Class TestCasesApplySnp
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
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- org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
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public class TestCasesApplySnp extends TestCasesBaseApply
Test cases: apply a variant (SNP) to a transcript
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description TestCasesApplySnp()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_apply_variant_01()
Variant before exonvoid
test_apply_variant_02()
Variant ending right before exon startvoid
test_apply_variant_04()
Variant at exon startvoid
test_apply_variant_05()
Variant in exonvoid
test_apply_variant_06()
Variant right before exon endvoid
test_apply_variant_08()
Variant right after exon endvoid
test_apply_variant_09()
Variant after exon end-
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
initSnpEffPredictor
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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, prependSequenceToFirstExon, showTranscripts
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Method Detail
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test_apply_variant_01
public void test_apply_variant_01()
Variant before exon
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test_apply_variant_02
public void test_apply_variant_02()
Variant ending right before exon start
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test_apply_variant_04
public void test_apply_variant_04()
Variant at exon start
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test_apply_variant_05
public void test_apply_variant_05()
Variant in exon
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test_apply_variant_06
public void test_apply_variant_06()
Variant right before exon end
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test_apply_variant_08
public void test_apply_variant_08()
Variant right after exon end
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test_apply_variant_09
public void test_apply_variant_09()
Variant after exon end
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