LICENSE
README.md
pyproject.toml
archive/obsolete_workflow_scripts/classify_sample_v2.py
archive/obsolete_workflow_scripts/collapse_reads.py
archive/obsolete_workflow_scripts/collapse_reads_v2.py
archive/obsolete_workflow_scripts/expand_to_samples.py
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/analysis/__init__.py
trace_crispr/analysis/aggregation.py
trace_crispr/analysis/comparison.py
trace_crispr/analysis/plotting.py
trace_crispr/analysis/statistics.py
trace_crispr/analysis/types.py
trace_crispr/core/__init__.py
trace_crispr/core/alignment_classifier.py
trace_crispr/core/cigar.py
trace_crispr/core/classification.py
trace_crispr/core/edit_distance_hdr.py
trace_crispr/core/models.py
trace_crispr/core/multi_ref_classifier.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/io/sqlite_cache.py
trace_crispr/multi_template/__init__.py
trace_crispr/multi_template/batch_processor.py
trace_crispr/obsolete/combinatorial_hdr.py
trace_crispr/obsolete/kmer.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/multi_ref_builder.py
trace_crispr/utils/sequence.py
workflow/scripts/aggregate_crispresso2.py
workflow/scripts/aggregate_results.py
workflow/scripts/align_unique_sequences.py
workflow/scripts/align_unique_sequences_triple.py
workflow/scripts/alignment_cache_index.py
workflow/scripts/auto_detect_trim.py
workflow/scripts/classify_group.py
workflow/scripts/classify_per_guide_donor.py
workflow/scripts/classify_sample.py
workflow/scripts/classify_unique_sequences.py
workflow/scripts/collapse_reads.py
workflow/scripts/create_pooled_summary.py
workflow/scripts/create_unified_comparison_table.py
workflow/scripts/detect_primer_offsets.py
workflow/scripts/detect_primer_trim.py
workflow/scripts/expand_to_samples.py
workflow/scripts/extract_alignment_cache.py
workflow/scripts/extract_global_unique_seqs.py
workflow/scripts/generate_crispresso_batch_settings.py
workflow/scripts/merge_unique_sequences.py