├── .github ├── codecov.yml ├── dependabot.yml └── workflows │ ├── ci.yml │ └── publish.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CHANGES.md ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── api.rst ├── cli.rst ├── concepts.rst ├── conf.py ├── cooler_logo.png ├── datamodel.rst ├── glossary.rst ├── index.rst ├── make_cli_rst.py ├── quickstart.rst ├── releasenotes.md ├── requirements.txt ├── schema.rst ├── schema_v1.rst ├── schema_v2.rst └── schema_v3.rst ├── pyproject.toml ├── src └── cooler │ ├── __init__.py │ ├── __main__.py │ ├── _balance.py │ ├── _logging.py │ ├── _reduce.py │ ├── _typing.py │ ├── _version.py │ ├── api.py │ ├── cli │ ├── __init__.py │ ├── _util.py │ ├── balance.py │ ├── cload.py │ ├── coarsen.py │ ├── csort.py │ ├── digest.py │ ├── dump.py │ ├── fileops.py │ ├── info.py │ ├── load.py │ ├── makebins.py │ ├── merge.py │ ├── show.py │ └── zoomify.py │ ├── core │ ├── __init__.py │ ├── _rangequery.py │ ├── _selectors.py │ └── _tableops.py │ ├── create │ ├── __init__.py │ ├── _constants.py │ ├── _create.py │ └── _ingest.py │ ├── fileops.py │ ├── parallel.py │ ├── sandbox │ ├── __init__.py │ └── dask.py │ └── util.py └── tests ├── _common.py ├── conftest.py ├── data ├── aag2.chrom.sizes ├── aag2.sample1.pairs ├── dec2_20_pluslig_1pGene_grch38_UBR4_D_1nt.pairwise.sorted.cool ├── hg19.GM12878-MboI.matrix.2000kb.bg2.gz ├── hg19.GM12878-MboI.matrix.2000kb.coo.txt ├── hg19.GM12878-MboI.matrix.2000kb.cool ├── hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz ├── hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2 ├── hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz ├── hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz.tbi ├── hg19.IMR90-MboI.matrix.2000kb.npy ├── hg19.bins.2000kb.bed.gz ├── hg19.sample1.pairs ├── manycontigs.1.coo ├── manycontigs.1.cool ├── manycontigs.chrom.sizes ├── mm9.sample1.pairs ├── odd.1.coo ├── odd.1.cool ├── odd.4.cool ├── odd.chrom.sizes ├── scool_test_file.scool ├── toy.asymm.16.bg2 ├── toy.asymm.16.cool ├── toy.asymm.2.bg2 ├── toy.asymm.2.cool ├── toy.asymm.32.bg2 ├── toy.asymm.32.cool ├── toy.asymm.4.bg2 ├── toy.asymm.4.cool ├── toy.asymm.8.bg2 ├── toy.asymm.8.cool ├── toy.bins.8.bed ├── toy.bins.var.bed ├── toy.chrom.sizes ├── toy.fasta ├── toy.fasta.fai ├── toy.pairs ├── toy.symm.upper.1.ob.bg2 ├── toy.symm.upper.1.ob.coo ├── toy.symm.upper.1.zb.bg2 ├── toy.symm.upper.1.zb.coo ├── toy.symm.upper.2.2x.cool ├── toy.symm.upper.2.bg2 ├── toy.symm.upper.2.cool ├── toy.symm.upper.2.mcool ├── toy.symm.upper.4.bg2 ├── toy.symm.upper.4.cool ├── toy.symm.upper.var.cool ├── toy.symm.upper.var2x.cool ├── toy_hash.pairs ├── toy_hash.pairs.gz └── yeast.10kb.cool ├── test_api.py ├── test_balance.py ├── test_cli.py ├── test_cli_export.py ├── test_cli_fileops.py ├── test_cli_ingest.py ├── test_cli_ops.py ├── test_core.py ├── test_create.py ├── test_create_ingest.py ├── test_create_sanitize.py ├── test_fileops.py ├── test_parallel.py ├── test_reduce.py ├── 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