LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
constraints/cibuildwheel-test.txt
src/AlignAIR.egg-info/PKG-INFO
src/AlignAIR.egg-info/SOURCES.txt
src/AlignAIR.egg-info/dependency_links.txt
src/AlignAIR.egg-info/entry_points.txt
src/AlignAIR.egg-info/requires.txt
src/AlignAIR.egg-info/top_level.txt
src/alignair/__init__.py
src/alignair/aligner.py
src/alignair/api.py
src/alignair/compare.py
src/alignair/align/__init__.py
src/alignair/align/backend.py
src/alignair/align/batch.py
src/alignair/align/bio.py
src/alignair/align/parasail.py
src/alignair/align/seed_prefilter.py
src/alignair/align/wfa.py
src/alignair/analyze/__init__.py
src/alignair/analyze/report.py
src/alignair/analyze/validate.py
src/alignair/cli/__init__.py
src/alignair/cli/analyze.py
src/alignair/cli/benchmark.py
src/alignair/cli/compare.py
src/alignair/cli/convert.py
src/alignair/cli/demo.py
src/alignair/cli/doctor.py
src/alignair/cli/export_reference.py
src/alignair/cli/genotype.py
src/alignair/cli/info.py
src/alignair/cli/main.py
src/alignair/cli/models.py
src/alignair/cli/predict.py
src/alignair/cli/reference.py
src/alignair/cli/train.py
src/alignair/cli/validate_airr.py
src/alignair/core/__init__.py
src/alignair/core/config.py
src/alignair/core/gene_branch.py
src/alignair/core/layers.py
src/alignair/core/losses.py
src/alignair/core/model.py
src/alignair/data/__init__.py
src/alignair/data/collate.py
src/alignair/data/column_schema.py
src/alignair/data/dataset.py
src/alignair/data/encoders.py
src/alignair/data/experiment_presets.py
src/alignair/data/genairr.py
src/alignair/data/readers.py
src/alignair/data/record_adapter.py
src/alignair/data/sample_builder.py
src/alignair/data/synthetic.py
src/alignair/data/tokenizer.py
src/alignair/evaluate/__init__.py
src/alignair/evaluate/benchmark.py
src/alignair/genotype/__init__.py
src/alignair/genotype/aggregate.py
src/alignair/genotype/airr.py
src/alignair/genotype/benchmark.py
src/alignair/genotype/calibrate.py
src/alignair/genotype/constraint.py
src/alignair/genotype/geometry.py
src/alignair/genotype/infer.py
src/alignair/genotype/observe.py
src/alignair/genotype/polymorphism.py
src/alignair/genotype/report.py
src/alignair/genotype/study.py
src/alignair/genotype/zygosity.py
src/alignair/io/airr.py
src/alignair/io/airr_field_map.py
src/alignair/io/airr_validate.py
src/alignair/io/sequence_reader.py
src/alignair/metrics/__init__.py
src/alignair/metrics/accumulator.py
src/alignair/metrics/allele_auc.py
src/alignair/metrics/average_last_label.py
src/alignair/metrics/boundary.py
src/alignair/metrics/entropy.py
src/alignair/model_file/__init__.py
src/alignair/model_file/container.py
src/alignair/model_file/serialize.py
src/alignair/nn/__init__.py
src/alignair/nn/weighting.py
src/alignair/nn/heads/__init__.py
src/alignair/nn/heads/orientation.py
src/alignair/nn/heads/region.py
src/alignair/nn/heads/state.py
src/alignair/predict/__init__.py
src/alignair/predict/_derive_cy.c
src/alignair/predict/_derive_cy.pyx
src/alignair/predict/calibrate.py
src/alignair/predict/clean.py
src/alignair/predict/config.py
src/alignair/predict/forward.py
src/alignair/predict/germline.py
src/alignair/predict/heuristic_matcher.py
src/alignair/predict/pipeline.py
src/alignair/predict/segment.py
src/alignair/predict/state.py
src/alignair/predict/threshold.py
src/alignair/predict/airr/__init__.py
src/alignair/predict/airr/alignment.py
src/alignair/predict/airr/builder.py
src/alignair/predict/airr/constants.py
src/alignair/predict/airr/quality.py
src/alignair/predict/airr/regions.py
src/alignair/reference/__init__.py
src/alignair/reference/reference_set.py
src/alignair/registry/__init__.py
src/alignair/registry/cache.py
src/alignair/registry/hf.py
src/alignair/registry/publish.py
src/alignair/registry/sources.py
src/alignair/registry/updates.py
src/alignair/registry/validate.py
src/alignair/train/__init__.py
src/alignair/train/build.py
src/alignair/train/guards.py
src/alignair/train/trainer.py
src/alignair/train/transfer.py
src/alignair/train/gym/__init__.py
src/alignair/train/gym/collate.py
src/alignair/train/gym/crop.py
src/alignair/train/gym/dataset.py
src/alignair/train/gym/experiment.py
src/alignair/train/gym/factored.py
src/alignair/train/gym/gym.py
src/alignair/train/gym/sharing.py
src/alignair/train/gym/targeting.py
src/alignair/train/gym/targets.py
src/alignair/train/gym/transformer.py
src/alignair/train/gym/control/__init__.py
src/alignair/train/gym/control/config.py
src/alignair/train/gym/control/controller.py
src/alignair/train/gym/control/exam.py
src/alignair/train/gym/control/gate.py
src/alignair/train/gym/control/hud.py
src/alignair/train/gym/control/ladder.py
src/alignair/train/gym/control/plateau.py
src/alignair/train/gym/control/reporter.py
src/alignair/train/gym/control/rigor.py
src/alignair/train/gym/control/state.py
src/alignair/train/gym/curriculum/__init__.py
src/alignair/train/gym/curriculum/base.py
src/alignair/train/gym/curriculum/factored.py
src/alignair/train/gym/curriculum/stratified.py
src/alignair/train/gym/curriculum/targeted.py
src/alignair/train/gym/instrument/__init__.py
src/alignair/train/gym/instrument/band_metrics.py
src/alignair/train/gym/instrument/competence.py
src/alignair/train/gym/instrument/lattice.py
src/alignair/train/gym/instrument/stats.py
src/alignair/train/gym/instrument/task_space.py
src/alignair/validation/__init__.py
src/alignair/validation/gates.py
src/alignair/xray/__init__.py
src/alignair/xray/deep_probe.py
src/alignair/xray/dynamics.py
src/alignair/xray/geometry.py
src/alignair/xray/model_xray.py
src/alignair/xray/network.py