.gitignore
CITATION.cff
LICENSE
README.md
SPEC.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/publish.yml
docs/superpowers/plans/2026-04-07-perf-html-report.md
examples/sample_exon_output.tsv
examples/sample_raw_output.tsv
examples/sample_report.md
examples/sample_report_guardrails.md
recipes/conda/build.sh
recipes/conda/meta.yaml
recipes/conda/test_generate_bam.py
recipes/conda/test_verify_html.py
recipes/conda/test_verify_report.py
recipes/conda/test_verify_tsv.py
scripts/build_gene_index.py
src/covsnap/__init__.py
src/covsnap/annotation.py
src/covsnap/bed.py
src/covsnap/cli.py
src/covsnap/engines.py
src/covsnap/html_report.py
src/covsnap/metrics.py
src/covsnap/report.py
src/covsnap.egg-info/PKG-INFO
src/covsnap.egg-info/SOURCES.txt
src/covsnap.egg-info/dependency_links.txt
src/covsnap.egg-info/entry_points.txt
src/covsnap.egg-info/requires.txt
src/covsnap.egg-info/top_level.txt
src/covsnap/data/.gitkeep
src/covsnap/data/hg38_exons.bed.gz
src/covsnap/data/hg38_exons.bed.gz.tbi
src/covsnap/data/hg38_gene_aliases.json.gz
src/covsnap/data/hg38_genes.tsv.gz
src/covsnap/data/hg38_genes.tsv.gz.tbi
tests/__init__.py
tests/conftest.py
tests/test_annotation.py
tests/test_cli_smoke.py
tests/test_engines.py
tests/test_guardrails.py
tests/test_html_report.py
tests/test_metrics.py
tests/test_report.py