Package org.snpeff.snpEffect.testCases.integration

Class TestCasesAnn

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.integration.TestCasesAnn

public class TestCasesAnn
extends TestCasesBase

Test case

Field Summary

Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesAnn()

Method Summary

Modifier and Type	Method	Description
void	test_01_Annotation_Stop()
void	test_01_VcfRawAlt()	Check that RAW alt fields are kept in 'Allele/Genotype'
void	test_02_Annotation_SpliceRegion()
void	test_03_Annotation_NonSyn()
void	test_04_Annotation_Intergenic()
void	test_05_Annotation_EndOfChromosome()

Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase

after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, prependSequenceToFirstExon, showTranscripts

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestCasesAnn

public TestCasesAnn()

Method Detail

test_01_Annotation_Stop

public void test_01_Annotation_Stop()

test_01_VcfRawAlt

public void test_01_VcfRawAlt()

Check that RAW alt fields are kept in 'Allele/Genotype'

test_02_Annotation_SpliceRegion

public void test_02_Annotation_SpliceRegion()

test_03_Annotation_NonSyn

public void test_03_Annotation_NonSyn()

test_04_Annotation_Intergenic

public void test_04_Annotation_Intergenic()

test_05_Annotation_EndOfChromosome

public void test_05_Annotation_EndOfChromosome()