Uses of Class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase (SnpEff 5.1 API)

Packages that use TestCasesIntegrationBase

Package

Description

org.snpeff.snpEffect.testCases.integration

Uses of TestCasesIntegrationBase in org.snpeff.snpEffect.testCases.integration

Subclasses of TestCasesIntegrationBase in org.snpeff.snpEffect.testCases.integration

Modifier and Type

Class

Description

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

Uses of Classorg.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase

Uses of TestCasesIntegrationBase in org.snpeff.snpEffect.testCases.integration

Uses of Class
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase