├── .coveragerc ├── .gitattributes ├── .github └── workflows │ └── tests.yml ├── .github_changelog_generator ├── .gitignore ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASING.md ├── code-of-conduct.md ├── deploy.sh ├── examples └── varcode-quick_start.ipynb ├── lint-and-test.sh ├── lint.sh ├── pylintrc ├── requirements.txt ├── setup.py ├── test.sh ├── tests ├── __init__.py ├── benchmark_vcf_load.py ├── common.py ├── data.py ├── data │ ├── dbnsfp_validation_set.csv │ ├── different-samples.1.vcf │ ├── different-samples.2.vcf │ ├── duplicate-id.1.vcf │ ├── duplicate-id.2.vcf │ ├── duplicates.maf │ ├── duplicates.vcf │ ├── mouse_vcf_dbsnp_chr1_partial.vcf │ ├── multiallelic.vcf │ ├── mutect-example-headerless.vcf │ ├── mutect-example.vcf │ ├── ov.wustle.subset5.maf │ ├── same-samples.1.vcf │ ├── same-samples.2.vcf │ ├── simple.1.vcf │ ├── simple.2.vcf │ ├── somatic_hg19_14muts.space_in_sample_name.vcf │ ├── somatic_hg19_14muts.vcf │ ├── somatic_hg19_14muts.vcf.gz │ ├── strelka-example.vcf │ ├── tcga_ov.head.maf │ └── tcga_ov.head.xychr.maf ├── test_cli_effects.py ├── test_cli_genes.py ├── test_collection_filtering.py ├── test_common.py ├── test_cosmic_mutations.py ├── test_dbnsfp_validation.py ├── test_effect_annotation_errors.py ├── test_effect_classes.py ├── test_effect_collection.py ├── test_effect_collection_serialization.py ├── test_effects_from_mutagenix_variants.py ├── test_exonic_splice_site.py ├── test_frameshift_helpers.py ├── test_maf.py ├── test_mm10_klf6_frameshift.py ├── test_mouse.py ├── test_mutate.py ├── test_no_duplicate_variants.py ├── test_problematic_variants.py ├── test_reference.py ├── test_string_helpers.py ├── test_timings.py ├── test_variant.py ├── test_variant_collection.py ├── test_vcf.py └── test_vcf_output.py └── varcode ├── __init__.py ├── cli ├── __init__.py ├── effects_script.py ├── genes_script.py ├── logging.conf ├── variant_args.py └── version_info.py ├── common.py ├── effects ├── __init__.py ├── common.py ├── effect_classes.py ├── effect_collection.py ├── effect_helpers.py ├── effect_ordering.py ├── effect_prediction.py ├── effect_prediction_coding.py ├── effect_prediction_coding_frameshift.py ├── effect_prediction_coding_in_frame.py ├── mutate.py ├── transcript_helpers.py └── translate.py ├── maf.py ├── nucleotides.py ├── reference.py ├── string_helpers.py ├── ucsc_reference_names.py ├── util.py ├── variant.py ├── variant_collection.py ├── vcf.py ├── vcf_output.py └── version.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/varcode/HEAD/.coveragerc -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | varcode/_version.py export-subst 2 | -------------------------------------------------------------------------------- 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