.coveragerc
.gitignore
.readthedocs.yaml
CHANGELOG.md
LICENSE
README.md
codecov.yml
config.yml
environment.yml
pyproject.toml
setup.cfg
setup.py
testing.yml
.github/workflows/publish-to-test-pypi.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/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/Makefile
docs/caprcruncher.rst
docs/cli.rst
docs/conf.py
docs/faq_pipeline.rst
docs/glossary.rst
docs/index.rst
docs/installing.rst
docs/make.bat
docs/requirements.txt
docs/running_the_pipeline.rst
docs/_static/capcruncher_statistics.html
docs/capcruncher_module_documentation/capcruncher.cli.rst
docs/capcruncher_module_documentation/capcruncher.pipeline.rst
docs/capcruncher_module_documentation/capcruncher.rst
docs/capcruncher_module_documentation/capcruncher.tools.rst
docs/capcruncher_module_documentation/capcruncher.utils.rst
docs/capcruncher_module_documentation/modules.rst
docs/ext/sphinx-click_napolean.py
docs/images/pipeline_flow.svg
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_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
tests/data/data_for_pipeline_run/SAMPLE-A
tests/data/data_for_pipeline_run/SAMPLE-A_REP1_1.fastq
tests/data/data_for_pipeline_run/SAMPLE-A_REP1_2.fastq
tests/data/data_for_pipeline_run/SAMPLE-A_REP2_1.fastq
tests/data/data_for_pipeline_run/SAMPLE-A_REP2_2.fastq
tests/data/data_for_pipeline_run/SAMPLE-B
tests/data/data_for_pipeline_run/SAMPLE-B_REP1_1.fastq
tests/data/data_for_pipeline_run/SAMPLE-B_REP1_2.fastq
tests/data/data_for_pipeline_run/SAMPLE-B_REP2_1.fastq
tests/data/data_for_pipeline_run/SAMPLE-B_REP2_2.fastq
tests/data/data_for_pipeline_run/chr14.fa.fai
tests/data/data_for_pipeline_run/chr14.fa.gz
tests/data/data_for_pipeline_run/design_matrix.tsv
tests/data/data_for_pipeline_run/get_test_data.ipynb
tests/data/data_for_pipeline_run/mm9_capture_oligos_Slc25A37.bed
tests/data/data_for_pipeline_run/mm9_chr14_genes.bed
tests/data/data_for_pipeline_run/mm9_chr14_genes.bed.bgz
tests/data/data_for_pipeline_run/mm9_chr14_genes.bed.bgz.tbi
tests/data/data_for_pipeline_run/plot_coords.bed
tests/data/data_for_pipeline_run/regions_for_norm.bed
tests/data/data_for_pipeline_run/.ipynb_checkpoints/SAMPLE-A-checkpoint
tests/data/data_for_pipeline_run/.ipynb_checkpoints/SAMPLE-B-checkpoint
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_1_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_1_2.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_2_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_2_2.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_3_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-1x_3_2.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_1_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_1_2.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_2_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_2_2.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_3_1.fastq.gz
tests/data/data_for_pipeline_run/old/Slc25A37-test-2x_3_2.fastq.gz
tests/data/fastq_deduplication/duplicated_1.fastq.gz
tests/data/fastq_deduplication/duplicated_2.fastq.gz
tests/data/fastq_deduplication/fq_dedup_1.fastq
tests/data/fastq_deduplication/fq_dedup_2.fastq
tests/data/fastq_deduplication/identified.pkl
tests/data/fastq_deduplication/parsed.json
tests/data/fastq_deduplication/parsed.pickle
tests/data/fastq_digestion/chrom_to_digest.fa
tests/data/fastq_digestion/digest_1.fastq.gz
tests/data/fastq_digestion/digest_2.fastq.gz
tests/data/fastq_digestion/digested_test_files.log
tests/data/io/Slc25A37-test_1_1.fastq.gz
tests/data/io/Slc25A37-test_1_2.fastq.gz
tests/data/old/Slc25A37-test_1_1.fastq.gz
tests/data/old/Slc25A37-test_1_2.fastq.gz
tests/data/old/Slc25A37_reporter_counts.tsv.gz
tests/data/old/Slc25A37_reporters.tsv.gz
tests/data/old/capture_oligos.bed
tests/data/old/ccslicefilter_test.yml
tests/data/old/design_matrix.tsv
tests/data/old/mm9_capture_oligos.bed
tests/data/old/mm9_capture_oligos_Slc25A37.bed
tests/data/old/mm9_chr14.gtf
tests/data/old/mm9_chr14_genes.bed
tests/data/old/mm9_chr14_genes.bed.bgz
tests/data/old/mm9_chr14_genes.bed.bgz.tbi
tests/data/old/reporters_duplicated.tsv
tests/data/old/test.Slc25A37.hdf5
tests/data/old/test_capture_bad_format.bed
tests/data/old/test_capture_blank.bed
tests/data/old/test_slices_to_filter_capture.tsv
tests/data/old/test_slices_to_filter_capture_rf.tsv
tests/data/reporter_count/SAMPLE-A_REP1.parquet/_common_metadata
tests/data/reporter_count/SAMPLE-A_REP1.parquet/_metadata
tests/data/reporter_count/SAMPLE-A_REP1.parquet/part.0.parquet
tests/data/reporter_count/SAMPLE-A_REP1.parquet/part.1.parquet
tests/data/reporters_count/bins.bed.gz
tests/data/reporters_count/viewpoints.bed
tests/data/reporters_store/SAMPLE-A_REP1.hdf5
tests/data/test_bigwigs/Slc25A37-test-1x_1.normalised.Slc25A37.bigWig
tests/data/test_bigwigs/Slc25A37-test-1x_2.normalised.Slc25A37.bigWig
tests/data/test_bigwigs/Slc25A37-test-1x_3.normalised.Slc25A37.bigWig
tests/data/test_bigwigs/Slc25A37-test-2x_1.normalised.Slc25A37.bigWig
tests/data/test_bigwigs/Slc25A37-test-2x_2.normalised.Slc25A37.bigWig
tests/data/test_bigwigs/Slc25A37-test-2x_3.normalised.Slc25A37.bigWig
tests/data/utils/viewpoints.fa
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