| CompareEffects |
Compare effects in tests cases
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| CompareToEnsembl |
Compare our results to ENSEML's Variant Effect predictor's output
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| CompareToVep |
Compare our results to ENSEML's Variant Effect predictor's output
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| CreateSpliceSiteTestCase |
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| IntegrationTest |
Base class for integration tests
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| TestCasesAnn |
Test case
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| TestCasesHgvsBase |
Test random SNP changes
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| TestCasesIntegrationAlphaFold |
Test case
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| TestCasesIntegrationApply |
Test 'apply' method (apply variant to marker)
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| TestCasesIntegrationBase |
Base class: Provides common methods used for testing
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| TestCasesIntegrationBuildPdb |
Test cases for annotation of protein interaction loci
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| TestCasesIntegrationCancer |
Test cases for cancer effect (difference betwee somatic an germline tissue)
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| TestCasesIntegrationCanonical |
Test cases for canonical transcript selection
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| TestCasesIntegrationCircularGenome |
Test case
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| TestCasesIntegrationCodingTag |
Test case: Make sure VCF entries have some 'coding' (transcript biotype), even
when biotype info is not available (e.g.
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| TestCasesIntegrationConfig |
Test case
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| TestCasesIntegrationCovid19 |
Test COVID19 build
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| TestCasesIntegrationCutsomIntervals |
Test Loss of Function prediction
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| TestCasesIntegrationDelEtc |
Test cases on deletions
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| TestCasesIntegrationDup |
Test case
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| TestCasesIntegrationEff |
Test cases for other 'effect' issues
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| TestCasesIntegrationEmbl |
Test case for EMBL file parsing (database creation)
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| TestCasesIntegrationErrors |
Test cases for error reporting
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| TestCasesIntegrationExonFrame |
Test case for exon frames
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| TestCasesIntegrationFilterTranscripts |
Filter transcripts
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| TestCasesIntegrationGenBank |
Test case for EMBL file parsing (database creation)
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| TestCasesIntegrationGenomicSequences |
Test case for genomic sequences
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| TestCasesIntegrationGff3 |
Test case for GFF3 file parsing
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| TestCasesIntegrationGtf22 |
Test case for GTF22 file parsing
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| TestCasesIntegrationHgvs |
Test random SNP changes
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| TestCasesIntegrationHgvsDel |
Test cases for HGVS notation on insertions
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| TestCasesIntegrationHgvsDnaDup |
Test case
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| TestCasesIntegrationHgvsFrameShift |
Test case
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| TestCasesIntegrationHgvsHard |
Test case HGSV: Hard cases
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| TestCasesIntegrationHgvsIns |
Test cases for HGVS notation on insertions
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| TestCasesIntegrationHgvsLarge |
Test random SNP changes
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| TestCasesIntegrationHgvsMnps |
Test case HGSV for MNPs
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| TestCasesIntegrationHgvsUpDownStream |
Test cases for HGVS notation
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| TestCasesIntegrationInsEtc |
Test random SNP changes
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| TestCasesIntegrationInsVep |
Test random SNP changes
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| TestCasesIntegrationLargeDeletion |
Test case where VCF entries are huge (e.g.
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| TestCasesIntegrationLof |
Test Loss of Function prediction
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| TestCasesIntegrationMarkerSeq |
Test case
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| TestCasesIntegrationMissenseSilentRatio |
Calculate missense over silent ratio
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| TestCasesIntegrationMixedVariants |
Test mixed variants
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| TestCasesIntegrationMnp |
Test random SNP changes
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| TestCasesIntegrationMotif |
Test Motif databases
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| TestCasesIntegrationNextProt |
Test NextProt databases
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| TestCasesIntegrationNmd |
Test Nonsense mediated decay prediction
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| TestCasesIntegrationNoChange |
Test case where VCF entries has no sequence change (either REF=ALT or ALT=".")
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| TestCasesIntegrationProtein |
Protein translation test case
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| TestCasesIntegrationProteinInteraction |
Test cases for annotation of protein interaction loci
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| TestCasesIntegrationRefSeq |
Test case for GTF22 file parsing
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| TestCasesIntegrationRegulation |
Test case
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| TestCasesIntegrationSequenceOntology |
Test case for sequence ontology
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| TestCasesIntegrationSnp |
Test SNP variants
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| TestCasesIntegrationSnpEff |
Invoke all integration test cases
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| TestCasesIntegrationSnpEffMultiThread |
Invoke multi thread integration test
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| TestCasesIntegrationSnpEnsembl |
Test random SNP changes
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| TestCasesIntegrationSpliceRegion |
Test cases for variants
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| TestCasesIntegrationStructural |
Test SNP variants
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| TestCasesIntegrationTranscript |
Test random SNP changes
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| TestCasesIntegrationTranscriptError |
Test case where VCF entries hit a transcript that has errors
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| TestCasesIntegrationVariant |
Test cases for variants
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| TestCasesIntegrationVcfs |
VCF annotations test cases
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| TestCasesIntegrationZzz |
Test case
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