CHANGELOG.md
LICENSE
MANIFEST.in
README.md
deploy.sh
lint.sh
pyproject.toml
release_upload.py
requirements.txt
test.sh
docs/sv-rna.md
examples/osteosarc_sv_validation.py
isovar/__init__.py
isovar/__main__.py
isovar/aligned_reference_prefix.py
isovar/alignment_score.py
isovar/allele_interpretations.py
isovar/allele_read.py
isovar/allele_read_helpers.py
isovar/assembly.py
isovar/cell_evidence.py
isovar/cell_umi.py
isovar/chimeric_alignment.py
isovar/common.py
isovar/dataframe_builder.py
isovar/dataframe_helpers.py
isovar/default_parameters.py
isovar/dna.py
isovar/effect_prediction.py
isovar/filtering.py
isovar/fusion.py
isovar/fusion_visualization.py
isovar/genetic_code.py
isovar/germline_evidence.py
isovar/isovar_result.py
isovar/isovar_result_provider.py
isovar/known_variants.py
isovar/locus_read.py
isovar/logging.py
isovar/main.py
isovar/mutant_transcript_source.py
isovar/orf_inclusion.py
isovar/orf_start.py
isovar/phase_group.py
isovar/phasing.py
isovar/protein_comparison.py
isovar/protein_hypotheses.py
isovar/protein_sequence.py
isovar/protein_sequence_creator.py
isovar/protein_sequence_helpers.py
isovar/read_collector.py
isovar/read_end_inference.py
isovar/read_evidence.py
isovar/read_identity.py
isovar/read_lineage.py
isovar/read_metadata.py
isovar/read_phasing.py
isovar/reference_coding_sequence_key.py
isovar/reference_context.py
isovar/reference_context_helpers.py
isovar/reference_sequence_key.py
isovar/rna_evidence.py
isovar/sid_data.py
isovar/string_helpers.py
isovar/sv_rna.py
isovar/sv_rna_comparison.py
isovar/sv_rna_orf_export.py
isovar/sv_rna_orfs.py
isovar/sv_rna_relations.py
isovar/transcript_assembly_edit.py
isovar/transcript_compatibility.py
isovar/transcript_edit_helpers.py
isovar/translation.py
isovar/translation_helpers.py
isovar/translation_key.py
isovar/value_object.py
isovar/variant_helpers.py
isovar/variant_orf.py
isovar/variant_orf_helpers.py
isovar/variant_sequence.py
isovar/variant_sequence_creator.py
isovar/variant_sequence_helpers.py
isovar/visualization.py
isovar.egg-info/PKG-INFO
isovar.egg-info/SOURCES.txt
isovar.egg-info/dependency_links.txt
isovar.egg-info/entry_points.txt
isovar.egg-info/requires.txt
isovar.egg-info/top_level.txt
isovar/cli/__init__.py
isovar/cli/commands.py
isovar/cli/filter_args.py
isovar/cli/isovar_allele_counts.py
isovar/cli/isovar_allele_interpretations.py
isovar/cli/isovar_allele_reads.py
isovar/cli/isovar_fusion.py
isovar/cli/isovar_main.py
isovar/cli/isovar_plot.py
isovar/cli/isovar_protein_hypotheses.py
isovar/cli/isovar_protein_sequences.py
isovar/cli/isovar_reference_contexts.py
isovar/cli/isovar_sv_rna.py
isovar/cli/isovar_translations.py
isovar/cli/isovar_variant_reads.py
isovar/cli/isovar_variant_sequences.py
isovar/cli/main_args.py
isovar/cli/output_args.py
isovar/cli/protein_sequence_args.py
isovar/cli/reference_context_args.py
isovar/cli/rna_args.py
isovar/cli/translation_args.py
isovar/cli/validation.py
isovar/cli/variant_sequences_args.py
isovar/data/sid-reads/acquisition.json
isovar/data/sid-reads/manifest.json
isovar/data/sid-reads/recipe.json
isovar/data/sid-reads/sources/1281e68167d4640a28783c86.bam
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isovar/data/sid-reads/sources/196160e703256c72b0bc992a.bam
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isovar/data/sid-reads/sources/ffc2634225ae966b32ebd383.header.json
tests/__init__.py
tests/osteosarc_protein_helpers.py
tests/reference_identity.py
tests/test_aligned_reading_frame.py
tests/test_alignment_score.py
tests/test_allele_counts.py
tests/test_allele_interpretations.py
tests/test_allele_reads.py
tests/test_argparser_helpers.py
tests/test_assembly.py
tests/test_cell_evidence.py
tests/test_cell_umi.py
tests/test_chimeric_phasing.py
tests/test_ci_scripts.py
tests/test_cli.py
tests/test_cli_csv_columns.py
tests/test_cli_defaults.py
tests/test_cli_input_errors.py
tests/test_cli_subcommands.py
tests/test_coding_fusion_examples.py
tests/test_common.py
tests/test_coordinate_sharing_performance_results.py
tests/test_dataframe_builder.py
tests/test_deploy_script.py
tests/test_dna_helpers.py
tests/test_docs.py
tests/test_edit_attribution.py
tests/test_effect_prediction.py
tests/test_extended_footprints.py
tests/test_filtering.py
tests/test_fusion.py
tests/test_fusion_extraction.py
tests/test_fusion_visualization.py
tests/test_gate_scripts.py
tests/test_gather_variant_reads_wgs.py
tests/test_genetic_code.py
tests/test_germline_evidence.py
tests/test_insertion_boundaries.py
tests/test_isovar_result.py
tests/test_locus_reads.py
tests/test_logging.py
tests/test_main.py
tests/test_mutant_amino_acids_in_protein_sequence.py
tests/test_mutant_transcript_source.py
tests/test_nr2f2_evidence.py
tests/test_nr2f2_libraries.py
tests/test_orf_inclusion.py
tests/test_orf_start.py
tests/test_osteosarc_audit.py
tests/test_osteosarc_expansion_corpus.py
tests/test_osteosarc_expansion_inventory.py
tests/test_osteosarc_expansion_matrix.py
tests/test_osteosarc_expansion_report.py
tests/test_osteosarc_expansion_stress.py
tests/test_osteosarc_expansion_validation.py
tests/test_osteosarc_figures.py
tests/test_osteosarc_footprints.py
tests/test_osteosarc_proteins.py
tests/test_osteosarc_rna.py
tests/test_phasing.py
tests/test_protein_comparison.py
tests/test_protein_hypotheses.py
tests/test_protein_sequence_selection.py
tests/test_protein_sequences.py
tests/test_read_collection_memory.py
tests/test_read_collection_performance_results.py
tests/test_read_contig_aliases.py
tests/test_read_end_inference.py
tests/test_read_helpers.py
tests/test_read_identity.py
tests/test_read_lineage.py
tests/test_read_metadata.py
tests/test_read_phasing.py
tests/test_real_rna.py
tests/test_reference_coding_sequence_key.py
tests/test_reference_context_limits.py
tests/test_reference_contexts.py
tests/test_reference_identity.py
tests/test_reference_sequence_key.py
tests/test_release_upload.py
tests/test_rna_path_schema.py
tests/test_rna_performance_results.py
tests/test_rna_performance_tools.py
tests/test_rna_support_record.py
tests/test_shared_support_index.py
tests/test_sid_data.py
tests/test_somatic_variant_with_0_supporting_rna_reads.py
tests/test_somatic_variant_with_2_supporting_rna_reads.py
tests/test_source_distribution.py
tests/test_spliced_indels.py
tests/test_sv_record_acquisition.py
tests/test_sv_rna.py
tests/test_sv_rna_comparison.py
tests/test_sv_rna_intergenic.py
tests/test_sv_rna_orf_export.py
tests/test_sv_rna_orf_orientation.py
tests/test_sv_rna_orfs.py
tests/test_sv_rna_three_fusions.py
tests/test_symbolic_variants.py
tests/test_transcript_compatibility.py
tests/test_transcript_edits.py
tests/test_translation.py
tests/test_translation_helpers.py
tests/test_translation_regressions.py
tests/test_value_object.py
tests/test_variant_helpers.py
tests/test_variant_orf.py
tests/test_variant_reads_with_dummy_samfile.py
tests/test_variant_sequence_support.py
tests/test_variant_sequences.py
tests/test_visualization.py
tests/testing_helpers.py
tests/data/fusions/README.md
tests/data/fusions/audit_three_fusions.py
tests/data/fusions/build_coding_examples.py
tests/data/fusions/build_osteosarc.py
tests/data/fusions/build_validation_events.py
tests/data/fusions/validation-events.json
tests/data/fusions/coding-corpus/ATP5MG--KMT2A.input.json.gz
tests/data/fusions/coding-corpus/BCR--ABL1.input.json.gz
tests/data/fusions/coding-corpus/README.md
tests/data/fusions/coding-corpus/manifest.json
tests/data/fusions/corpus/FOXO3--STRADA-CCDC47-T1.input.json.gz
tests/data/fusions/corpus/FOXO3--STRADA-CCDC47-T2.input.json.gz
tests/data/fusions/corpus/PARD3B--CDKN2B-AS1-CDKN2B-T1.input.json.gz
tests/data/fusions/corpus/TPST1--CRCP-T1.input.json.gz
tests/data/fusions/corpus/TPST1--CRCP-T2.input.json.gz
tests/data/fusions/corpus/manifest.json
tests/data/fusions/long-read/README.md
tests/data/fusions/long-read/manifest.json
tests/data/fusions/three-fusions/GABBR1--SLC29A1.ONT-T1.json.gz
tests/data/fusions/three-fusions/GABBR1--SLC29A1.ONT-T2.json.gz
tests/data/fusions/three-fusions/GABBR1--SLC29A1.ONT-T3.json.gz
tests/data/fusions/three-fusions/GABBR1--SLC29A1.PacBio-T1.json.gz
tests/data/fusions/three-fusions/OTUD7A--FMN1.ONT-T1.json.gz
tests/data/fusions/three-fusions/OTUD7A--FMN1.ONT-T2.json.gz
tests/data/fusions/three-fusions/OTUD7A--FMN1.ONT-T3.json.gz
tests/data/fusions/three-fusions/OTUD7A--FMN1.PacBio-T1.json.gz
tests/data/fusions/three-fusions/PARD3B--CDKN2B-AS1-CDKN2B.ONT-T1.json.gz
tests/data/fusions/three-fusions/PARD3B--CDKN2B-AS1-CDKN2B.ONT-T2.json.gz
tests/data/fusions/three-fusions/PARD3B--CDKN2B-AS1-CDKN2B.ONT-T3.json.gz
tests/data/fusions/three-fusions/PARD3B--CDKN2B-AS1-CDKN2B.PacBio-T1.json.gz
tests/data/fusions/three-fusions/README.md
tests/data/fusions/three-fusions/SPEC.md
tests/data/fusions/three-fusions/manifest.json
tests/data/fusions/three-fusions/references.json.gz
tests/data/fusions/three-fusions/source-inventory.json.gz
tests/data/osteosarc/protein_references.py
tests/data/osteosarc/expansion/inventory.py
tests/data/osteosarc/expansion/references.py