Class TestCasesStructuralDup
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
Test case for structural variants: Duplications
-
Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected voidcheckEffects(Variant variant, EffectType[] expEffs, String[] expHgvsp, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns) protected voidinit()voidDuplication Whole genevoidDuplication whole transcriptvoidtest02()Duplication One coding exonvoidtest03()Duplication two coding exons (within the same gene)voidtest04()Duplication Part of one coding exonvoidtest05()Duplication Part of two coding exons (within the same gene)voidtest06()Duplication Two genesvoidtest07()Duplication After gene's coding region (LOW impact)voidtest08()Duplication Part of two genes cutting on intronsvoidtest09()Duplication Part of two genes cutting exonsvoidtest10()Duplication IntronMethods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
-
Constructor Details
-
TestCasesStructuralDup
public TestCasesStructuralDup()
-
-
Method Details
-
checkEffects
protected void checkEffects(Variant variant, EffectType[] expEffs, String[] expHgvsp, String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, String[] expAnns) -
init
protected void init()- Overrides:
initin classTestCasesBase
-
test01_dupGene
@Test public void test01_dupGene()Duplication Whole gene -
test01_dupTr
@Test public void test01_dupTr()Duplication whole transcript -
test02
@Test public void test02()Duplication One coding exon -
test03
@Test public void test03()Duplication two coding exons (within the same gene) -
test04
@Test public void test04()Duplication Part of one coding exon -
test05
@Test public void test05()Duplication Part of two coding exons (within the same gene) -
test06
@Test public void test06()Duplication Two genes -
test07
@Test public void test07()Duplication After gene's coding region (LOW impact) -
test08
@Test public void test08()Duplication Part of two genes cutting on introns -
test09
@Test public void test09()Duplication Part of two genes cutting exons -
test10
@Test public void test10()Duplication Intron
-