LICENSE
MANIFEST.in
README.md
pyproject.toml
tests/test_data_utils.py
tests/test_orchestration.py
vntyper/__init__.py
vntyper/cli.py
vntyper/config.json
vntyper/version.py
vntyper.egg-info/PKG-INFO
vntyper.egg-info/SOURCES.txt
vntyper.egg-info/dependency_links.txt
vntyper.egg-info/entry_points.txt
vntyper.egg-info/requires.txt
vntyper.egg-info/top_level.txt
vntyper/dependencies/kestrel/commons-lang3-3.4.jar
vntyper/dependencies/kestrel/java-getopt-1.0.14.jar
vntyper/dependencies/kestrel/kanalyze.jar
vntyper/dependencies/kestrel/kestrel.jar
vntyper/dependencies/kestrel/logback-classic-1.1.3.jar
vntyper/dependencies/kestrel/logback-core-1.1.3.jar
vntyper/dependencies/kestrel/slf4j-api-1.7.12.jar
vntyper/modules/__init__.py
vntyper/modules/advntr/__init__.py
vntyper/modules/advntr/advntr_config.json
vntyper/modules/advntr/advntr_genotyping.py
vntyper/modules/shark/__init__.py
vntyper/modules/shark/shark_config.json
vntyper/modules/shark/shark_filtering.py
vntyper/scripts/__init__.py
vntyper/scripts/alignment_processing.py
vntyper/scripts/chromosome_utils.py
vntyper/scripts/cohort_summary.py
vntyper/scripts/confidence_assignment.py
vntyper/scripts/cross_match.py
vntyper/scripts/extract_unmapped_from_offset.py
vntyper/scripts/fastq_bam_processing.py
vntyper/scripts/file_processing.py
vntyper/scripts/flagging.py
vntyper/scripts/generate_report.py
vntyper/scripts/install_references.py
vntyper/scripts/install_references_config.json
vntyper/scripts/kestrel_config.json
vntyper/scripts/kestrel_genotyping.py
vntyper/scripts/motif_processing.py
vntyper/scripts/online_mode.py
vntyper/scripts/pipeline.py
vntyper/scripts/reference_registry.py
vntyper/scripts/region_utils.py
vntyper/scripts/report_config.json
vntyper/scripts/scoring.py
vntyper/scripts/summary.py
vntyper/scripts/utils.py
vntyper/scripts/variant_parsing.py
vntyper/templates/cohort_summary_template.html
vntyper/templates/report_template.html