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