.gitignore
.gitmodules
.zenodo.json
AUTHORS
CODE_OF_CONDUCT.md
LICENCE
README.md
decombinator-runner.py
pyproject.toml
.github/workflows/package-build-test.yml
.github/workflows/publish-to-pypi.yml
assets/decombinator-logo.png
examples/cli_example.sh
examples/Logs/2025_08_29_alpha__Decombinator_Summary.csv
examples/Logs/2025_08_29_beta__Decombinator_Summary.csv
examples/Logs/2025_08_29_beta__Decombinator_Summary2.csv
examples/Logs/2025_08_29_beta__Decombinator_Summary3.csv
examples/Logs/2025_08_29_dcr_TINY_1_alpha_CDR3_Translation_Summary.csv
examples/Logs/2025_08_29_dcr_TINY_1_alpha_Collapsing_Summary.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary2.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_CDR3_Translation_Summary3.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_Collapsing_Summary.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_Collapsing_Summary2.csv
examples/Logs/2025_08_29_dcr_TINY_1_beta_Collapsing_Summary3.csv
examples/expected_output/dcr_TINY_1_alpha.freq
examples/expected_output/dcr_TINY_1_alpha.n12
examples/expected_output/dcr_TINY_1_alpha.tsv
examples/expected_output/dcr_TINY_1_beta.freq
examples/expected_output/dcr_TINY_1_beta.n12
examples/expected_output/dcr_TINY_1_beta.tsv
examples/expected_output/Logs/2023_01_31_alpha_TINY_1_Decombinator_Summary.csv
examples/expected_output/Logs/2023_01_31_beta_TINY_1_Decombinator_Summary.csv
examples/expected_output/Logs/2023_01_31_dcr_TINY_1_alpha_CDR3_Translation_Summary.csv
examples/expected_output/Logs/2023_01_31_dcr_TINY_1_alpha_Collapsing_Summary.csv
examples/expected_output/Logs/2023_01_31_dcr_TINY_1_beta_CDR3_Translation_Summary.csv
examples/expected_output/Logs/2023_01_31_dcr_TINY_1_beta_Collapsing_Summary.csv
examples/input/TINY_1.fq
examples/input/TINY_2.fq
src/decombinator/__init__.py
src/decombinator/__main__.py
src/decombinator/collapse.py
src/decombinator/decombine.py
src/decombinator/io.py
src/decombinator/pipeline.py
src/decombinator/translate.py
src/decombinator.egg-info/PKG-INFO
src/decombinator.egg-info/SOURCES.txt
src/decombinator.egg-info/dependency_links.txt
src/decombinator.egg-info/entry_points.txt
src/decombinator.egg-info/requires.txt
src/decombinator.egg-info/top_level.txt
tests/__init__.py
tests/conftest.py
tests/test_cli.py
tests/test_collapse.py
tests/test_decombine.py
tests/test_pipeline.py
tests/test_subparsers.py
tests/resources/2023_01_31_alpha_TINY_1_Decombinator_Summary.csv
tests/resources/2023_01_31_beta_TINY_1_Decombinator_Summary.csv
tests/resources/2023_01_31_dcr_TINY_1_alpha_CDR3_Translation_Summary.csv
tests/resources/2023_01_31_dcr_TINY_1_alpha_Collapsing_Summary.csv
tests/resources/2023_01_31_dcr_TINY_1_beta_CDR3_Translation_Summary.csv
tests/resources/2023_01_31_dcr_TINY_1_beta_Collapsing_Summary.csv
tests/resources/TINY_1.fq
tests/resources/TINY_2.fq
tests/resources/dcr_TINY_1_alpha.freq
tests/resources/dcr_TINY_1_alpha.n12
tests/resources/dcr_TINY_1_alpha.tsv
tests/resources/dcr_TINY_1_beta.freq
tests/resources/dcr_TINY_1_beta.n12
tests/resources/dcr_TINY_1_beta.tsv