LICENSE.txt
MANIFEST.in
README.md
pyproject.toml
setup.py
geniml/__init__.py
geniml/_version.py
geniml/cli.py
geniml/const.py
geniml/exceptions.py
geniml/utils.py
geniml.egg-info/PKG-INFO
geniml.egg-info/SOURCES.txt
geniml.egg-info/dependency_links.txt
geniml.egg-info/entry_points.txt
geniml.egg-info/requires.txt
geniml.egg-info/top_level.txt
geniml/assess/__init__.py
geniml/assess/assess.py
geniml/assess/cli.py
geniml/assess/distance.py
geniml/assess/intersection.py
geniml/assess/likelihood.py
geniml/assess/utils.py
geniml/atacformer/__init__.py
geniml/atacformer/const.py
geniml/atacformer/main.py
geniml/atacformer/training.py
geniml/atacformer/utils.py
geniml/bbclient/__init__.py
geniml/bbclient/bbclient.py
geniml/bbclient/cli.py
geniml/bbclient/const.py
geniml/bbclient/utils.py
geniml/bedshift/BedshiftYAMLHandler.py
geniml/bedshift/__init__.py
geniml/bedshift/_version.py
geniml/bedshift/arguments.py
geniml/bedshift/bedshift.py
geniml/bedspace/__init__.py
geniml/bedspace/_version.py
geniml/bedspace/argparsers.py
geniml/bedspace/cli.py
geniml/bedspace/const.py
geniml/eval/__init__.py
geniml/eval/cli.py
geniml/eval/const.py
geniml/eval/ctt.py
geniml/eval/gdst.py
geniml/eval/npt.py
geniml/eval/rct.py
geniml/eval/utils.py
geniml/io/__init__.py
geniml/io/const.py
geniml/io/exceptions.py
geniml/io/io.py
geniml/io/utils.py
geniml/likelihood/__init__.py
geniml/likelihood/build_model.py
geniml/likelihood/cli.py
geniml/models/__init__.py
geniml/models/main.py
geniml/nn/__init__.py
geniml/nn/main.py
geniml/region2vec/__init__.py
geniml/region2vec/cli.py
geniml/region2vec/const.py
geniml/region2vec/experimental.py
geniml/region2vec/main.py
geniml/region2vec/main_legacy.py
geniml/region2vec/models.py
geniml/region2vec/pooling.py
geniml/region2vec/region2vec_train.py
geniml/region2vec/region_shuffling.py
geniml/region2vec/utils.py
geniml/scembed/__init__.py
geniml/scembed/_version.py
geniml/scembed/annotation.py
geniml/scembed/argparser.py
geniml/scembed/cli.py
geniml/scembed/const.py
geniml/scembed/exceptions.py
geniml/scembed/main.py
geniml/scembed/models.py
geniml/scembed/utils.py
geniml/search/__init__.py
geniml/search/const.py
geniml/search/filebackend_tools.py
geniml/search/search_eval.py
geniml/search/utils.py
geniml/search/backends/__init__.py
geniml/search/backends/abstract.py
geniml/search/backends/bivecbackend.py
geniml/search/backends/dbbackend.py
geniml/search/backends/filebackend.py
geniml/search/interfaces/__init__.py
geniml/search/interfaces/abstract.py
geniml/search/interfaces/bed2bed.py
geniml/search/interfaces/mlfree.py
geniml/search/interfaces/text2bed.py
geniml/search/query2vec/__init__.py
geniml/search/query2vec/abstract.py
geniml/search/query2vec/bed2vec.py
geniml/search/query2vec/text2vec.py
geniml/text2bednn/__init__.py
geniml/text2bednn/const.py
geniml/text2bednn/text2bednn.py
geniml/text2bednn/utils.py
geniml/tokenization/__init__.py
geniml/tokenization/bedtools_tokenizer.py
geniml/tokenization/cli.py
geniml/tokenization/hard_tokenization_batch.py
geniml/tokenization/main.py
geniml/tokenization/split_file.py
geniml/tokenization/utils.py
geniml/universe/__init__.py
geniml/universe/cc_universe.py
geniml/universe/ccf_universe.py
geniml/universe/cli.py
geniml/universe/const.py
geniml/universe/custom_distribution.py
geniml/universe/hmm_universe.py
geniml/universe/ml_universe.py
geniml/universe/models.py
geniml/universe/utils.py
requirements/requirements-basic.txt
requirements/requirements-ml.txt
requirements/requirements-test.txt
requirements/requirements-train.txt
tests/test_atacformer.py
tests/test_batch_correction.py
tests/test_bbclient.py
tests/test_bedshift.py
tests/test_finetuning.py
tests/test_io.py
tests/test_region2vec.py
tests/test_scembed.py
tests/test_search.py
tests/test_text2bednn.py
tests/test_tokenization.py