├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── __init__.py ├── examples ├── jobscript.sh ├── score_variants.crc.sh ├── score_variants.neuro.sh └── score_variants.sherlock.neuro.sh ├── pyproject.toml ├── scripts └── get_caqtl_data.sh ├── src ├── __init__.py ├── archive │ ├── old.variant_scoring.per_chrom.shuf_pvals.py │ ├── old_chunks.py │ └── variant_scoring.per_chunk.py ├── generators │ ├── __init__.py │ ├── peak_generator.py │ └── variant_generator.py ├── hitcaller_variant.py ├── utils │ ├── __init__.py │ ├── argmanager.py │ ├── helpers.py │ ├── io.py │ ├── losses.py │ ├── one_hot.py │ └── shap_utils.py ├── variant_annotation.py ├── variant_scoring.per_chrom.py ├── variant_scoring.py ├── variant_shap.py └── variant_summary_across_folds.py └── tests ├── archive ├── annotations │ └── test.annotations.tsv ├── test.annotations.sh ├── test.forward_only.sh ├── test.per_chrom.forward_only.sh ├── test.per_chrom.sh └── test.sh ├── conftest.py ├── data ├── caqtls.african.lcls.benchmarking.subset.tsv ├── test.anno_input.tsv ├── test.bed ├── test.chrombpnet.incorrect.tsv ├── test.chrombpnet.incorrect2.tsv ├── test.chrombpnet.no_chr.tsv ├── test.chrombpnet.tsv ├── test.genes.bed ├── test.hits.bed ├── test.incorrect.bed ├── test.original.tsv ├── test.peaks.bed └── test.plink.tsv ├── test_load_bed_files.py ├── test_load_variant_table.py ├── test_one_hot.py ├── test_variant_annotation.py └── test_variant_scoring.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kundajelab/variant-scorer/HEAD/.gitignore -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kundajelab/variant-scorer/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: 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