LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
capcruncher/__init__.py
capcruncher/utils.py
capcruncher.egg-info/PKG-INFO
capcruncher.egg-info/SOURCES.txt
capcruncher.egg-info/dependency_links.txt
capcruncher.egg-info/entry_points.txt
capcruncher.egg-info/not-zip-safe
capcruncher.egg-info/requires.txt
capcruncher.egg-info/top_level.txt
capcruncher/cli/__init__.py
capcruncher/cli/alignments_annotate.py
capcruncher/cli/alignments_deduplicate.py
capcruncher/cli/alignments_filter.py
capcruncher/cli/cli_alignments.py
capcruncher/cli/cli_fastq.py
capcruncher/cli/cli_genome.py
capcruncher/cli/cli_pipeline.py
capcruncher/cli/cli_plot.py
capcruncher/cli/cli_reporters.py
capcruncher/cli/cli_utilities.py
capcruncher/cli/fastq_deduplicate.py
capcruncher/cli/fastq_digest.py
capcruncher/cli/fastq_split.py
capcruncher/cli/genome_digest.py
capcruncher/cli/plot.py
capcruncher/cli/reporters_compare.py
capcruncher/cli/reporters_count.py
capcruncher/cli/reporters_differential.py
capcruncher/cli/reporters_pileup.py
capcruncher/cli/reporters_store.py
capcruncher/pipeline/__init__.py
capcruncher/pipeline/make_report.py
capcruncher/pipeline/pipeline.py
capcruncher/pipeline/report_text.yml
capcruncher/tools/__init__.py
capcruncher/tools/annotate.py
capcruncher/tools/count.py
capcruncher/tools/deduplicate.py
capcruncher/tools/digest.py
capcruncher/tools/filter.py
capcruncher/tools/io.py
capcruncher/tools/pileup.py
capcruncher/tools/plotting.py
capcruncher/tools/statistics.py
capcruncher/tools/storage.py
docs/conf.py
docs/ext/sphinx-click_napolean.py
tests/__init__.py
tests/test_annotate.py
tests/test_cli.py
tests/test_counting.py
tests/test_deduplication.py
tests/test_digest.py
tests/test_io.py
tests/test_pipeline.py
tests/test_slice_filtering.py
tests/test_utils.py
tests/data/__init__.py
tests/data/old/ccslicefilter_test.yml
tests/old/need_fixing/test_cli.py
tests/old/need_fixing/test_pileup.py
tests/old/need_fixing/test_plotting.py
tests/old/need_fixing/test_slice_filtering.py
tests/old/need_fixing/test_storage.py
tests/old/need_fixing/test_utils.py