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
All Methods Instance Methods Concrete Methods 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 genevoid
test01_dupTr()
Duplication whole transcriptvoid
test02()
Duplication One coding exonvoid
test03()
Duplication two coding exons (within the same gene)void
test04()
Duplication Part of one coding exonvoid
test05()
Duplication Part of two coding exons (within the same gene)void
test06()
Duplication Two genesvoid
test07()
Duplication After gene's coding region (LOW impact)void
test08()
Duplication Part of two genes cutting on intronsvoid
test09()
Duplication Part of two genes cutting exonsvoid
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
-
-
-
-
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 classTestCasesBase
-
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
-
-