Package org.snpeff.snpEffect.testCases.unity

Class TestCasesStructuralDup

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup

public class TestCasesStructuralDup
extends TestCasesBase

Test case for structural variants: Duplications

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
TestCasesStructuralDup()

Method Summary

Modifier and Type	Method	Description
protected void	checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void	init()
void	test01_dupGene()	Duplication Whole gene
void	test01_dupTr()	Duplication whole transcript
void	test02()	Duplication One coding exon
void	test03()	Duplication two coding exons (within the same gene)
void	test04()	Duplication Part of one coding exon
void	test05()	Duplication Part of two coding exons (within the same gene)
void	test06()	Duplication Two genes
void	test07()	Duplication After gene's coding region (LOW impact)
void	test08()	Duplication Part of two genes cutting on introns
void	test09()	Duplication Part of two genes cutting exons
void	test10()	Duplication Intron

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

after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, 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

TestCasesStructuralDup

public TestCasesStructuralDup()

Method Detail

checkEffects

protected void checkEffects(Variant variant,
                            EffectType[] expEffs,
                            java.lang.String[] expHgvsp,
                            java.lang.String[] expHgvsc,
                            VariantEffect.EffectImpact expectedImpact,
                            java.lang.String[] expAnns)

init

protected void init()

Overrides:

init in class TestCasesBase

test01_dupGene

public void test01_dupGene()

Duplication Whole gene

test01_dupTr

public void test01_dupTr()

Duplication whole transcript

test02

public void test02()

Duplication One coding exon

test03

public void test03()

Duplication two coding exons (within the same gene)

test04

public void test04()

Duplication Part of one coding exon

test05

public void test05()

Duplication Part of two coding exons (within the same gene)

test06

public void test06()

Duplication Two genes

test07

public void test07()

Duplication After gene's coding region (LOW impact)

test08

public void test08()

Duplication Part of two genes cutting on introns

test09

public void test09()

Duplication Part of two genes cutting exons

test10

public void test10()

Duplication Intron