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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TestCasesHgvsExon |
Test random SNP changes
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TestCasesHgvsIntron |
Test random SNP changes
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TestCasesIntegratioBuildPdb |
Test cases for annotation of protein interaction loci
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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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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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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
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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
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TestCasesIntegrationHgvsUpDownStream |
Test cases for HGVS notation
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TestCasesIntegrationHugeDeletions |
Test case where VCF entries are huge (e.g.
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TestCasesIntegrationInsEtc |
Test random SNP changes
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TestCasesIntegrationInsVep |
Test random SNP changes
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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
WARNING: JUnit doesn't seem to work if you use multi-threading....
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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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