AUTHORS.rst
CHANGELOG.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
docs/Makefile
docs/authors.rst
docs/conf.py
docs/history.rst
docs/index.rst
docs/installation.rst
docs/license.rst
docs/make.bat
requirements/base.txt
requirements/develop.txt
requirements/test.txt
requirements/test_black.txt
tests/__init__.py
tests/conftest.py
tests/test_import.py
tests/test_parse_ped.py
tests/cli/__init__.py
tests/cli/test_base.py
tests/cli/test_cases.py
tests/cli/test_importer.py
tests/cli/test_projects.py
tests/cli/test_tools.py
tests/cli/test_varannos.py
tests/cli/__snapshots__/test_cases.ambr
tests/cli/__snapshots__/test_importer.ambr
tests/cli/__snapshots__/test_projects.ambr
tests/cli/__snapshots__/test_tools.ambr
tests/cli/__snapshots__/test_varannos.ambr
tests/cli/data/caseimportinfo-list.len-2.json
tests/cli/data/cases_case-list.len-1.json
tests/cli/data/projects_project-list.len-2.json
tests/cli/data/varannos_varannoset-list.len-1.json
tests/cli/data/varannos_varannosetentry-list.len-1.json
tests/cli/data/dragen_qc/sample.mapping_metrics.csv
tests/cli/data/dragen_qc/sample.qc-coverage-region-1_coverage_metrics.csv
tests/cli/data/dragen_qc/sample2.mapping_metrics.csv
tests/cli/data/dragen_qc/sample2.qc-coverage-region-1_coverage_metrics.csv
tests/cli/data/dragen_qc/samples.ped
tests/data/cases_import/FAM_Case_3_father.bam.bamstats.txt
tests/data/cases_import/FAM_Case_3_father.bam.flagstats.txt
tests/data/cases_import/FAM_Case_3_father.bam.idxstats.txt
tests/data/cases_import/FAM_Case_3_index.bam.bamstats.txt
tests/data/cases_import/FAM_Case_3_index.bam.flagstats.txt
tests/data/cases_import/FAM_Case_3_index.bam.idxstats.txt
tests/data/cases_import/FAM_Case_3_mother.bam.bamstats.txt
tests/data/cases_import/FAM_Case_3_mother.bam.flagstats.txt
tests/data/cases_import/FAM_Case_3_mother.bam.idxstats.txt
tests/data/config/varfishrc.toml
tests/data/importer/Case_3_index-N1-DNA1-WGS1.ped
tests/data/importer/Case_3_index-N1-DNA1-WGS1.ped.md5
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.db-infos.tsv.gz
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.db-infos.tsv.gz.md5
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.feature-effects.tsv.gz
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.feature-effects.tsv.gz.md5
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.gts.tsv.gz
tests/data/importer/bwa.delly2.varfish_annotated.Case_3_index-N1-DNA1-WGS1.gts.tsv.gz.md5
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.bam-qc.tsv.gz
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.bam-qc.tsv.gz.md5
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.db-infos.tsv.gz
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.db-infos.tsv.gz.md5
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.gts.tsv.gz
tests/data/importer/bwa.gatk_hc.varfish_annotated.Case_3_index-N1-DNA1-WGS1.gts.tsv.gz.md5
tests/data/parse_ped/trio.ped
varfish_cli/__init__.py
varfish_cli/__main__.py
varfish_cli/common.py
varfish_cli/config.py
varfish_cli/exceptions.py
varfish_cli/parse_ped.py
varfish_cli/version.py
varfish_cli.egg-info/PKG-INFO
varfish_cli.egg-info/SOURCES.txt
varfish_cli.egg-info/dependency_links.txt
varfish_cli.egg-info/entry_points.txt
varfish_cli.egg-info/not-zip-safe
varfish_cli.egg-info/requires.txt
varfish_cli.egg-info/top_level.txt
varfish_cli/api/__init__.py
varfish_cli/api/case.py
varfish_cli/api/common.py
varfish_cli/api/models.py
varfish_cli/api/project.py
varfish_cli/api/varannos.py
varfish_cli/cli/__init__.py
varfish_cli/cli/cases.py
varfish_cli/cli/common.py
varfish_cli/cli/projects.py
varfish_cli/cli/varannos.py
varfish_cli/cli/importer/__init__.py
varfish_cli/cli/importer/create.py
varfish_cli/cli/tools/__init__.py
varfish_cli/cli/tools/models.py