MANIFEST.in
README.md
pyproject.toml
scripts/__init__.py
scripts/annotate_vcf_csv_by_ncbi_gtf.py
scripts/annotate_wgs_gtex.py
scripts/bcftools_preprocess.sh
scripts/compound_het_filter.py
scripts/filter_dbsnp.py
scripts/merge_filter_clinvar_with_distance.py
scripts/vcf_to_gt_csv.py
scripts/genos/1_build_variant_ref_csv.py
scripts/genos/2_export_attention_by_variant_no_vcf.py
scripts/genos/3_plot_variant_reference_logfc.py
scripts/genos/4_check_truth_peak.py
src/seekrare/__init__.py
src/seekrare/pipeline.py
src/seekrare.egg-info/PKG-INFO
src/seekrare.egg-info/SOURCES.txt
src/seekrare.egg-info/dependency_links.txt
src/seekrare.egg-info/requires.txt
src/seekrare.egg-info/top_level.txt
src/seekrare/annotation/__init__.py
src/seekrare/annotation/alphafold3.py
src/seekrare/annotation/clinvar_loader.py
src/seekrare/annotation/combiner.py
src/seekrare/annotation/gtex_eqtl.py
src/seekrare/annotation/hpo_matcher.py
src/seekrare/io/__init__.py
src/seekrare/io/csv_writer.py
src/seekrare/io/vcf_parser.py
src/seekrare/llm/__init__.py
src/seekrare/llm/alphafold_client.py
src/seekrare/llm/genos_client.py
src/seekrare/llm/symptom_parser.py
src/seekrare/preprocess/__init__.py
src/seekrare/preprocess/bcftools_wrapper.py
src/seekrare/preprocess/clinvar_annotation.py
src/seekrare/preprocess/dbsnp_filter.py
src/seekrare/preprocess/eqtl_annotation.py
src/seekrare/preprocess/gene_annotation.py
src/seekrare/preprocess/stage1_family.py
src/seekrare/preprocess/stage4_alphafold.py
src/seekrare/preprocess/stage4_genos.py
src/seekrare/preprocess/vcf_to_gt.py
src/seekrare/scoring/__init__.py
src/seekrare/scoring/engine.py
src/seekrare/scoring/ranker.py
src/seekrare/scoring/stage3_annotate.py
src/seekrare/scoring/stage3_prep.py