LICENSE
README.md
pyproject.toml
speconsense/__init__.py
speconsense/_help.py
speconsense/cli.py
speconsense/context.py
speconsense/distances.py
speconsense/msa.py
speconsense/outliers.py
speconsense/qctx.py
speconsense/quality_report.py
speconsense/significance.py
speconsense/synth.py
speconsense/types.py
speconsense.egg-info/PKG-INFO
speconsense.egg-info/SOURCES.txt
speconsense.egg-info/dependency_links.txt
speconsense.egg-info/entry_points.txt
speconsense.egg-info/requires.txt
speconsense.egg-info/top_level.txt
speconsense/core/__init__.py
speconsense/core/__main__.py
speconsense/core/cli.py
speconsense/core/clusterer.py
speconsense/core/workers.py
speconsense/error_models/dorado-v3.5.yaml
speconsense/error_models/dorado-v5.0.yaml
speconsense/fit_error_model/__init__.py
speconsense/fit_error_model/__main__.py
speconsense/fit_error_model/analyze.py
speconsense/fit_error_model/cli.py
speconsense/fit_error_model/compare.py
speconsense/fit_error_model/extract.py
speconsense/fit_error_model/nonhp.py
speconsense/fit_error_model/output.py
speconsense/fit_error_model/selection.py
speconsense/profiles/__init__.py
speconsense/profiles/compressed.yaml
speconsense/profiles/example.yaml
speconsense/profiles/herbarium.yaml
speconsense/profiles/largedata.yaml
speconsense/profiles/nostalgia.yaml
speconsense/profiles/strict.yaml
speconsense/scalability/__init__.py
speconsense/scalability/base.py
speconsense/scalability/config.py
speconsense/scalability/vsearch.py
speconsense/summarize/__init__.py
speconsense/summarize/__main__.py
speconsense/summarize/analysis.py
speconsense/summarize/cli.py
speconsense/summarize/clustering.py
speconsense/summarize/fields.py
speconsense/summarize/full_consensus.py
speconsense/summarize/io.py
speconsense/summarize/iupac.py
speconsense/summarize/merging.py
speconsense/summarize/tree.py
tests/test_ambiguity_calling.py
tests/test_augment_input.py
tests/test_cer_factor.py
tests/test_complement_flags.py
tests/test_context.py
tests/test_err_factor.py
tests/test_fields.py
tests/test_fit_error_model.py
tests/test_haplotype_filtering.py
tests/test_hp_threshold.py
tests/test_logging.py
tests/test_metadata_cer.py
tests/test_orientation.py
tests/test_outliers.py
tests/test_overlap_merge.py
tests/test_overlap_merge_integration.py
tests/test_profiles.py
tests/test_qctx.py
tests/test_quality_report.py
tests/test_regression.py
tests/test_scalability_parity.py
tests/test_summarize.py
tests/test_synth.py
tests/test_truncated_distance.py
tests/test_variant_phasing.py
tests/test_variant_tree.py