LICENSE
MANIFEST.in
README.md
pyproject.toml
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/assets/NOTICE.md
vntyper/assets/igv-3.0.2.min.js.gz
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_calibration.json
vntyper/modules/advntr/advntr_config.json
vntyper/modules/advntr/advntr_genotyping.py
vntyper/modules/advntr/advntr_result_io.py
vntyper/modules/advntr/advntr_variant_annotations.py
vntyper/modules/advntr/model_provenance.py
vntyper/modules/shark/__init__.py
vntyper/modules/shark/shark_config.json
vntyper/modules/shark/shark_filtering.py
vntyper/scripts/__init__.py
vntyper/scripts/algorithm_rules.py
vntyper/scripts/alignment_binding.py
vntyper/scripts/alignment_consumer_commands.py
vntyper/scripts/alignment_contract.py
vntyper/scripts/alignment_fastq_conversion.py
vntyper/scripts/alignment_index.py
vntyper/scripts/alignment_index_binding.py
vntyper/scripts/alignment_index_provenance.py
vntyper/scripts/alignment_preflight.py
vntyper/scripts/alignment_preflight_logs.py
vntyper/scripts/alignment_processing.py
vntyper/scripts/alignment_scan.py
vntyper/scripts/alignment_target_io.py
vntyper/scripts/archive_safety.py
vntyper/scripts/artifact_names.py
vntyper/scripts/assembly_guard.py
vntyper/scripts/calibration.json
vntyper/scripts/chromosome_utils.py
vntyper/scripts/cli_handlers.py
vntyper/scripts/cli_lazy_imports.py
vntyper/scripts/cli_logging_safety.py
vntyper/scripts/cli_parser.py
vntyper/scripts/cli_report.py
vntyper/scripts/cohort_categories.py
vntyper/scripts/cohort_exports.py
vntyper/scripts/cohort_inputs.py
vntyper/scripts/cohort_pseudonyms.py
vntyper/scripts/cohort_summary.py
vntyper/scripts/cohort_tables.py
vntyper/scripts/command_builders.py
vntyper/scripts/comparator_rules.py
vntyper/scripts/confidence_assignment.py
vntyper/scripts/coverage_presentation.py
vntyper/scripts/coverage_qc.py
vntyper/scripts/coverage_stats.py
vntyper/scripts/cross_match.py
vntyper/scripts/cross_match_presentation.py
vntyper/scripts/css_escaping.py
vntyper/scripts/extract_unmapped_from_offset.py
vntyper/scripts/fastp_cutoffs.py
vntyper/scripts/fastq_bam_processing.py
vntyper/scripts/file_processing.py
vntyper/scripts/flagging.py
vntyper/scripts/generate_report.py
vntyper/scripts/idxstats_parsing.py
vntyper/scripts/igv_report.py
vntyper/scripts/install_references.py
vntyper/scripts/install_references_config.json
vntyper/scripts/install_references_logging.py
vntyper/scripts/kestrel_command.py
vntyper/scripts/kestrel_config.json
vntyper/scripts/kestrel_count.py
vntyper/scripts/kestrel_counting.py
vntyper/scripts/kestrel_execution.py
vntyper/scripts/kestrel_genotyping.py
vntyper/scripts/kestrel_vcf_contract.py
vntyper/scripts/motif_decisions.py
vntyper/scripts/motif_processing.py
vntyper/scripts/nomenclature.py
vntyper/scripts/nomenclature_annotate.py
vntyper/scripts/nomenclature_bam.py
vntyper/scripts/nomenclature_config.json
vntyper/scripts/online_mode.py
vntyper/scripts/output_paths.py
vntyper/scripts/pipeline.py
vntyper/scripts/pipeline_advntr_cleanup.py
vntyper/scripts/pipeline_advntr_preflight.py
vntyper/scripts/pipeline_advntr_run_context.py
vntyper/scripts/pipeline_alignment.py
vntyper/scripts/pipeline_cleanup.py
vntyper/scripts/pipeline_coverage.py
vntyper/scripts/pipeline_guards.py
vntyper/scripts/pipeline_inputs.py
vntyper/scripts/pipeline_kestrel.py
vntyper/scripts/pipeline_read_routing.py
vntyper/scripts/preflight_command_io.py
vntyper/scripts/preflight_error_io.py
vntyper/scripts/preflight_input_io.py
vntyper/scripts/read_layout.py
vntyper/scripts/reference_binding.py
vntyper/scripts/reference_bundle.py
vntyper/scripts/reference_cache_binding.py
vntyper/scripts/reference_download.py
vntyper/scripts/reference_integrity.py
vntyper/scripts/reference_provenance.py
vntyper/scripts/reference_registry.py
vntyper/scripts/reference_resolution.py
vntyper/scripts/reference_resolution_environment.py
vntyper/scripts/reference_uri_policy.py
vntyper/scripts/region_utils.py
vntyper/scripts/report_assets.py
vntyper/scripts/report_config.json
vntyper/scripts/report_context_contract.py
vntyper/scripts/report_formatting.py
vntyper/scripts/report_identity.py
vntyper/scripts/samtools_command_fragments.py
vntyper/scripts/scoring.py
vntyper/scripts/screening_summary.py
vntyper/scripts/subthreshold.py
vntyper/scripts/summary.py
vntyper/scripts/summary_steps.py
vntyper/scripts/utils.py
vntyper/scripts/variant_parsing.py
vntyper/scripts/verify_seeds.py
vntyper/templates/_report_base.html
vntyper/templates/cohort_summary_template.html
vntyper/templates/igv_report_template.html
vntyper/templates/report_template.html