LICENSE
README.md
pyproject.toml
speconsense/__init__.py
speconsense/cli.py
speconsense/msa.py
speconsense/quality_report.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/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/io.py
speconsense/summarize/iupac.py
speconsense/summarize/merging.py
tests/test_ambiguity_calling.py
tests/test_augment_input.py
tests/test_complement_flags.py
tests/test_fields.py
tests/test_haplotype_filtering.py
tests/test_orientation.py
tests/test_overlap_merge.py
tests/test_overlap_merge_integration.py
tests/test_profiles.py
tests/test_regression.py
tests/test_summarize.py
tests/test_synth.py
tests/test_variant_phasing.py