LICENSE
README.md
pyproject.toml
tests/__init__.py
tests/test_config.py
tests/test_core.py
tests/test_utils.py
trace_crispr/__init__.py
trace_crispr/__main__.py
trace_crispr/cli.py
trace_crispr/config.py
trace_crispr/pipeline.py
trace_crispr.egg-info/PKG-INFO
trace_crispr.egg-info/SOURCES.txt
trace_crispr.egg-info/dependency_links.txt
trace_crispr.egg-info/entry_points.txt
trace_crispr.egg-info/requires.txt
trace_crispr.egg-info/top_level.txt
trace_crispr/core/__init__.py
trace_crispr/core/cigar.py
trace_crispr/core/classification.py
trace_crispr/core/kmer.py
trace_crispr/core/scoring.py
trace_crispr/integrations/__init__.py
trace_crispr/integrations/aligners.py
trace_crispr/integrations/crispresso.py
trace_crispr/io/__init__.py
trace_crispr/io/output.py
trace_crispr/io/sample_key.py
trace_crispr/preprocessing/__init__.py
trace_crispr/preprocessing/contamination.py
trace_crispr/preprocessing/detection.py
trace_crispr/preprocessing/preprocess.py
trace_crispr/preprocessing/trimming.py
trace_crispr/qc/__init__.py
trace_crispr/utils/__init__.py
trace_crispr/utils/barcode_templates.py
trace_crispr/utils/manifest.py
trace_crispr/utils/sequence.py