.coveragerc
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CITATION.cff
LICENSE
README.md
pyproject.toml
.github/CODEOWNERS
.github/ISSUE_TEMPLATE/bug-report.yaml
.github/ISSUE_TEMPLATE/feature-request.yaml
.github/workflows/checks.yaml
.github/workflows/pr-priority-label.yaml
.github/workflows/release.yml
.github/workflows/stale.yaml
docs/Makefile
docs/make.bat
docs/source/changelog.rst
docs/source/conf.py
docs/source/contributing.rst
docs/source/index.rst
docs/source/install.rst
docs/source/license.rst
docs/source/transcript_selection.rst
docs/source/usage.rst
docs/source/_static/img/biomart.png
docs/source/_templates/module_summary.rst
docs/source/reference/index.rst
src/cool_seq_tool/__init__.py
src/cool_seq_tool/app.py
src/cool_seq_tool/schemas.py
src/cool_seq_tool/utils.py
src/cool_seq_tool.egg-info/PKG-INFO
src/cool_seq_tool.egg-info/SOURCES.txt
src/cool_seq_tool.egg-info/dependency_links.txt
src/cool_seq_tool.egg-info/requires.txt
src/cool_seq_tool.egg-info/top_level.txt
src/cool_seq_tool/handlers/__init__.py
src/cool_seq_tool/handlers/seqrepo_access.py
src/cool_seq_tool/mappers/__init__.py
src/cool_seq_tool/mappers/alignment.py
src/cool_seq_tool/mappers/exon_genomic_coords.py
src/cool_seq_tool/mappers/feature_overlap.py
src/cool_seq_tool/mappers/liftover.py
src/cool_seq_tool/mappers/mane_transcript.py
src/cool_seq_tool/resources/__init__.py
src/cool_seq_tool/resources/data_files.py
src/cool_seq_tool/resources/status.py
src/cool_seq_tool/resources/transcript_mapping.tsv
src/cool_seq_tool/sources/__init__.py
src/cool_seq_tool/sources/mane_transcript_mappings.py
src/cool_seq_tool/sources/transcript_mappings.py
src/cool_seq_tool/sources/uta_database.py
tests/conftest.py
tests/test_utils.py
tests/handlers/test_feature_overlap.py
tests/handlers/test_seqrepo_access.py
tests/mappers/test_alignment.py
tests/mappers/test_exon_genomic_coords.py
tests/mappers/test_liftover.py
tests/mappers/test_mane_transcript.py
tests/sources/test_mane_transcript_mappings.py
tests/sources/test_uta_database.py