.coveragerc
AGENTS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
RELEASING.md
deploy.sh
develop.sh
lint.sh
mkdocs.yml
pyproject.toml
requirements.txt
test.sh
docs/annotator_contract.md
docs/api.md
docs/api_annotators.md
docs/api_effects.md
docs/api_phasing.md
docs/api_rna.md
docs/api_variants.md
docs/changelog.md
docs/csv.md
docs/development_audit.md
docs/effect_annotation.md
docs/effect_types.md
docs/errors.md
docs/experimental_annotators.md
docs/genotype.md
docs/germline.md
docs/getting_started.md
docs/index.md
docs/library_roles.md
docs/phasing.md
docs/rna_structures.md
docs/sample_identity.md
docs/splice_variants.md
docs/structural_variants.md
docs/sv_comparison.md
docs/sv_reference.md
docs/transcript_models.md
docs/transforms.md
examples/vcf_header_usage.py
tests/README.md
tests/__init__.py
tests/benchmark_vcf_load.py
tests/collect_osteosarc_variants.py
tests/common.py
tests/conftest.py
tests/data.py
tests/osteosarc_variants.py
tests/test_annotator_divergence_scenarios.py
tests/test_annotator_haplotypes.py
tests/test_annotator_parity_adversarial.py
tests/test_annotators.py
tests/test_bnd_retained_segments.py
tests/test_cli_effects.py
tests/test_cli_genes.py
tests/test_cli_records.py
tests/test_cli_without_pkg_resources.py
tests/test_collection_filtering.py
tests/test_collection_variants_attr_consistency.py
tests/test_common.py
tests/test_cosmic_mutations.py
tests/test_cryptic_exons.py
tests/test_csv_roundtrip.py
tests/test_dbnsfp_validation.py
tests/test_default_structural_helpers.py
tests/test_deploy_script.py
tests/test_documentation_examples.py
tests/test_effect_annotation_errors.py
tests/test_effect_candidates.py
tests/test_effect_classes.py
tests/test_effect_collection.py
tests/test_effect_collection_serialization.py
tests/test_effect_collection_sort_order.py
tests/test_effect_hypotheses.py
tests/test_effects_from_mutagenix_variants.py
tests/test_exacto_fusions.py
tests/test_exacto_reference_mapping.py
tests/test_exonic_splice_site.py
tests/test_fast_path.py
tests/test_frameshift_cterminus_regression.py
tests/test_frameshift_helpers.py
tests/test_fusion_insertions.py
tests/test_fusion_partner_candidates.py
tests/test_genome_contig_validation.py
tests/test_genome_sequence.py
tests/test_genomic_layout.py
tests/test_genotype.py
tests/test_genotype_from_vcf.py
tests/test_germline_context.py
tests/test_germline_effects.py
tests/test_germline_overlap.py
tests/test_haplotype_effect.py
tests/test_intragenic_breakends.py
tests/test_local_sv_insertions.py
tests/test_maf.py
tests/test_mitochondrial.py
tests/test_mixed_haplotypes.py
tests/test_mm10_klf6_frameshift.py
tests/test_mouse.py
tests/test_mutant_transcript.py
tests/test_mutate.py
tests/test_native_reference_dna.py
tests/test_no_duplicate_variants.py
tests/test_nonlocal_layout.py
tests/test_nonlocal_sv_transcripts.py
tests/test_osteosarc_dataset.py
tests/test_osteosarc_fusions.py
tests/test_osteosarc_shared_fusions.py
tests/test_osteosarc_shared_reads.py
tests/test_osteosarc_shared_svs.py
tests/test_osteosarc_shared_targets.py
tests/test_osteosarc_variants.py
tests/test_partial_annotators.py
tests/test_premature_stop_short_description.py
tests/test_problematic_variants.py
tests/test_protein_diff_parity.py
tests/test_read_phase_resolver.py
tests/test_real_world_callers.py
tests/test_reference.py
tests/test_reference_completion.py
tests/test_reference_fixture.py
tests/test_reference_mismatch_error.py
tests/test_reference_segments.py
tests/test_rna_evidence.py
tests/test_rna_haplotype_sequences.py
tests/test_rna_read_phasing_source.py
tests/test_sample_identity.py
tests/test_selenocysteine.py
tests/test_selenocysteine_proteins.py
tests/test_silent_aa_pos.py
tests/test_silent_hgvs_description.py
tests/test_source_distribution.py
tests/test_splice_graph.py
tests/test_splice_outcomes.py
tests/test_splice_site_effects.py
tests/test_stop_codon_classification_bugs.py
tests/test_string_helpers.py
tests/test_structural_serialization.py
tests/test_structural_variant_annotator.py
tests/test_structural_variants.py
tests/test_sv_comparison.py
tests/test_sv_consequences.py
tests/test_sv_selenocysteine.py
tests/test_sv_sequence_changes.py
tests/test_sv_tabular_metadata.py
tests/test_symbolic_alleles.py
tests/test_symbolic_sv_padding.py
tests/test_test_script.py
tests/test_timings.py
tests/test_transcript_layout.py
tests/test_transcript_model.py
tests/test_transcript_model_start_codons.py
tests/test_transforms_left_align.py
tests/test_transforms_pair_breakends.py
tests/test_upstream_fusion_partners.py
tests/test_variant.py
tests/test_variant_collection.py
tests/test_vcf.py
tests/test_vcf_export_integrity.py
tests/test_vcf_limits.py
tests/test_vcf_output.py
tests/test_vcf_parsing.py
tests/test_vcf_phase_resolver.py
tests/test_vcf_spec_examples.py
tests/data/README.md
tests/data/SHA256SUMS
tests/data/dbnsfp_validation_set.csv
tests/data/different-samples.1.vcf
tests/data/different-samples.2.vcf
tests/data/duplicate-id.1.vcf
tests/data/duplicate-id.2.vcf
tests/data/duplicates.maf
tests/data/duplicates.vcf
tests/data/mouse_vcf_dbsnp_chr1_partial.vcf
tests/data/multiallelic.vcf
tests/data/mutect-example-headerless.vcf
tests/data/mutect-example.vcf
tests/data/osteosarc_esvee_shared_svs.vcf
tests/data/osteosarc_esvee_somatic.vcf
tests/data/osteosarc_observed_junctions.json
tests/data/osteosarc_snapshot_2026-09-18t.zip
tests/data/osteosarc_variants.json
tests/data/ov.wustle.subset5.maf
tests/data/same-samples.1.vcf
tests/data/same-samples.2.vcf
tests/data/simple.1.vcf
tests/data/simple.2.vcf
tests/data/somatic_hg19_14muts.space_in_sample_name.vcf
tests/data/somatic_hg19_14muts.vcf
tests/data/somatic_hg19_14muts.vcf.gz
tests/data/strelka-example.vcf
tests/data/tcga_ov.head.maf
tests/data/tcga_ov.head.xychr.maf
tests/data/documentation/merged_phased.vcf
tests/data/documentation/normal.vcf
tests/data/documentation/structural_variants.vcf
tests/data/documentation/variants.vcf
tests/data/real_callers/README.md
tests/data/real_callers/mutect2_example.vcf
tests/data/real_callers/strelka2_somatic_snvs.vcf
tests/data/real_callers/vep_annotated_csq.vcf
tests/data/spec_examples/README.md
tests/data/spec_examples/vcf42_spec_trio.vcf
tests/data/spec_examples/vcf43_spec_sv.vcf
varcode/__init__.py
varcode/_sample_vcf.py
varcode/common.py
varcode/cryptic_exons.py
varcode/csv_helpers.py
varcode/effect_candidates.py
varcode/effect_hypotheses.py
varcode/errors.py
varcode/exacto.py
varcode/genome.py
varcode/genome_sequence.py
varcode/genomic_layout.py
varcode/genotype.py
varcode/germline.py
varcode/maf.py
varcode/mutant_transcript.py
varcode/nucleotides.py
varcode/phasing.py
varcode/realized_effects.py
varcode/reference.py
varcode/reference_completion.py
varcode/rna_evidence.py
varcode/rna_read_phasing.py
varcode/sample_identity.py
varcode/splice_graph.py
varcode/splice_outcomes.py
varcode/string_helpers.py
varcode/structural_variant.py
varcode/sv_allele_parser.py
varcode/sv_comparison.py
varcode/transcript_layout.py
varcode/transcript_model.py
varcode/ucsc_reference_names.py
varcode/util.py
varcode/variant.py
varcode/variant_collection.py
varcode/vcf.py
varcode/vcf_output.py
varcode/vcf_parsing.py
varcode/version.py
varcode.egg-info/PKG-INFO
varcode.egg-info/SOURCES.txt
varcode.egg-info/dependency_links.txt
varcode.egg-info/entry_points.txt
varcode.egg-info/requires.txt
varcode.egg-info/top_level.txt
varcode/annotators/__init__.py
varcode/annotators/fast.py
varcode/annotators/protein_diff.py
varcode/annotators/registry.py
varcode/cli/__init__.py
varcode/cli/effects_script.py
varcode/cli/genes_script.py
varcode/cli/logging.conf
varcode/cli/main.py
varcode/cli/sample_checks.py
varcode/cli/variant_args.py
varcode/cli/version_info.py
varcode/effects/__init__.py
varcode/effects/classify.py
varcode/effects/codon_tables.py
varcode/effects/common.py
varcode/effects/effect_classes.py
varcode/effects/effect_collection.py
varcode/effects/effect_helpers.py
varcode/effects/effect_ordering.py
varcode/effects/effect_prediction.py
varcode/effects/effect_prediction_coding.py
varcode/effects/effect_prediction_coding_frameshift.py
varcode/effects/effect_prediction_coding_in_frame.py
varcode/effects/fast_path.py
varcode/effects/mutate.py
varcode/effects/selenocysteine.py
varcode/effects/sequence_change.py
varcode/effects/structural.py
varcode/effects/structural_serialization.py
varcode/effects/transcript_helpers.py
varcode/effects/translate.py
varcode/transforms/__init__.py