.gitignore
.pre-commit-config.yaml
LICENSE
MANIFEST.in
README.md
codecov.yml
conftest.py
environment.yml
mkdocs.yml
pyproject.toml
requirements-minimal.txt
requirements.txt
setup.py
.github/dependabot.yml
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/CD.yml
.github/workflows/CI.yml
.github/workflows/docs.yml
capcruncher/__init__.py
capcruncher/_version.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/requires.txt
capcruncher.egg-info/top_level.txt
capcruncher/api/__init__.py
capcruncher/api/annotate.py
capcruncher/api/deduplicate.py
capcruncher/api/filter.py
capcruncher/api/io.py
capcruncher/api/pileup.py
capcruncher/api/plotting.py
capcruncher/api/statistics.py
capcruncher/api/storage.py
capcruncher/cli/__init__.py
capcruncher/cli/alignments_annotate.py
capcruncher/cli/alignments_filter.py
capcruncher/cli/cli_alignments.py
capcruncher/cli/cli_fastq.py
capcruncher/cli/cli_genome.py
capcruncher/cli/cli_interactions.py
capcruncher/cli/cli_pipeline.py
capcruncher/cli/cli_plot.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/interactions_compare.py
capcruncher/cli/interactions_count.py
capcruncher/cli/interactions_deduplicate.py
capcruncher/cli/interactions_differential.py
capcruncher/cli/interactions_pileup.py
capcruncher/cli/interactions_store.py
capcruncher/data/logo.txt
capcruncher/pipeline/utils.py
capcruncher/pipeline/config/cookiecutter.json
capcruncher/pipeline/config/{{cookiecutter.date}}_{{cookiecutter.__project_id}}_{{cookiecutter.__assay}}/capcruncher_config.yml
capcruncher/pipeline/workflow/Snakefile
capcruncher/pipeline/workflow/data/annotation_defaults.json
capcruncher/pipeline/workflow/envs/environment.yml
capcruncher/pipeline/workflow/envs/profiles/profile_drmaa_singularity/config.yaml
capcruncher/pipeline/workflow/envs/profiles/profile_singularity/config.yaml
capcruncher/pipeline/workflow/report/capcruncher_report.qmd
capcruncher/pipeline/workflow/report/make_report.py
capcruncher/pipeline/workflow/report/report_text.yml
capcruncher/pipeline/workflow/rules/align.smk
capcruncher/pipeline/workflow/rules/annotate.smk
capcruncher/pipeline/workflow/rules/compare.smk
capcruncher/pipeline/workflow/rules/digest.smk
capcruncher/pipeline/workflow/rules/fastq.smk
capcruncher/pipeline/workflow/rules/filter.smk
capcruncher/pipeline/workflow/rules/optional.smk
capcruncher/pipeline/workflow/rules/pileup.smk
capcruncher/pipeline/workflow/rules/qc.smk
capcruncher/pipeline/workflow/rules/statistics.smk
capcruncher/pipeline/workflow/rules/visualise.smk
capcruncher/pipeline/workflow/scripts/count_identified_viewpoints.py
capcruncher/pipeline/workflow/scripts/extract_flash_data.py
capcruncher/pipeline/workflow/scripts/extract_trimming_data.py
capcruncher/pipeline/workflow/scripts/fastqc_wrapper.py
capcruncher/pipeline/workflow/scripts/identify_viewpoints_with_interactions.py
capcruncher/pipeline/workflow/scripts/make_ucsc_hub.py
capcruncher/pipeline/workflow/scripts/plot.py
capcruncher/pipeline/workflow/scripts/remove_duplicate_coordinates.py
capcruncher/pipeline/workflow/scripts/validation_check_n_bins_per_viewpoint.py
capcruncher/pipeline/workflow/scripts/validation_confirm_annotated_viewpoints_present.py
docs/cli.md
docs/cluster_config.md
docs/gen_ref_pages.py
docs/index.md
docs/installation.md
docs/pipeline.md
docs/plotting.ipynb
docs/tips.md
docs/usage.md
docs/examples/capcruncher_config.yml
docs/img/capcruncher_logo.png
tests/__init__.py
tests/test_annotate.py
tests/test_cli.py
tests/test_counting.py
tests/test_digest.py
tests/test_pileup.py
tests/test_pipeline.py
tests/test_plotting.py
tests/test_slice_filtering.py
tests/test_utils.py
tests/data/__init__.py
tests/data/alignment_annotation/bad_bed.bed
tests/data/alignment_annotation/blank.bed
tests/data/alignment_annotation/test.pe.bam
tests/data/alignment_annotation/test_capture.bed
tests/data/alignment_annotation/test_exlcusions.bed
tests/data/alignment_annotation/test_rf.bed
tests/data/alignment_annotation/test_slices.bed
tests/data/alignment_annotation/test_slices_sorted.bed
tests/data/alignment_deduplication/duplicates.flashed.pkl
tests/data/alignment_deduplication/duplicates.pe.pkl
tests/data/alignment_deduplication/fragments.flashed.parquet
tests/data/alignment_deduplication/fragments.pe.parquet
tests/data/alignment_deduplication/slices.flashed.parquet
tests/data/alignment_deduplication/slices.pe.parquet
tests/data/alignment_filtering/test.annotations.parquet
tests/data/alignment_filtering/test.annotations.tsv
tests/data/alignment_filtering/test.flashed.bam
tests/data/alignment_filtering/test.pe.bam
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