AUTHORS
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
puzzle/__init__.py
puzzle/__main__.py
puzzle/_compat.py
puzzle/constants.py
puzzle/log.py
puzzle.egg-info/PKG-INFO
puzzle.egg-info/SOURCES.txt
puzzle.egg-info/dependency_links.txt
puzzle.egg-info/entry_points.txt
puzzle.egg-info/not-zip-safe
puzzle.egg-info/requires.txt
puzzle.egg-info/top_level.txt
puzzle/cli/__init__.py
puzzle/cli/base.py
puzzle/cli/cases.py
puzzle/cli/delete.py
puzzle/cli/individuals.py
puzzle/cli/init.py
puzzle/cli/load.py
puzzle/cli/utils.py
puzzle/cli/view.py
puzzle/exceptions/__init__.py
puzzle/exceptions/database.py
puzzle/models/__init__.py
puzzle/models/case.py
puzzle/models/compound.py
puzzle/models/dotdict.py
puzzle/models/gene.py
puzzle/models/genotype.py
puzzle/models/individual.py
puzzle/models/mixins.py
puzzle/models/transcript.py
puzzle/models/variant.py
puzzle/models/sql/__init__.py
puzzle/models/sql/comment.py
puzzle/models/sql/genelist.py
puzzle/models/sql/models.py
puzzle/models/sql/phenotypeterm.py
puzzle/models/sql/query.py
puzzle/models/sql/resource.py
puzzle/models/sql/suspect.py
puzzle/plugins/__init__.py
puzzle/plugins/base.py
puzzle/plugins/base_case_mixin.py
puzzle/plugins/base_variant_mixin.py
puzzle/plugins/constants.py
puzzle/plugins/gemini/__init__.py
puzzle/plugins/gemini/plugin.py
puzzle/plugins/gemini/mixins/__init__.py
puzzle/plugins/gemini/mixins/case.py
puzzle/plugins/gemini/mixins/variant.py
puzzle/plugins/gemini/mixins/variant_extras/__init__.py
puzzle/plugins/gemini/mixins/variant_extras/consequences.py
puzzle/plugins/gemini/mixins/variant_extras/core.py
puzzle/plugins/gemini/mixins/variant_extras/frequencies.py
puzzle/plugins/gemini/mixins/variant_extras/genes.py
puzzle/plugins/gemini/mixins/variant_extras/genotypes.py
puzzle/plugins/gemini/mixins/variant_extras/transcripts.py
puzzle/plugins/sql/__init__.py
puzzle/plugins/sql/store.py
puzzle/plugins/sql/mixins/__init__.py
puzzle/plugins/sql/mixins/case.py
puzzle/plugins/sql/mixins/variant.py
puzzle/plugins/sql/mixins/actions/__init__.py
puzzle/plugins/sql/mixins/actions/comment.py
puzzle/plugins/sql/mixins/actions/core.py
puzzle/plugins/sql/mixins/actions/gemini.py
puzzle/plugins/sql/mixins/actions/genelist.py
puzzle/plugins/sql/mixins/actions/phenotype.py
puzzle/plugins/sql/mixins/actions/resource.py
puzzle/plugins/sql/mixins/actions/suspect.py
puzzle/plugins/vcf/__init__.py
puzzle/plugins/vcf/vcf.py
puzzle/plugins/vcf/mixins/__init__.py
puzzle/plugins/vcf/mixins/case_mixin.py
puzzle/plugins/vcf/mixins/variant_mixin.py
puzzle/plugins/vcf/mixins/variant_extras/__init__.py
puzzle/plugins/vcf/mixins/variant_extras/annotations.py
puzzle/plugins/vcf/mixins/variant_extras/consequences.py
puzzle/plugins/vcf/mixins/variant_extras/core.py
puzzle/plugins/vcf/mixins/variant_extras/frequencies.py
puzzle/plugins/vcf/mixins/variant_extras/genes.py
puzzle/plugins/vcf/mixins/variant_extras/genotype.py
puzzle/plugins/vcf/mixins/variant_extras/transcripts.py
puzzle/server/__init__.py
puzzle/server/ext.py
puzzle/server/factory.py
puzzle/server/settings.py
puzzle/server/blueprints/__init__.py
puzzle/server/blueprints/public/__init__.py
puzzle/server/blueprints/public/views.py
puzzle/server/blueprints/public/templates/case.html
puzzle/server/blueprints/public/templates/gene_list.html
puzzle/server/blueprints/public/templates/index.html
puzzle/server/blueprints/public/templates/individual.html
puzzle/server/blueprints/public/templates/individuals.html
puzzle/server/blueprints/public/templates/public_utils.html
puzzle/server/blueprints/public/templates/resource.html
puzzle/server/blueprints/variants/__init__.py
puzzle/server/blueprints/variants/views.py
puzzle/server/blueprints/variants/templates/sv_variant.html
puzzle/server/blueprints/variants/templates/sv_variants.html
puzzle/server/blueprints/variants/templates/variant.html
puzzle/server/blueprints/variants/templates/variants.html
puzzle/server/blueprints/variants/templates/macros/compounds.html
puzzle/server/blueprints/variants/templates/macros/filters.html
puzzle/server/blueprints/variants/templates/macros/genes.html
puzzle/server/blueprints/variants/templates/macros/gt_calls.html
puzzle/server/blueprints/variants/templates/macros/links.html
puzzle/server/blueprints/variants/templates/macros/transcripts.html
puzzle/server/static/styles.css
puzzle/server/templates/layouts/base.html
puzzle/server/templates/macros/comments.html
puzzle/server/templates/macros/form_utils.html
puzzle/utils/__init__.py
puzzle/utils/constants.py
puzzle/utils/get_file_info.py
puzzle/utils/get_info.py
puzzle/utils/headers.py
puzzle/utils/ped.py
puzzle/utils/phenomizer.py
puzzle/utils/puzzle_database.py
puzzle/utils/test_cytoband.py
puzzle/utils/test_gemini.py
puzzle/utils/test_grep.py
puzzle/utils/resources/cytoBand.txt.gz
puzzle/utils/resources/hgnc_to_omim.json
requirements/dev.txt
tests/conftest.py
tests/test_puzzle.py
tests/cli/test_cli.py
tests/fixtures/.gitkeep
tests/fixtures/HapMapSv.ped
tests/fixtures/P575-101E.bam
tests/fixtures/P575-101E.bam.bai
tests/fixtures/P575-105E.bam
tests/fixtures/P575-105E.bam.bai
tests/fixtures/P575-106E.bam
tests/fixtures/P575-106E.bam.bai
tests/fixtures/gene-list.txt
tests/fixtures/hapmap.ped
tests/fixtures/hapmap.sv.vep.vcf.gz
tests/fixtures/hapmap.sv.vep.vcf.gz.tbi
tests/fixtures/hapmap.vcf
tests/fixtures/hapmap.vcf.gz
tests/fixtures/hapmap_no_individuals.vcf
tests/fixtures/hapmap_pos.vcf.gz
tests/fixtures/hapmap_pos.vcf.gz.tbi
tests/fixtures/hapmap_regions.csv
tests/fixtures/minimal.vcf
tests/fixtures/no_ind.vcf
tests/models/test_models_case.py
tests/models/test_variant.py
tests/models/sql/test_genelist.py
tests/models/sql/test_sql.py
tests/plugins/gemini/test_gemini_case_mixin.py
tests/plugins/gemini/test_gemini_init.py
tests/plugins/gemini/test_gemini_variant_extras.py
tests/plugins/gemini/test_gemini_variant_mixin.py
tests/plugins/store/test_sqlstore.py
tests/plugins/store/mixins/test_mixin_case.py
tests/plugins/store/mixins/test_mixin_comment.py
tests/plugins/store/mixins/test_mixin_gemini.py
tests/plugins/store/mixins/test_mixin_genelist.py
tests/plugins/store/mixins/test_mixin_phenotype.py
tests/plugins/store/mixins/test_mixin_resource.py
tests/plugins/store/mixins/test_mixin_variant.py
tests/plugins/vcf/test_annotations_mixin.py
tests/plugins/vcf/test_consequence_extras.py
tests/plugins/vcf/test_vcf_case_mixin.py
tests/plugins/vcf/test_vcf_init.py
tests/plugins/vcf/test_vcf_variant_mixin.py
tests/server/test_settings.py
tests/utils/test_constants.py
tests/utils/test_get_file_info.py
tests/utils/test_get_info.py
tests/utils/test_headers.py
tests/utils/test_ped.py