MANIFEST.in
README.md
setup.cfg
setup.py
adagenes/__init__.py
adagenes.egg-info/PKG-INFO
adagenes.egg-info/SOURCES.txt
adagenes.egg-info/dependency_links.txt
adagenes.egg-info/requires.txt
adagenes.egg-info/top_level.txt
adagenes/app/__init__.py
adagenes/app/bframe_to_dataframe.py
adagenes/app/filter.py
adagenes/app/load_data.py
adagenes/app/sample_data.py
adagenes/app/table.py
adagenes/app/sites/__init__.py
adagenes/app/sites/about.py
adagenes/clients/__init__.py
adagenes/clients/client.py
adagenes/clients/annotate/__init__.py
adagenes/clients/annotate/blosum_client.py
adagenes/clients/annotate/liftover_annotation.py
adagenes/clients/annotate/type_recognition.py
adagenes/clients/filter/__init__.py
adagenes/clients/filter/allele_filter.py
adagenes/clients/filter/chrom_filter.py
adagenes/clients/filter/defined_variant_filter.py
adagenes/clients/filter/filter_feature.py
adagenes/clients/filter/position_filter.py
adagenes/clients/filter/random_variant_filter.py
adagenes/clients/filter/section_filter.py
adagenes/clients/filter/type_filter.py
adagenes/clients/network/__init__.py
adagenes/clients/network/rest_client.py
adagenes/clients/plot/__init__.py
adagenes/clients/reader/__init__.py
adagenes/clients/reader/avf_reader.py
adagenes/clients/reader/csv_reader.py
adagenes/clients/reader/fasta_reader.py
adagenes/clients/reader/gtf_reader.py
adagenes/clients/reader/json_reader.py
adagenes/clients/reader/maf_reader.py
adagenes/clients/reader/reader.py
adagenes/clients/reader/tsv_reader.py
adagenes/clients/reader/txt_reader.py
adagenes/clients/reader/vcf_reader.py
adagenes/clients/reader/xlsx_reader.py
adagenes/clients/sort/__init__.py
adagenes/clients/sort/positional_sort.py
adagenes/clients/transform/__init__.py
adagenes/clients/transform/combination_client.py
adagenes/clients/transform/dataframe.py
adagenes/clients/transform/dragen_to_vcf_client.py
adagenes/clients/transform/liftover_client.py
adagenes/clients/transform/normalize.py
adagenes/clients/writer/__init__.py
adagenes/clients/writer/avf_writer.py
adagenes/clients/writer/csv_writer.py
adagenes/clients/writer/json_writer.py
adagenes/clients/writer/maf_writer.py
adagenes/clients/writer/normalized_data_writer.py
adagenes/clients/writer/pandas_writer.py
adagenes/clients/writer/pdf_writer.py
adagenes/clients/writer/tsv_writer.py
adagenes/clients/writer/txt_writer.py
adagenes/clients/writer/vcf_writer.py
adagenes/clients/writer/writer.py
adagenes/clients/writer/xlsx_writer.py
adagenes/conf/__init__.py
adagenes/conf/config.ini
adagenes/conf/read_config.py
adagenes/conf/vcf_config.py
adagenes/conf/data/hg19ToHg38.over.chain.gz
adagenes/conf/data/hg19ToHs1.over.chain.gz
adagenes/conf/data/hg38ToGCA_009914755.4.over.chain.gz
adagenes/conf/data/hg38ToHg19.over.chain.gz
adagenes/conf/data/hs1ToHg19.over.chain.gz
adagenes/conf/data/hs1ToHg38.over.chain.gz
adagenes/plot/__init__.py
adagenes/plot/generate_plot_graph_data.py
adagenes/plot/generate_upset_plot_data.py
adagenes/plot/generate_data/__init__.py
adagenes/plot/generate_data/generate_aa_features_heatmap_data.py
adagenes/plot/generate_data/generate_chromosome_positions_data.py
adagenes/plot/generate_data/generate_needleplot_data.py
adagenes/plot/generate_data/generate_protein_pathogenicity_heatmap_data.py
adagenes/plot/generate_data/generate_protein_plot.py
adagenes/plot/generate_data/generate_radarplot_data.py
adagenes/plot/generate_data/generate_sunburst_plot_data.py
adagenes/plot/generate_data/generate_upset_plot_data.py
adagenes/plot/generate_data/plot_config.py
adagenes/plot/generate_plots/__init__.py
adagenes/plot/generate_plots/drug_classification_intersections.py
adagenes/plot/generate_plots/generate_aa_features_heatmap_plots.py
adagenes/plot/generate_plots/generate_network_graph.py
adagenes/plot/generate_plots/generate_protein_pathogenicity_heatmap.py
adagenes/plot/generate_plots/generate_radarplot.py
adagenes/plot/generate_plots/generate_sunburst_plots.py
adagenes/plot/generate_plots/generate_upset_plots.py
adagenes/processing/__init__.py
adagenes/processing/json_biomarker.py
adagenes/processing/parse_http_responses.py
adagenes/processing/process_files.py
adagenes/processing/protein_to_genomic.py
adagenes/run_scripts/__init__.py
adagenes/tools/__init__.py
adagenes/tools/biomarker_types.py
adagenes/tools/client_mgt.py
adagenes/tools/data_io.py
adagenes/tools/data_structures.py
adagenes/tools/dataframe.py
adagenes/tools/format_requests.py
adagenes/tools/hgvs_re.py
adagenes/tools/identify_biomarkers.py
adagenes/tools/json_mgt.py
adagenes/tools/log.py
adagenes/tools/maf_mgt.py
adagenes/tools/module_requests.py
adagenes/tools/normalize_variants.py
adagenes/tools/parse_annotations.py
adagenes/tools/parse_args.py
adagenes/tools/parse_cancer_type_labels.py
adagenes/tools/parse_dataframes.py
adagenes/tools/parse_drug_names.py
adagenes/tools/parse_genomic_data.py
adagenes/tools/parse_indel_locations.py
adagenes/tools/parse_vcf.py
adagenes/tools/preprocessing.py
adagenes/tools/reference_genomes.py
adagenes/tools/seqcat_genetogenomic_client.py
adagenes/tools/seqcat_genomictogene_client.py
adagenes/tools/sequential_annotation.py
plots/__init__.py
plots/tcga_single_patient.py
tests/__init__.py
tests/annotation/__init__.py
tests/annotation/test_blosum_client.py
tests/annotation/test_liftover_annotation.py
tests/annotation/test_type_recognition.py
tests/formats/__init__.py
tests/formats/test_bframe.py
tests/formats/test_clients_read_excel_write_vcf.py
tests/formats/test_clients_read_json_write_json.py
tests/formats/test_clients_read_json_write_tsv.py
tests/formats/test_clients_read_json_write_vcf.py
tests/formats/test_clients_read_tsv_write_tsv.py
tests/formats/test_clients_read_vcf_write_json.py
tests/formats/test_clients_vcf_read_vcf_write_vcf.py
tests/formats/test_avf/__init__.py
tests/formats/test_avf/test_avf_reader.py
tests/formats/test_avf/test_avf_writer.py
tests/formats/test_json/__init__.py
tests/formats/test_json/test_json_annotation.py
tests/formats/test_json/test_json_reader_writer.py
tests/formats/test_transformations/__init__.py
tests/formats/test_transformations/test_txt2csv.py
tests/formats/test_transformations/test_vcf_to_csv.py
tests/preprocessing/__init__.py
tests/preprocessing/test_aa_exchange_biomarker_detection.py
tests/preprocessing/test_biomarker_type_recognition.py
tests/preprocessing/test_biomarker_type_recognition_indels.py
tests/preprocessing/test_biomarker_type_recognition_transcripts.py
tests/preprocessing/test_gene_request.py
tests/preprocessing/test_multiple_biomarker_requests.py
tests/preprocessing/test_preprocessing.py
tests/preprocessing/test_protein_to_genomic.py
tests/preprocessing/test_request_type_identification.py
tests/preprocessing/test_variant_type_recognition_proteins.py
tests/processing/__init__.py
tests/processing/read_files_with_mapping.py
tests/read/__init__.py
tests/read/test_csv_reader.py
tests/read/test_fasta_reader.py
tests/read/test_maf_reader.py
tests/read/test_vcf_reader.py
tests/read/test_xlsx_reader.py
tests/tools/__init__.py
tests/tools/test_alternate_alleles.py
tests/tools/test_dna_normalization.py
tests/tools/test_file_types.py
tests/tools/test_identify_biomarkers.py
tests/tools/test_parse_genome_position.py
tests/tools/test_parse_indel.py
tests/tools/test_protein_normalization.py
tests/tools/test_remove_duplicate_pmids.py
tests/tools/test_seqcat_gene_to_genomic.py
tests/tools/test_seqcat_genomic_to_gene.py
tests/tools/test_wildtype_variant_filter.py
tests/write/__init__.py
tests/write/test_csv_write.py
tests/write/test_vcf_writer.py
tests/write/test_writer.py