CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
pytest.ini
setup.py
genomics_data_index/__init__.py
genomics_data_index.egg-info/PKG-INFO
genomics_data_index.egg-info/SOURCES.txt
genomics_data_index.egg-info/dependency_links.txt
genomics_data_index.egg-info/entry_points.txt
genomics_data_index.egg-info/requires.txt
genomics_data_index.egg-info/top_level.txt
genomics_data_index/api/__init__.py
genomics_data_index/api/query/GenomicsDataIndex.py
genomics_data_index/api/query/SamplesQuery.py
genomics_data_index/api/query/TreeBuilder.py
genomics_data_index/api/query/__init__.py
genomics_data_index/api/query/features/FeaturesComparator.py
genomics_data_index/api/query/features/FeaturesFromIndexComparator.py
genomics_data_index/api/query/features/MLSTFeaturesComparator.py
genomics_data_index/api/query/features/MutationFeaturesFromIndexComparator.py
genomics_data_index/api/query/features/SampleCategoriesClustererExperimental.py
genomics_data_index/api/query/features/__init__.py
genomics_data_index/api/query/impl/ClusterScorer.py
genomics_data_index/api/query/impl/DataFrameSamplesQuery.py
genomics_data_index/api/query/impl/ExperimentalTreeSamplesQuery.py
genomics_data_index/api/query/impl/KmerTreeSamplesQuery.py
genomics_data_index/api/query/impl/MutationTreeSamplesQuery.py
genomics_data_index/api/query/impl/QueriesCollection.py
genomics_data_index/api/query/impl/SamplesQueryIndex.py
genomics_data_index/api/query/impl/TreeBuilderKmers.py
genomics_data_index/api/query/impl/TreeBuilderReferenceMutations.py
genomics_data_index/api/query/impl/TreeSamplesQuery.py
genomics_data_index/api/query/impl/TreeSamplesQueryFactory.py
genomics_data_index/api/query/impl/WrappedSamplesQuery.py
genomics_data_index/api/query/impl/__init__.py
genomics_data_index/api/query/impl/cluster/ClusterScoreMRCAJaccard.py
genomics_data_index/api/query/impl/cluster/ClusterScoreMethod.py
genomics_data_index/api/query/impl/cluster/__init__.py
genomics_data_index/api/query/kind/IsaKind.py
genomics_data_index/api/query/kind/__init__.py
genomics_data_index/api/query/kind/isa/DelegateIsaKind.py
genomics_data_index/api/query/kind/isa/__init__.py
genomics_data_index/api/query/kind/isa/typing/ExperimentalSARSCov2ConstellationsTyper.py
genomics_data_index/api/query/kind/isa/typing/SamplesTypingIsaKind.py
genomics_data_index/api/query/kind/isa/typing/__init__.py
genomics_data_index/api/viewer/TreeSamplesVisual.py
genomics_data_index/api/viewer/TreeStyler.py
genomics_data_index/api/viewer/__init__.py
genomics_data_index/api/viewer/samples_visuals/AbstractAnnotationTreeSamplesVisual.py
genomics_data_index/api/viewer/samples_visuals/AnnotateTreeSamplesVisual.py
genomics_data_index/api/viewer/samples_visuals/AnnotationSpacingTreeSamplesVisual.py
genomics_data_index/api/viewer/samples_visuals/HighlightTreeSamplesVisual.py
genomics_data_index/api/viewer/samples_visuals/__init__.py
genomics_data_index/cli/__init__.py
genomics_data_index/cli/gdi.py
genomics_data_index/configuration/ConfigFile.py
genomics_data_index/configuration/Project.py
genomics_data_index/configuration/__init__.py
genomics_data_index/configuration/connector/DataIndexConnection.py
genomics_data_index/configuration/connector/FilesystemStorage.py
genomics_data_index/configuration/connector/__init__.py
genomics_data_index/pipelines/ExecutorResults.py
genomics_data_index/pipelines/PipelineExecutor.py
genomics_data_index/pipelines/SnakemakePipelineExecutor.py
genomics_data_index/pipelines/__init__.py
genomics_data_index/pipelines/snakemake/main/README.md
genomics_data_index/pipelines/snakemake/main/clean.sh
genomics_data_index/pipelines/snakemake/main/config/config-all-data.yaml
genomics_data_index/pipelines/snakemake/main/config/config-reads-single.yaml
genomics_data_index/pipelines/snakemake/main/config/config-reads-snpeff.yaml
genomics_data_index/pipelines/snakemake/main/config/config-reads.yaml
genomics_data_index/pipelines/snakemake/main/config/config-snpeff.yaml
genomics_data_index/pipelines/snakemake/main/config/config.yaml
genomics_data_index/pipelines/snakemake/main/config/samples-all-data.tsv
genomics_data_index/pipelines/snakemake/main/config/samples-reads-single.tsv
genomics_data_index/pipelines/snakemake/main/config/samples-reads-snpeff.tsv
genomics_data_index/pipelines/snakemake/main/config/samples-reads.tsv
genomics_data_index/pipelines/snakemake/main/config/samples-snpeff.tsv
genomics_data_index/pipelines/snakemake/main/config/samples.tsv
genomics_data_index/pipelines/snakemake/main/input-data/NC_011083-5000-snpeff.gbk.gz
genomics_data_index/pipelines/snakemake/main/input-data/README.md
genomics_data_index/pipelines/snakemake/main/input-data/SampleA-snpeff.fasta.gz
genomics_data_index/pipelines/snakemake/main/input-data/SampleA-snpeff_1.fastq.gz
genomics_data_index/pipelines/snakemake/main/input-data/SampleA-snpeff_2.fastq.gz
genomics_data_index/pipelines/snakemake/main/input-data/SampleA.fasta
genomics_data_index/pipelines/snakemake/main/input-data/SampleA_1.fastq.gz
genomics_data_index/pipelines/snakemake/main/input-data/SampleA_2.fastq.gz
genomics_data_index/pipelines/snakemake/main/input-data/reference.fasta
genomics_data_index/pipelines/snakemake/main/input-data/reference.fasta.fai
genomics_data_index/pipelines/snakemake/main/workflow/.gitignore
genomics_data_index/pipelines/snakemake/main/workflow/Snakefile
genomics_data_index/pipelines/snakemake/main/workflow/envs/bcftools.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/bedtools.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/gdi.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/main.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/minimap2.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/mlst.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/snippy.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/snpeff.yaml
genomics_data_index/pipelines/snakemake/main/workflow/envs/sourmash.yaml
genomics_data_index/pipelines/snakemake/main/workflow/scripts/create-snippy-mask.py
genomics_data_index/pipelines/snakemake/main/workflow/scripts/fasta-to-genome-bedtools.py
genomics_data_index/pipelines/snakemake/main/workflow/scripts/gdi-create-fofn.py
genomics_data_index/pipelines/snakemake/main/workflow/scripts/prepare-reference.py
genomics_data_index/pipelines/snakemake/main/workflow/scripts/prepare-snpeff-database.py
genomics_data_index/pipelines/snakemake/main/workflow/scripts/variant-snpeff.py
genomics_data_index/storage/MaskedGenomicRegions.py
genomics_data_index/storage/SampleSet.py
genomics_data_index/storage/__init__.py
genomics_data_index/storage/index/KmerIndexer.py
genomics_data_index/storage/index/KmerSearchManager.py
genomics_data_index/storage/index/__init__.py
genomics_data_index/storage/io/FeaturesReader.py
genomics_data_index/storage/io/SampleData.py
genomics_data_index/storage/io/SampleDataPackage.py
genomics_data_index/storage/io/SampleDataPackageFactory.py
genomics_data_index/storage/io/SampleFilesProcessor.py
genomics_data_index/storage/io/__init__.py
genomics_data_index/storage/io/mlst/MLSTChewbbacaReader.py
genomics_data_index/storage/io/mlst/MLSTFeaturesReader.py
genomics_data_index/storage/io/mlst/MLSTSampleData.py
genomics_data_index/storage/io/mlst/MLSTSampleDataPackage.py
genomics_data_index/storage/io/mlst/MLSTSistrReader.py
genomics_data_index/storage/io/mlst/MLSTTSeemannFeaturesReader.py
genomics_data_index/storage/io/mlst/__init__.py
genomics_data_index/storage/io/mutation/NucleotideFeaturesReader.py
genomics_data_index/storage/io/mutation/NucleotideSampleData.py
genomics_data_index/storage/io/mutation/NucleotideSampleDataBedMask.py
genomics_data_index/storage/io/mutation/NucleotideSampleDataPackage.py
genomics_data_index/storage/io/mutation/NucleotideSampleDataPackageFactory.py
genomics_data_index/storage/io/mutation/NucleotideSampleDataSequenceMask.py
genomics_data_index/storage/io/mutation/SequenceFile.py
genomics_data_index/storage/io/mutation/SnpEffDatabase.py
genomics_data_index/storage/io/mutation/VariationFile.py
genomics_data_index/storage/io/mutation/VcfSnpEffAnnotationParser.py
genomics_data_index/storage/io/mutation/VcfVariantsReader.py
genomics_data_index/storage/io/mutation/__init__.py
genomics_data_index/storage/io/mutation/templates/snpEff.config
genomics_data_index/storage/io/mutation/variants_processor/MultipleProcessVcfVariantsTableProcessor.py
genomics_data_index/storage/io/mutation/variants_processor/SerialVcfVariantsTableProcessor.py
genomics_data_index/storage/io/mutation/variants_processor/VcfVariantsTableProcessor.py
genomics_data_index/storage/io/mutation/variants_processor/__init__.py
genomics_data_index/storage/io/processor/MultipleProcessSampleFilesProcessor.py
genomics_data_index/storage/io/processor/NullSampleFilesProcessor.py
genomics_data_index/storage/io/processor/SerialSampleFilesProcessor.py
genomics_data_index/storage/io/processor/__init__.py
genomics_data_index/storage/model/NucleotideMutationTranslater.py
genomics_data_index/storage/model/QueryFeature.py
genomics_data_index/storage/model/QueryFeatureFactory.py
genomics_data_index/storage/model/QueryFeatureHGVS.py
genomics_data_index/storage/model/QueryFeatureHGVSGN.py
genomics_data_index/storage/model/QueryFeatureMLST.py
genomics_data_index/storage/model/QueryFeatureMutation.py
genomics_data_index/storage/model/QueryFeatureMutationSPDI.py
genomics_data_index/storage/model/__init__.py
genomics_data_index/storage/model/db/DatabasePathTranslator.py
genomics_data_index/storage/model/db/__init__.py
genomics_data_index/storage/service/CoreAlignmentService.py
genomics_data_index/storage/service/FeatureService.py
genomics_data_index/storage/service/KmerService.py
genomics_data_index/storage/service/MLSTService.py
genomics_data_index/storage/service/ReferenceService.py
genomics_data_index/storage/service/SampleService.py
genomics_data_index/storage/service/TreeService.py
genomics_data_index/storage/service/VariationService.py
genomics_data_index/storage/service/__init__.py
genomics_data_index/storage/util/ListSliceIter.py
genomics_data_index/storage/util/SamplesProgressLogger.py
genomics_data_index/storage/util/__init__.py
genomics_data_index/test/__init__.py
genomics_data_index/test/integration/__init__.py
genomics_data_index/test/integration/api/__init__.py
genomics_data_index/test/integration/api/test_GenomicsDataIndex_api_import.py
genomics_data_index/test/integration/api/query/__init__.py
genomics_data_index/test/integration/api/query/conftest.py
genomics_data_index/test/integration/api/query/test_ClusterScorer.py
genomics_data_index/test/integration/api/query/test_GenomicsDataIndex.py
genomics_data_index/test/integration/api/query/test_GenomicsDataIndex_from_project.py
genomics_data_index/test/integration/api/query/test_GenomicsDataIndex_samples_query.py
genomics_data_index/test/integration/api/query/test_TreeBuilderReferenceMutations.py
genomics_data_index/test/integration/api/query/test_TreeSamplesQueryExperimental.py
genomics_data_index/test/integration/api/query/features/__init__.py
genomics_data_index/test/integration/api/query/features/test_MLSTFeaturesComparator.py
genomics_data_index/test/integration/api/query/features/test_MutationFromIndexFeaturesComparator.py
genomics_data_index/test/integration/configuration/__init__.py
genomics_data_index/test/integration/configuration/test_Project.py
genomics_data_index/test/integration/configuration/connector/__init__.py
genomics_data_index/test/integration/configuration/connector/test_DataIndexConnection.py
genomics_data_index/test/integration/data/consensus/SampleA-consensus-nomask.fasta.gz
genomics_data_index/test/integration/data/consensus/SampleA-consensus-withmask-over-mutation.fasta.gz
genomics_data_index/test/integration/data/consensus/SampleA-consensus-withmask.fasta.gz
genomics_data_index/test/integration/data/empty_vcfs/SampleA/snps.aligned.fa
genomics_data_index/test/integration/data/empty_vcfs/SampleA/snps.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB-empty.snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB-empty.snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB2.snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB2.snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB3.snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB3.snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB4.snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB4.snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5-different-allele-ambiguous.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5-different-allele-ambiguous.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5-different-allele.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5-different-allele.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5.snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/extra-snippy-samples/SampleB5.snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/mlst/mlst-basic.tsv
genomics_data_index/test/integration/data/mlst/mlst-chewbbaca-small.tsv
genomics_data_index/test/integration/data/mlst/mlst-single-scheme.tsv
genomics_data_index/test/integration/data/mlst/mlst-single-scheme2.tsv
genomics_data_index/test/integration/data/mlst/mlst-single-scheme3.tsv
genomics_data_index/test/integration/data/mlst/mlst-sistr.csv
genomics_data_index/test/integration/data/mlst/mlst-snippy-data.csv
genomics_data_index/test/integration/data/mlst/mlst-unknown.tsv
genomics_data_index/test/integration/data/regular-vcf/SampleA.vcf.gz
genomics_data_index/test/integration/data/regular-vcf/SampleB.vcf.gz
genomics_data_index/test/integration/data/regular-vcf/SampleC.vcf.gz
genomics_data_index/test/integration/data/snippy/README.md
genomics_data_index/test/integration/data/snippy/features_in_A_not_BC.txt
genomics_data_index/test/integration/data/snippy/features_in_BC_not_A.txt
genomics_data_index/test/integration/data/snippy/genome.fasta.bz2
genomics_data_index/test/integration/data/snippy/genome.fasta.gz
genomics_data_index/test/integration/data/snippy/genome.fasta.xz
genomics_data_index/test/integration/data/snippy/missing-all.bed.gz
genomics_data_index/test/integration/data/snippy/missing-any-AB.bed.gz
genomics_data_index/test/integration/data/snippy/missing-any-BC.bed.gz
genomics_data_index/test/integration/data/snippy/missing-both-AB.bed.gz
genomics_data_index/test/integration/data/snippy/missing-both-AC.bed.gz
genomics_data_index/test/integration/data/snippy/missing-both-BC.bed.gz
genomics_data_index/test/integration/data/snippy/position-in-beds.py
genomics_data_index/test/integration/data/snippy/print-length-bed.py
genomics_data_index/test/integration/data/snippy/print-nucleotide-position.py
genomics_data_index/test/integration/data/snippy/print-positions-bed.py
genomics_data_index/test/integration/data/snippy/print-unknown-missing.py
genomics_data_index/test/integration/data/snippy/sequence_vcf_to_mask.py
genomics_data_index/test/integration/data/snippy/snippy.core.aln
genomics_data_index/test/integration/data/snippy/snippy.full.aln
genomics_data_index/test/integration/data/snippy/tree.tre
genomics_data_index/test/integration/data/snippy/SampleA/mutations-dataframe.all.tsv
genomics_data_index/test/integration/data/snippy/SampleA/mutations-dataframe.snps.tsv
genomics_data_index/test/integration/data/snippy/SampleA/snps.aligned.bed.gz
genomics_data_index/test/integration/data/snippy/SampleA/snps.aligned.fa
genomics_data_index/test/integration/data/snippy/SampleA/snps.aligned.minus-vcf.bed.gz
genomics_data_index/test/integration/data/snippy/SampleA/snps.aligned.nogap.fa.gz
genomics_data_index/test/integration/data/snippy/SampleA/snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleA/snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/snippy/SampleA/snps.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleA/snps.vcf.gz.csi
genomics_data_index/test/integration/data/snippy/SampleB/mutations-dataframe.all.tsv
genomics_data_index/test/integration/data/snippy/SampleB/mutations-dataframe.snps.tsv
genomics_data_index/test/integration/data/snippy/SampleB/snps.aligned.bed.gz
genomics_data_index/test/integration/data/snippy/SampleB/snps.aligned.fa
genomics_data_index/test/integration/data/snippy/SampleB/snps.aligned.minus-vcf.bed.gz
genomics_data_index/test/integration/data/snippy/SampleB/snps.aligned.nogap.fa.gz
genomics_data_index/test/integration/data/snippy/SampleB/snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleB/snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/snippy/SampleB/snps.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleB/snps.vcf.gz.csi
genomics_data_index/test/integration/data/snippy/SampleC/mutations-dataframe.all.tsv
genomics_data_index/test/integration/data/snippy/SampleC/mutations-dataframe.snps.tsv
genomics_data_index/test/integration/data/snippy/SampleC/snps.aligned.bed.gz
genomics_data_index/test/integration/data/snippy/SampleC/snps.aligned.fa
genomics_data_index/test/integration/data/snippy/SampleC/snps.aligned.minus-vcf.bed.gz
genomics_data_index/test/integration/data/snippy/SampleC/snps.aligned.nogap.fa.gz
genomics_data_index/test/integration/data/snippy/SampleC/snps.fill-tags.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleC/snps.fill-tags.vcf.gz.csi
genomics_data_index/test/integration/data/snippy/SampleC/snps.vcf.gz
genomics_data_index/test/integration/data/snippy/SampleC/snps.vcf.gz.csi
genomics_data_index/test/integration/data/snpeff-database/NC_011083-5000.gbk.gz
genomics_data_index/test/integration/data/snpeff-database/NC_011083_CP001602-5000.gbk.gz
genomics_data_index/test/integration/data/snpeff-database/README.md
genomics_data_index/test/integration/data/snpeff-database/SampleA.vcf.gz
genomics_data_index/test/integration/data/snpeff-database/ref.fasta.gz
genomics_data_index/test/integration/data/snpeff-database/input/SampleA.fasta.gz
genomics_data_index/test/integration/data/snpeff-vcf/NC_011083.fasta.gz
genomics_data_index/test/integration/data/snpeff-vcf/README.md
genomics_data_index/test/integration/data/snpeff-vcf/SH10-014-dup-gene-variant-2.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH10-014-dup-gene-variant.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH10-014.bed.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH10-014.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH14-001.bed.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH14-001.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH14-014.bed.gz
genomics_data_index/test/integration/data/snpeff-vcf/SH14-014.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/USA__CA-CDPH-3000143037__2021.noann.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/USA__CA-CDPH-3000143037__2021.vcf.gz
genomics_data_index/test/integration/data/snpeff-vcf/sh10-uniq.txt
genomics_data_index/test/integration/data/snpeff-vcf/tree.txt
genomics_data_index/test/integration/data/sourmash/README.md
genomics_data_index/test/integration/data/sourmash/SampleA.sig.gz
genomics_data_index/test/integration/data/sourmash/SampleB.sig.gz
genomics_data_index/test/integration/data/sourmash/SampleC.sig.gz
genomics_data_index/test/integration/data/test_project_dir/gdi-config.yaml
genomics_data_index/test/integration/data/test_project_dir/.gdi-data/gdi-db.sqlite
genomics_data_index/test/integration/data/variation/SampleA-mask-over-mutation.bed.gz
genomics_data_index/test/integration/data/variation/SampleA.bcf
genomics_data_index/test/integration/data/variation/SampleA.bcf.csi
genomics_data_index/test/integration/data/variation/SampleA.bed.gz
genomics_data_index/test/integration/data/variation/SampleA.vcf.gz
genomics_data_index/test/integration/pipelines/__init__.py
genomics_data_index/test/integration/pipelines/test_SnakemakePipelineExecutor.py
genomics_data_index/test/integration/pipelines/data/assemblies/README.md
genomics_data_index/test/integration/pipelines/data/assemblies/genome.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleA-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleB-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleC-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleD-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleD.bed.gz
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleE-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleE.bed.gz
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleF-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleF.bed.gz
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleH-mutations.txt
genomics_data_index/test/integration/pipelines/data/assemblies/expected/SampleH.bed.gz
genomics_data_index/test/integration/pipelines/data/assemblies/expected/empty.bed.gz
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleA.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleB.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleC.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleD.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleE.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleF.fasta
genomics_data_index/test/integration/pipelines/data/assemblies/samples/SampleH.fasta
genomics_data_index/test/integration/pipelines/data/reads/SampleA-single-snpeff.fastq.gz
genomics_data_index/test/integration/pipelines/data/reads/SampleA-snpeff_1.fastq.gz
genomics_data_index/test/integration/pipelines/data/reads/SampleA-snpeff_2.fastq.gz
genomics_data_index/test/integration/storage/__init__.py
genomics_data_index/test/integration/storage/index/__init__.py
genomics_data_index/test/integration/storage/index/test_KmerIndexManager.py
genomics_data_index/test/integration/storage/index/test_KmerIndexer.py
genomics_data_index/test/integration/storage/index/test_KmerSearchManager.py
genomics_data_index/test/integration/storage/io/__init__.py
genomics_data_index/test/integration/storage/io/test_MLSTChewbbacaReader.py
genomics_data_index/test/integration/storage/io/test_MLSTSampleDataPackage.py
genomics_data_index/test/integration/storage/io/test_MLSTSistrReader.py
genomics_data_index/test/integration/storage/io/test_MLSTTSeemannFeaturesReader.py
genomics_data_index/test/integration/storage/io/test_VcfVariantsReader.py
genomics_data_index/test/integration/storage/io/mutation/__init__.py
genomics_data_index/test/integration/storage/io/mutation/conftest.py
genomics_data_index/test/integration/storage/io/mutation/test_NucleotideSampleData.py
genomics_data_index/test/integration/storage/io/mutation/test_NucleotideSampleDataBedMask.py
genomics_data_index/test/integration/storage/io/mutation/test_NucleotideSampleDataPackage.py
genomics_data_index/test/integration/storage/io/mutation/test_NucleotideSampleDataPackageFactory.py
genomics_data_index/test/integration/storage/io/mutation/test_NucleotideSampleDataSequenceMask.py
genomics_data_index/test/integration/storage/io/mutation/test_SequenceFile.py
genomics_data_index/test/integration/storage/io/mutation/test_SnpEffDatabase.py
genomics_data_index/test/integration/storage/io/mutation/test_VariationFile.py
genomics_data_index/test/integration/storage/service/__init__.py
genomics_data_index/test/integration/storage/service/conftest.py
genomics_data_index/test/integration/storage/service/test_CoreAlignmentService.py
genomics_data_index/test/integration/storage/service/test_DatabaseConnection.py
genomics_data_index/test/integration/storage/service/test_KmerService.py
genomics_data_index/test/integration/storage/service/test_MLSTService.py
genomics_data_index/test/integration/storage/service/test_ReferenceService.py
genomics_data_index/test/integration/storage/service/test_SampleService.py
genomics_data_index/test/integration/storage/service/test_TreeService.py
genomics_data_index/test/integration/storage/service/test_VariationService.py
genomics_data_index/test/unit/__init__.py
genomics_data_index/test/unit/api/__init__.py
genomics_data_index/test/unit/api/query/__init__.py
genomics_data_index/test/unit/api/query/kind/__init__.py
genomics_data_index/test/unit/api/query/kind/test_ExperimentalSARSCov2ConstellationsTyper.py
genomics_data_index/test/unit/data/NC_045512.2.gb.gz
genomics_data_index/test/unit/variant/__init__.py
genomics_data_index/test/unit/variant/test_MaskedGenomicRegions.py
genomics_data_index/test/unit/variant/test_SampleSet.py
genomics_data_index/test/unit/variant/data/snps-for-mask.vcf.gz
genomics_data_index/test/unit/variant/io/__init__.py
genomics_data_index/test/unit/variant/io/test_MLSTSampleData.py
genomics_data_index/test/unit/variant/io/mutation/__init__.py
genomics_data_index/test/unit/variant/io/mutation/test_NucleotideSampleData.py
genomics_data_index/test/unit/variant/io/mutation/test_SequenceFile.py
genomics_data_index/test/unit/variant/io/mutation/test_VcfSnpEffAnnotationParser.py
genomics_data_index/test/unit/variant/model/__init__.py
genomics_data_index/test/unit/variant/model/test_NucleotideMutationTranslater.py
genomics_data_index/test/unit/variant/model/test_QueryFeatureFactory.py
genomics_data_index/test/unit/variant/model/test_QueryFeatureHGVS.py
genomics_data_index/test/unit/variant/model/test_QueryFeatureHGVSGN.py
genomics_data_index/test/unit/variant/model/test_QueryFeatureMLST.py
genomics_data_index/test/unit/variant/model/test_QueryFeatureMutationSPDI.py
genomics_data_index/test/unit/variant/model/db/__init__.py
genomics_data_index/test/unit/variant/model/db/test_DatabasePathTranslator.py
genomics_data_index/test/unit/variant/model/db/test_MLSTAllelesSamples.py
genomics_data_index/test/unit/variant/model/db/test_NucleotideVariantsSamples.py
genomics_data_index/test/unit/variant/pipelines/__init__.py
genomics_data_index/test/unit/variant/pipelines/test_SnakemakePipelineExecutor.py
genomics_data_index/test/unit/variant/service/__init__.py
genomics_data_index/test/unit/variant/service/test_SQLQueryInBatcher.py
genomics_data_index/test/unit/variant/util/__init__.py
genomics_data_index/test/unit/variant/util/test_ListSliceIter.py