.gitignore
LICENSE
Readme.md
analyse_allele_frequencies.py
remove_overlapping_indels.py
setup.py
.github/workflows/install-and-test.yml
example_data/few_variants.vcf
example_data/few_variants_two_chromosomes.vcf
example_data/small_reference.fa
example_data/small_reference_two_chromosomes.fa
example_data/vcf_with_genotypes.vcf
kage/__init__.py
kage/command_line_interface.py
kage/configuration.py
kage/io.py
kage/naive_genotyper.py
kage/node_counts.py
kage/util.py
kage/variant_filtering.py
kage/analysis/__init__.py
kage/analysis/analysis.py
kage/analysis/debugging.py
kage/analysis/genotype_accuracy.py
kage/analysis/variant_kmer_analyser.py
kage/benchmarking/__init__.py
kage/benchmarking/vcf_preprocessing.py
kage/genotyping/__init__.py
kage/genotyping/combination_model_genotyper.py
kage/genotyping/multiallelic.py
kage/glimpse/__init__.py
kage/glimpse/glimpse_wrapper.py
kage/indexing/__init__.py
kage/indexing/div.py
kage/indexing/graph.py
kage/indexing/index_bundle.py
kage/indexing/kmer_scoring.py
kage/indexing/main.py
kage/indexing/modulo_filter.py
kage/indexing/path_based_count_model.py
kage/indexing/path_variant_indexing.py
kage/indexing/paths.py
kage/indexing/signatures.py
kage/indexing/sparse_haplotype_matrix.py
kage/indexing/tricky_variants.py
kage/models/__init__.py
kage/models/helper_index.py
kage/models/helper_index_using_duplicate_counts.py
kage/models/helper_model.py
kage/models/joint_distribution.py
kage/models/mapping_model.py
kage/models/models.py
kage/models/sampling_combo_model.py
kage/modles/__init__.py
kage/preprocessing/__init__.py
kage/preprocessing/variants.py
kage/simulation/__init__.py
kage/simulation/read_simulation.py
kage/simulation/simulation.py
kage_genotyper.egg-info/PKG-INFO
kage_genotyper.egg-info/SOURCES.txt
kage_genotyper.egg-info/dependency_links.txt
kage_genotyper.egg-info/entry_points.txt
kage_genotyper.egg-info/not-zip-safe
kage_genotyper.egg-info/requires.txt
kage_genotyper.egg-info/top_level.txt
scripts/compare_kmer_index_and_modulo_filter.py
scripts/div.py
scripts/test_pruning_kmers.py
scripts/test_read_gzipped.py
tests/__init__.py
tests/biallelic.vcf
tests/div.py
tests/haplotype_matrix1.npy
tests/integration_test.py
tests/integration_test_special_cases.py
tests/multiallelic.fa
tests/multiallelic.vcf
tests/multiallelic2.vcf
tests/path_alleles1.npy
tests/ref_for_tricky_variants.fa
tests/test_biallelic_haplotype_matrix.npy
tests/test_fast_approx_counter.py
tests/test_find_good_helper_variants.py
tests/test_genotype_accuracy.py
tests/test_glimpse_wrapper.py
tests/test_graph.py
tests/test_haplotype_as_paths.py
tests/test_helper_model.py
tests/test_helper_model_genotyping.py
tests/test_io.py
tests/test_limited_frequency_model.py
tests/test_limited_frequency_sampling_model.py
tests/test_min_count_bloom_filter.py
tests/test_modulo_filter.py
tests/test_multiallelic_postprocessing.py
tests/test_multiallelic_variants.py
tests/test_path_based_count_model.py
tests/test_path_variant_indexing.py
tests/test_paths.py
tests/test_priors.py
tests/test_ray.py
tests/test_read_simulation.py
tests/test_samplemodel.py
tests/test_sampling_for_sample_model.py
tests/test_signatures.py
tests/test_sparse_haplotype_matrix.py
tests/test_sparse_observed_counts.py
tests/test_util.py
tests/test_variant_merger.py
tests/test_variants.py
tests/test_vcf_preprocessing.py
tests/test_window_kmers.py
tests/tricky_variants.vcf
tests/tricky_variants21.vcf
tests/vcf_with_missing.vcf
tests/test_data_sacCer3/filtered_population.vcf.gz
tests/test_data_sacCer3/filtered_population.vcf.gz.tbi
tests/test_data_sacCer3/reads.fq.gz
tests/test_data_sacCer3/reference.fa
tests/test_data_sacCer3/test_genotypes.vcf.gz
tests/test_data_sacCer3/test_genotypes.vcf.gz.tbi
tests/test_data_sacCer3/truth.vcf