_extract_clipped_edges.py
tests/test_extract_frame_rules.py
tests/test_extract_haplotype_fields.py
tests/test_extract_index.py
tests/test_family_retirement.py
tests/test_fibertools_frame.py
tests/test_fixed_likelihood_mixture.py
tests/test_footprint_model_bam.py
tests/test_footprint_pair_edge_tolerance.py
tests/test_frame_evidence_warning.py
tests/test_frame_invariant_roundtrip.py
tests/test_frame_resolution_compat.py
tests/test_frozen_transfer_cli.py
tests/test_frozen_transfer_lattice.py
tests/test_ft_integration.py
tests/test_fused_stages.py
tests/test_geometry_uncertainty.py
tests/test_hierarchical_state_model.py
tests/test_hmm.py
tests/test_hmm_cpg_mask.py
tests/test_inference_engine.py
tests/test_inference_parallel.py
tests/test_iterative_tf_geometry_stability_driver.py
tests/test_joint_geometry_catalog.py
tests/test_latent_tiling.py
tests/test_legacy_annotation_transport.py
tests/test_loader_sampling.py
tests/test_m5c.py
tests/test_m5c_cli_guards.py
tests/test_m6a_table_indexing.py
tests/test_ma_group_frame_callers.py
tests/test_mixed_geometry_graph.py
tests/test_mm_parser_vs_pysam.py
tests/test_mode_equivalence.py
tests/test_model_io.py
tests/test_model_registry.py
tests/test_molecule_footprint_pair.py
tests/test_native_footprint_grouping.py
tests/test_nuc_recaller.py
tests/test_output_permissions.py
tests/test_output_provenance.py
tests/test_package_consistency.py
tests/test_packaging.py
tests/test_pair_unified.py
tests/test_paper_family_replay.py
tests/test_pipeline.py
tests/test_pipeline_integrity.py
tests/test_pipeline_provenance.py
tests/test_population_rescue_posterior.py
tests/test_posterior_lifecycle.py
tests/test_predictive_decision_stop.py
tests/test_progress_and_numba_env.py
tests/test_publish_transactions.py
tests/test_qc.py
tests/test_qc_states.py
tests/test_read_filters.py
tests/test_recall_io.py
tests/test_recall_tfs_cli.py
tests/test_region_cleanup.py
tests/test_region_planning.py
tests/test_region_posteriors.py
tests/test_region_types.py
tests/test_release_defaults_3_0.py
tests/test_resume_integrity.py
tests/test_run_identity.py
tests/test_seq_validation.py
tests/test_snakemake_template.py
tests/test_snp_amplicon_ids.py
tests/test_soft_footprint_pair_groups.py
tests/test_staged_checkpoints.py
tests/test_staged_evidence_storage.py
tests/test_staged_families.py
tests/test_state_conflict_graph.py
tests/test_state_factor_graph.py
tests/test_state_geometry.py
tests/test_state_intervals.py
tests/test_stats.py
tests/test_strand_limited_flag.py
tests/test_strand_rescue.py
tests/test_strand_rescue_overlay.py
tests/test_strand_rescue_validation.py
tests/test_streaming_pipeline.py
tests/test_summarize_targeted_strand_rescue.py
tests/test_supplementary_calls.py
tests/test_tagging.py
tests/test_tf_configurations.py
tests/test_tf_family_tags.py
tests/test_tf_model_output.py
tests/test_tf_recaller.py
tests/test_tf_sites.py
tests/test_train_cli.py
tests/test_training_daf_path.py
tests/test_tsv_backend.py
tests/test_update_check.py
tests/test_verify_atomic_finalize.py
tests/test_verify_custom_chemistry.py
tests/test_verify_mm_question.py
tests/test_verify_platform_sniff.py
tests/test_workflow_regression.py
tests/benchmarks/__init__.py
tests/benchmarks/bench_encoding.py
tests/benchmarks/bench_hmm.py
tests/benchmarks/bench_io_vs_compute.py
tests/benchmarks/bench_memory.py
tests/benchmarks/bench_pysam_threads.py
tests/benchmarks/bench_scaling.py
tests/benchmarks/bench_throughput.py
tests/benchmarks/conftest.py
tests/fixtures/fake_dorado.py
tests/fixtures/hia5_nanopore_control_counts_k3.tsv.gz
tests/fixtures/advisories/geo_dddb_2167.header.txt
tests/fixtures/advisories/ont_hia5_2168_frozen_1ca7d0a.header.txt
tests/fixtures/advisories/ont_hia5_2168_frozen_dc7abba.header.txt
tests/fixtures/fibertools_frame/expected.json
tests/fixtures/fibertools_frame/fiberhmm3.0.0_call.bam
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tests/fixtures/fibertools_frame/ft0.13_predict_m6a.bam.bai
tests/fixtures/fibertools_frame/ft0.6.2_addnuc_fire.bam
tests/fixtures/fibertools_frame/ft0.6.2_addnuc_fire.bam.bai
tests/fixtures/frames/pre_c1ede9e_frames.json
tests/fixtures/paper_families/README.md
tests/fixtures/paper_families/manifest.json
tests/fixtures/paper_families/upstream_manifest.json
tests/fixtures/paper_families/cage/evidence_0.json.gz
tests/fixtures/paper_families/cage/evidence_1.json.gz
tests/fixtures/paper_families/cage/evidence_2.json.gz
tests/fixtures/paper_families/cage/evidence_3.json.gz
tests/fixtures/paper_families/cage/expected_0.json
tests/fixtures/paper_families/cage/expected_1.json
tests/fixtures/paper_families/cage/expected_2.json
tests/fixtures/paper_families/cage/expected_3.json
tests/fixtures/paper_families/cage/models.json.gz
tests/fixtures/paper_families/ctcf/evidence_0.json.gz
tests/fixtures/paper_families/ctcf/evidence_1.json.gz
tests/fixtures/paper_families/ctcf/evidence_2.json.gz
tests/fixtures/paper_families/ctcf/expected_0.json
tests/fixtures/paper_families/ctcf/expected_1.json
tests/fixtures/paper_families/ctcf/expected_2.json
tests/fixtures/paper_families/ctcf/models.json.gz
tests/fixtures/paper_families/gata_tal1/evidence_0.json.gz
tests/fixtures/paper_families/gata_tal1/evidence_1.json.gz
tests/fixtures/paper_families/gata_tal1/evidence_2.json.gz
tests/fixtures/paper_families/gata_tal1/expected_0.json
tests/fixtures/paper_families/gata_tal1/expected_1.json
tests/fixtures/paper_families/gata_tal1/expected_2.json
tests/fixtures/paper_families/gata_tal1/models.json.gz
tests/fixtures/paper_families/pause/evidence_0.json.gz
tests/fixtures/paper_families/pause/evidence_1.json.gz
tests/fixtures/paper_families/pause/evidence_2.json.gz
tests/fixtures/paper_families/pause/evidence_3.json.gz
tests/fixtures/paper_families/pause/expected_0.json
tests/fixtures/paper_families/pause/expected_1.json
tests/fixtures/paper_families/pause/expected_2.json
tests/fixtures/paper_families/pause/expected_3.json
tests/fixtures/paper_families/pause/models.json.gz
tests/fixtures/paper_families/tata/evidence_0.json.gz
tests/fixtures/paper_families/tata/evidence_1.json.gz
tests/fixtures/paper_families/tata/evidence_2.json.gz
tests/fixtures/paper_families/tata/evidence_3.json.gz
tests/fixtures/paper_families/tata/expected_0.json
tests/fixtures/paper_families/tata/expected_1.json
tests/fixtures/paper_families/tata/expected_2.json
tests/fixtures/paper_families/tata/expected_3.json
tests/fixtures/paper_families/tata/models.json.gz
tests/fixtures/paper_families/upstream_pause/evidence_0.json.gz
tests/fixtures/paper_families/upstream_pause/evidence_1.json.gz
tests/fixtures/paper_families/upstream_pause/evidence_2.json.gz
tests/fixtures/paper_families/upstream_pause/evidence_3.json.gz
tests/fixtures/paper_families/upstream_pause/expected_0.json
tests/fixtures/paper_families/upstream_pause/expected_1.json
tests/fixtures/paper_families/upstream_pause/expected_2.json
tests/fixtures/paper_families/upstream_pause/expected_3.json
tests/fixtures/paper_families/upstream_pause/models.json.gz
tools/build_advisory_index.py
tools/gen_cli_reference.py
workflows/snakemake/README.md
workflows/snakemake/Snakefile
workflows/snakemake/config.yaml
workflows/snakemake/samples.tsv
workflows/snakemake/profiles/local/config.yaml
workflows/snakemake/profiles/slurm/config.yaml