├── .gitignore ├── LICENSE ├── README.md ├── ampclasslib ├── __init__.py ├── _version.py ├── ac_annotation.py ├── ac_io.py ├── ac_util.py ├── amplicon_similarity.py ├── check_SV_support.py ├── config_params.py ├── convert_cycles_file.py ├── default_config.json ├── ecDNA_context.py ├── make_input.sh ├── profile_connections.py ├── radar_plotting.py ├── read_support_utils.py └── resources │ ├── combined_oncogene_list.txt │ ├── gencode_GRCh38_long_noncoding_RNAs.gff3.gz │ ├── gencode_hg19_long_noncoding_RNAs.gff3.gz │ ├── gencode_mm10_long_noncoding_RNAs.gff3.gz │ ├── patch_regions.tsv │ └── sorted_background_scores.txt ├── amplicon_classifier.py ├── feature_similarity.py ├── legacy_natgen_2020 ├── README.md └── legacy_natgen_scripts.tar.gz ├── make_input.sh ├── make_results_table.py └── scripts ├── amplicons_intersecting_bed.py ├── lift_AC_coords.py ├── make_sample_cnv_bed_map.sh ├── results_comparator.py └── softlink_images.py /.gitignore: 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