.github/CONTRIBUTING.md

.github/ISSUE_TEMPLATE/bug_report.md

.github/ISSUE_TEMPLATE/feature_request.md

.github/PULL_REQUEST_TEMPLATE.md

.github/markdownlint.yml

.github/workflows/linting.yml

CHANGELOG.md

CODE_OF_CONDUCT.md

Dockerfile

README.md

bin/mergeSAM.py

bin/scrape_software_versions.py

conf/base.config

conf/hicpro.config

conf/test.config

conf/test_full.config

docs/README.md

docs/output.md

docs/usage.md

environment.yml