LICENSE
README.md
apply_model.py
export_posteriors.py
extract_tags.py
fiberhmm_utils.py
generate_probs.py
pyproject.toml
train_model.py
fiberhmm/__init__.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/apply.py
fiberhmm/cli/call.py
fiberhmm/cli/common.py
fiberhmm/cli/consensus_tfs.py
fiberhmm/cli/daf_encode.py
fiberhmm/cli/export_posteriors.py
fiberhmm/cli/extract_tags.py
fiberhmm/cli/generate_probs.py
fiberhmm/cli/recall_tfs.py
fiberhmm/cli/run.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/daf/__init__.py
fiberhmm/daf/encoder.py
fiberhmm/inference/__init__.py
fiberhmm/inference/bam_output.py
fiberhmm/inference/circular.py
fiberhmm/inference/engine.py
fiberhmm/inference/fused_stages.py
fiberhmm/inference/legacy_pipeline.py
fiberhmm/inference/mp_context.py
fiberhmm/inference/parallel.py
fiberhmm/inference/read_filters.py
fiberhmm/inference/region_pipeline.py
fiberhmm/inference/region_planning.py
fiberhmm/inference/region_types.py
fiberhmm/inference/region_workers.py
fiberhmm/inference/stats.py
fiberhmm/inference/streaming_drain.py
fiberhmm/inference/streaming_pipeline.py
fiberhmm/inference/streaming_workers.py
fiberhmm/inference/tagging.py
fiberhmm/inference/tf_recaller.py
fiberhmm/inference/worker_results.py
fiberhmm/io/__init__.py
fiberhmm/io/autosql.py
fiberhmm/io/ma_tags.py
fiberhmm/models/__init__.py
fiberhmm/models/ddda_TF.json
fiberhmm/models/ddda_nuc.json
fiberhmm/models/dddb_nanopore.json
fiberhmm/models/hia5_nanopore.json
fiberhmm/models/hia5_pacbio.json
fiberhmm/models/legacy/ddda_pacbio.json
fiberhmm/models/legacy/hia5_pacbio_fp0.1x.json
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
tests/test_bam_output.py
tests/test_bam_reader.py
tests/test_call_cli.py
tests/test_call_pipeline.py
tests/test_circular_support.py
tests/test_cli_common.py
tests/test_consensus_tfs.py
tests/test_daf_encoder_lifecycle.py
tests/test_daf_iupac.py
tests/test_export_posteriors_cli.py
tests/test_extract_block_scores.py
tests/test_fused_stages.py
tests/test_hmm.py
tests/test_inference_engine.py
tests/test_inference_parallel.py
tests/test_mm_parser_vs_pysam.py
tests/test_mode_equivalence.py
tests/test_model_io.py
tests/test_package_consistency.py
tests/test_posterior_lifecycle.py
tests/test_read_filters.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_stats.py
tests/test_streaming_pipeline.py
tests/test_tagging.py
tests/test_tf_recaller.py
tests/test_train_cli.py
tests/test_tsv_backend.py
tests/test_workflow_regression.py