AUTHORS
CHANGELOG.rst
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
chanjo/__init__.py
chanjo/__main__.py
chanjo/_compat.py
chanjo/cli.py
chanjo/utils.py
chanjo.egg-info/PKG-INFO
chanjo.egg-info/SOURCES.txt
chanjo.egg-info/dependency_links.txt
chanjo.egg-info/entry_points.txt
chanjo.egg-info/not-zip-safe
chanjo.egg-info/requires.txt
chanjo.egg-info/top_level.txt
chanjo/annotator/__init__.py
chanjo/annotator/cli.py
chanjo/annotator/core.py
chanjo/annotator/stages.py
chanjo/builder/__init__.py
chanjo/builder/cli.py
chanjo/builder/consumers.py
chanjo/builder/core.py
chanjo/builder/stages.py
chanjo/config/__init__.py
chanjo/config/cli.py
chanjo/config/core.py
chanjo/config/questions.py
chanjo/config/utils.py
chanjo/converter/__init__.py
chanjo/converter/cli.py
chanjo/converter/core.py
chanjo/converter/stages.py
chanjo/demo/__init__.py
chanjo/demo/cli.py
chanjo/demo/files/CCDS.mini.txt
chanjo/demo/files/alignment.bai
chanjo/demo/files/alignment.bam
chanjo/demo/files/alignment.sam
chanjo/depth_reader/__init__.py
chanjo/depth_reader/core.py
chanjo/exporter/__init__.py
chanjo/exporter/cli.py
chanjo/exporter/core.py
chanjo/exporter/producers.py
chanjo/importer/__init__.py
chanjo/importer/cli.py
chanjo/importer/consumers.py
chanjo/importer/core.py
chanjo/importer/utils.py
chanjo/sex_checker/__init__.py
chanjo/sex_checker/cli.py
chanjo/sex_checker/core.py
chanjo/store/__init__.py
chanjo/store/core.py
chanjo/store/models.py
docs/Makefile
docs/api.rst
docs/code.rst
docs/conf.py
docs/developer.rst
docs/faq.rst
docs/index.rst
docs/installation.rst
docs/interface.rst
docs/introduction.rst
docs/make.bat
docs/release-notes.rst
requirements/conda.txt
requirements/development.txt
tests/test_utils.py
tests/annotator/test_annotator_core.py
tests/annotator/test_annotator_stages.py
tests/builder/test_builder_consumers.py
tests/builder/test_builder_core.py
tests/builder/test_builder_stages.py
tests/config/test_config_core.py
tests/config/test_config_questions.py
tests/config/test_config_utils.py
tests/converter/test_converter_core.py
tests/converter/test_converter_stages.py
tests/depth_reader/test_depth_reader_core.py
tests/exporter/test_exporter_core.py
tests/exporter/test_exporter_producers.py
tests/fixtures/CCDS.mini.bed
tests/fixtures/CCDS.mini.coverage.bed
tests/fixtures/CCDS.mini.txt
tests/fixtures/alignment.bai
tests/fixtures/alignment.bam
tests/fixtures/alignment.bed
tests/fixtures/alignment.sam
tests/fixtures/bad-syntax.json
tests/fixtures/conflict.json
tests/fixtures/something.json
tests/importer/test_importer_consumers.py
tests/importer/test_importer_utils.py
tests/sex_checker/test_sex_checker_core.py
tests/store/test_store_core.py
tests/store/test_store_models.py