Package org.snpeff.snpEffect.testCases.integration
package org.snpeff.snpEffect.testCases.integration
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ClassesClassDescriptionCompare effects in tests casesCompare our results to ENSEML's Variant Effect predictor's outputCompare our results to ENSEML's Variant Effect predictor's outputBase class for integration testsTest caseTest random SNP changesTest caseTest 'apply' method (apply variant to marker)Base class: Provides common methods used for testingTest cases for annotation of protein interaction lociTest cases for cancer effect (difference betwee somatic an germline tissue)Test cases for canonical transcript selectionTest caseTest case: Make sure VCF entries have some 'coding' (transcript biotype), even when biotype info is not available (e.g.Test caseTest COVID19 buildTest Loss of Function predictionTest cases on deletionsTest caseTest cases for other 'effect' issuesTest case for EMBL file parsing (database creation)Test cases for error reportingTest case for exon framesFilter transcriptsTest case for EMBL file parsing (database creation)Test case for genomic sequencesTest case for GFF3 file parsingTest case for GTF22 file parsingTest random SNP changesTest cases for HGVS notation on insertionsTest caseTest caseTest case HGSV: Hard casesTest cases for HGVS notation on insertionsTest random SNP changesTest case HGSV for MNPsTest cases for HGVS notationTest random SNP changesTest random SNP changesTest case where VCF entries are huge (e.g.Test Loss of Function predictionTest caseCalculate missense over silent ratioTest mixed variantsTest random SNP changesTest Motif databasesTest NextProt databasesTest Nonsense mediated decay predictionTest case where VCF entries has no sequence change (either REF=ALT or ALT=".")Protein translation test caseTest cases for annotation of protein interaction lociTest case for GTF22 file parsingTest caseTest case for sequence ontologyTest SNP variantsInvoke all integration test casesInvoke multi thread integration testTest random SNP changesTest cases for variantsTest SNP variantsTest random SNP changesTest case where VCF entries hit a transcript that has errorsTest cases for variantsVCF annotations test casesTest case