├── .gitattributes ├── .gitignore ├── LICENSE.txt ├── README.md ├── caller ├── __init__.py ├── call_variants.py ├── cnv_hybrid.py ├── construct_star_table.py ├── match_star_allele.py └── tests │ ├── __init__.py │ ├── test_call_variants.py │ ├── test_cnv_hybrid.py │ ├── test_data │ ├── HG00611.bam │ ├── HG00611.bam.bai │ ├── NA23275.bam │ └── NA23275.bam.bai │ └── test_match_star.py ├── data ├── CYP2D6_SNP_19.txt ├── CYP2D6_SNP_37.txt ├── CYP2D6_SNP_38.txt ├── CYP2D6_gmm.txt ├── CYP2D6_haplotype_19.txt ├── CYP2D6_haplotype_37.txt ├── CYP2D6_haplotype_38.txt ├── CYP2D6_region_19.bed ├── CYP2D6_region_37.bed ├── CYP2D6_region_38.bed ├── CYP2D6_target_variant_19.txt ├── CYP2D6_target_variant_37.txt ├── CYP2D6_target_variant_38.txt ├── CYP2D6_target_variant_homology_region_19.txt ├── CYP2D6_target_variant_homology_region_37.txt ├── CYP2D6_target_variant_homology_region_38.txt └── star_table.txt ├── depth_calling ├── __init__.py ├── bin_count.py ├── copy_number_call.py ├── gmm.py ├── haplotype.py ├── snp_count.py ├── tests │ ├── __init__.py │ ├── test_bin_count.py │ ├── test_copy_number_call.py │ ├── test_data │ │ ├── NA12878.bam │ │ ├── NA12878.bam.bai │ │ ├── NA12885.bam │ │ ├── NA12885.bam.bai │ │ ├── SMN_SNP_19.txt │ │ ├── SMN_SNP_37.txt │ │ ├── SMN_SNP_37_test.txt │ │ ├── SMN_SNP_38.txt │ │ ├── SMN_gmm.txt │ │ ├── SMN_region_19_short.bed │ │ └── SMN_region_37_short.bed │ ├── test_gmm.py │ ├── test_haplotype.py │ ├── test_snp_count.py │ └── test_utilities.py └── utilities.py ├── requirements.txt └── star_caller.py /.gitattributes: -------------------------------------------------------------------------------- 1 | * text=auto 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Illumina/Cyrius/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: 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