├── .coveragerc ├── .gitignore ├── .gitmodules ├── AUTHORS.md ├── CHANGES.md ├── CODEOWNERS ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Development-Getting-Started.md └── presentations │ ├── Fig2.pdf │ ├── fig1.pdf │ ├── fig3.pdf │ ├── plots.R │ └── recomb_2019_poster.pdf ├── indextools ├── __init__.py ├── bed.py ├── console │ ├── __init__.py │ ├── commands.py │ ├── features.py │ ├── partition.py │ └── split.py ├── index.py ├── intervals.py ├── regions.py └── utils.py ├── pyproject.toml ├── requirements-test.txt └── tests ├── __init__.py ├── conftest.py ├── data ├── contig_sizes.txt ├── small.bam └── small.bam.bai ├── test_index.py ├── test_integration_partition.py ├── test_intervals.py └── tests.test_integration_partition └── test_partition_index_w_contigs └── small_partitions.bed /.coveragerc: -------------------------------------------------------------------------------- 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