├── .github └── ISSUE_TEMPLATE │ └── issue-or-feature-request.md ├── .gitignore ├── CNAME ├── LICENSE ├── README.md ├── annotations ├── README.md ├── combine_PrimateAI_scores_and_gene_threshold_tables.py ├── combine_score_tables.py ├── convert_SpliceAI_annotation_input_format_to_bed.py ├── convert_gtf_to_SpliceAI_annotation_input_format.py ├── convert_primate_ai_to_indexed_table.sh ├── generate_transcript_annotation_json.py ├── list_current_homo_sapiens_ensembl_dbs.sh ├── update_SpliceAI_annotation_txt_files.sh ├── update_json_annotation_files.sh ├── update_pangolin_db_files.sh └── upload_annotations_to_server.sh ├── chm13v2-hg38.over.chain.gz ├── google_cloud_run_services ├── Makefile ├── README.md ├── build_and_deploy.py ├── connect_to_db.sh ├── create_pangolin_db.py ├── database_admin.sh ├── docker │ ├── pangolin │ │ ├── Dockerfile │ │ ├── requirements.txt │ │ ├── sha256_grch37.txt │ │ └── sha256_grch38.txt │ └── spliceai │ │ ├── Dockerfile │ │ ├── requirements.txt │ │ ├── sha256_grch37.txt │ │ └── sha256_grch38.txt ├── server.py └── test_score_consistency.py ├── hg19ToHg38.over.chain.gz ├── hg38-chm13v2.over.chain.gz ├── hg38ToHg19.over.chain.gz ├── icon.png ├── index.html ├── requirements.txt ├── restart_server.sh ├── run_tests.sh ├── server.py ├── start_local_server.sh ├── start_server.sh ├── stop_server.sh ├── t2t-chm13-v1.0.hg38.over.chain.gz ├── t2t-chm13-v1.1.grch38.over.chain.gz ├── temporarily_disable_liftover_rate_limit.py ├── test_data ├── run_spliceai_on_test_vcf.sh ├── spliceai_scores.masked.snv.hg38_subset.vcf.gz ├── spliceai_scores.masked.snv.hg38_subset.vcf.gz.tbi ├── spliceai_scores.raw.indel.hg38_subset.vcf.gz ├── spliceai_scores.raw.indel.hg38_subset.vcf.gz.tbi ├── spliceai_scores.raw.snv.hg38_subset.vcf.gz ├── spliceai_scores.raw.snv.hg38_subset.vcf.gz.tbi └── test.vcf └── test_spliceai.py /.github/ISSUE_TEMPLATE/issue-or-feature-request.md: -------------------------------------------------------------------------------- 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