├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── website_issue.md └── workflows │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── pints ├── __init__.py ├── _version.py ├── calling_engine.py ├── extension_engine.py ├── io_engine.py ├── qc_engine.py └── stats_engine.py ├── scripts ├── pints_boundary_extender ├── pints_caller ├── pints_counter ├── pints_normalizer ├── pints_sample_qc └── pints_visualizer ├── setup.cfg ├── setup.py ├── tests ├── datasets │ ├── ENCFF948HPU.bigBed │ ├── README │ ├── annotations.chr22.gtf.gz │ ├── chr22.bam │ ├── chr22.bam.bai │ ├── input.chr22.bam │ ├── input.chr22.bam.bai │ ├── mn.chr22.bw │ └── pl.chr22.bw ├── functional_test.py └── test_em.py └── versioneer.py /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hyulab/PINTS/HEAD/.github/ISSUE_TEMPLATE/bug_report.md 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