.gitignore
CHANGELOG.rst
LICENSE.rst
README.rst
ddrage.py
pyproject.toml
rage.py
ddrage/__init__.py
ddrage/__main__.py
ddrage/barcodes.py
ddrage/distributions.py
ddrage/generation.py
ddrage/initialization.py
ddrage/mutation_model.py
ddrage/output.py
ddrage/plotting.py
ddrage/postprocessors.py
ddrage/rad_locus.py
ddrage/rad_reads.py
ddrage/read_mutation_handling.py
ddrage.egg-info/PKG-INFO
ddrage.egg-info/SOURCES.txt
ddrage.egg-info/dependency_links.txt
ddrage.egg-info/entry_points.txt
ddrage.egg-info/requires.txt
ddrage.egg-info/top_level.txt
ddrage/barcode_handler/README.rst
ddrage/barcode_handler/__init__.py
ddrage/barcode_handler/barcode_file_parser.py
ddrage/barcode_handler/barcodes/barcodes.txt
ddrage/barcode_handler/barcodes/big.txt
ddrage/barcode_handler/barcodes/full.txt
ddrage/barcode_handler/barcodes/huge.txt
ddrage/barcode_handler/barcodes/small.txt
ddrage/quality_profiles/L100-Q70-A.qmodel.npz
ddrage/quality_profiles/L100-Q70-B.qmodel.npz
ddrage/quality_profiles/L126-Q70.qmodel.npz
ddrage/quality_profiles/L150-Q70.qmodel.npz
ddrage/tools/__init__.py
ddrage/tools/bbd_visualization.py
ddrage/tools/learn_qmodel.py
ddrage/tools/randomize_fastq.py
ddrage/tools/remove_annotation.py
ddrage/tools/split_by_p7_barcode.py
docs/.readthedocs.yaml
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/source/changelog.rst
docs/source/conf.py
docs/source/faqs.rst
docs/source/index.rst
docs/source/documentation/assumptions_and_notation.rst
docs/source/documentation/enzymes.rst
docs/source/documentation/index.rst
docs/source/documentation/input_format.rst
docs/source/documentation/output_format.rst
docs/source/documentation/parameters.rst
docs/source/documentation/tools.rst
docs/source/figures/overlap.svg
docs/source/figures/pd.svg
docs/source/figures/plot_coverage_distribution.py
docs/source/figures/plot_distribution_heatmap.py
docs/source/figures/plot_pd.py
docs/source/figures/plot_versus.py
docs/source/figures/plot_ztpd.py
docs/source/figures/quality_styles.svg
docs/source/figures/read_coverage_distribution.svg
docs/source/figures/read_structure.svg
docs/source/figures/truncation.svg
docs/source/figures/versus.svg
docs/source/figures/ztpd.svg
docs/source/getting-started/cookbook.rst
docs/source/getting-started/index.rst
docs/source/getting-started/tutorial.rst
docs/source/myhaiku/layout.html
docs/source/myhaiku/theme.conf
docs/source/myhaiku/static/alert_info_32.png
docs/source/myhaiku/static/alert_warning_32.png
docs/source/myhaiku/static/bg-page.png
docs/source/myhaiku/static/bullet_orange.png
docs/source/myhaiku/static/haiku.css_t